I: pbuilder: network access will be disabled during build I: Current time: Sat Apr 19 08:20:07 +14 2025 I: pbuilder-time-stamp: 1745000407 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [prody_2.4.1+dfsg-2.dsc] I: copying [./prody_2.4.1+dfsg.orig.tar.xz] I: copying [./prody_2.4.1+dfsg-2.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Feb 13 07:18:28 2024 gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./prody_2.4.1+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting prody in prody-2.4.1+dfsg dpkg-source: info: unpacking prody_2.4.1+dfsg.orig.tar.xz dpkg-source: info: unpacking prody_2.4.1+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no-network-access.patch dpkg-source: info: applying add-missing-test-files.patch dpkg-source: info: applying numpy-1.24.patch dpkg-source: info: applying 1816.patch dpkg-source: info: applying skip-equals-on-vector.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/17053/tmp/hooks/D01_modify_environment starting debug: Running on ionos6-i386. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Apr 18 18:20 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/17053/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/17053/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=2ecc8b27af5c4b4bbe62f9f4008fab3f LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=17053 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.pvkjNTt7/pbuilderrc_gugh --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.pvkjNTt7/b2 --logfile b2/build.log prody_2.4.1+dfsg-2.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 16 19:35 /bin -> usr/bin I: user script /srv/workspace/pbuilder/17053/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-biopython, python3-numpy, python3-pyparsing, python3-scipy, python3-setuptools, python3-zombie-imp dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19643 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pyparsing; however: Package python3-pyparsing is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-zombie-imp; however: Package python3-zombie-imp is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libcairo2{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libharfbuzz0b{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.11t64{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libraqm0{a} libreadline8t64{a} libsharpyuv0{a} libsub-override-perl{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxrender1{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-biopython{a} python3-cairo{a} python3-chardet{a} python3-decorator{a} python3-dev{a} python3-distutils{a} python3-freetype{a} python3-lib2to3{a} python3-minimal{a} python3-numpy{a} python3-pil{a} python3-pkg-resources{a} python3-pyparsing{a} python3-reportlab{a} python3-rlpycairo{a} python3-scipy{a} python3-setuptools{a} python3-zombie-imp{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tzdata{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-extra javascript-common libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx ncbi-blast+ python-biopython-doc python3-olefile shared-mime-info wget xdg-user-dirs 0 packages upgraded, 128 newly installed, 0 to remove and 0 not upgraded. Need to get 102 MB of archives. After unpacking 403 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 libpython3.11-minimal i386 3.11.8-3 [816 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.2-1 [107 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 python3.11-minimal i386 3.11.8-3 [1917 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 python3-minimal i386 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 tzdata all 2024a-1 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-3.1 [69.2 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-3.1 [171 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 libpython3.11-stdlib i386 3.11.8-3 [1794 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 python3.11 i386 3.11.8-3 [597 kB] Get: 12 http://deb.debian.org/debian unstable/main i386 libpython3-stdlib i386 3.11.8-1 [9336 B] Get: 13 http://deb.debian.org/debian unstable/main i386 python3 i386 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 libpython3.12-minimal i386 3.12.2-4 [807 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 python3.12-minimal i386 3.12.2-4 [2062 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 sgml-base all 1.31 [15.4 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3 [314 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3 [114 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3 [42.9 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 22 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 23 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-3+b1 [1195 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.39.3-10 [93.6 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.7-1+b2 [39.6 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 man-db i386 2.12.0-3 [1413 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 autoconf all 2.71-3 [332 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 autopoint all 0.21-14 [496 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.14.1 [85.6 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-7 [517 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian unstable/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 37 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 39 http://deb.debian.org/debian unstable/main i386 libelf1 i386 0.190-1+b1 [182 kB] Get: 40 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1 [118 kB] Get: 41 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 42 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.9.14+dfsg-1.3+b2 [727 kB] Get: 43 http://deb.debian.org/debian unstable/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 44 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 45 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 debhelper all 13.14.1 [890 kB] Get: 47 http://deb.debian.org/debian unstable/main i386 python3-lib2to3 all 3.12.2-3 [77.6 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 python3-distutils all 3.12.2-3 [131 kB] Get: 49 http://deb.debian.org/debian unstable/main i386 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 python3-setuptools all 68.1.2-2 [468 kB] Get: 51 http://deb.debian.org/debian unstable/main i386 dh-python all 6.20240310 [106 kB] Get: 52 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 53 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-core all 2.37-8 [840 kB] Get: 54 http://deb.debian.org/debian unstable/main i386 libfontenc1 i386 1:1.1.8-1 [23.1 kB] Get: 55 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b3 [314 kB] Get: 56 http://deb.debian.org/debian unstable/main i386 libpng16-16t64 i386 1.6.43-3 [286 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 libfreetype6 i386 2.13.2+dfsg-1+b2 [449 kB] Get: 58 http://deb.debian.org/debian unstable/main i386 x11-common all 1:7.7+23 [252 kB] Get: 59 http://deb.debian.org/debian unstable/main i386 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 60 http://deb.debian.org/debian unstable/main i386 xfonts-utils i386 1:7.7+6 [95.2 kB] Get: 61 http://deb.debian.org/debian unstable/main i386 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 62 http://deb.debian.org/debian unstable/main i386 fontconfig-config i386 2.15.0-1.1 [317 kB] Get: 63 http://deb.debian.org/debian unstable/main i386 libblas3 i386 3.12.0-3 [140 kB] Get: 64 http://deb.debian.org/debian unstable/main i386 libbsd0 i386 0.12.1-1 [132 kB] Get: 65 http://deb.debian.org/debian unstable/main i386 libfontconfig1 i386 2.15.0-1.1 [401 kB] Get: 66 http://deb.debian.org/debian unstable/main i386 libpixman-1-0 i386 0.42.2-1+b1 [555 kB] Get: 67 http://deb.debian.org/debian unstable/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 68 http://deb.debian.org/debian unstable/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 69 http://deb.debian.org/debian unstable/main i386 libxcb1 i386 1.15-1 [148 kB] Get: 70 http://deb.debian.org/debian unstable/main i386 libx11-data all 2:1.8.7-1 [328 kB] Get: 71 http://deb.debian.org/debian unstable/main i386 libx11-6 i386 2:1.8.7-1 [822 kB] Get: 72 http://deb.debian.org/debian unstable/main i386 libxcb-render0 i386 1.15-1 [116 kB] Get: 73 http://deb.debian.org/debian unstable/main i386 libxcb-shm0 i386 1.15-1 [106 kB] Get: 74 http://deb.debian.org/debian unstable/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 75 http://deb.debian.org/debian unstable/main i386 libxrender1 i386 1:0.9.10-1.1 [34.1 kB] Get: 76 http://deb.debian.org/debian unstable/main i386 libcairo2 i386 1.18.0-2 [587 kB] Get: 77 http://deb.debian.org/debian unstable/main i386 libdeflate0 i386 1.19-1 [41.9 kB] Get: 78 http://deb.debian.org/debian unstable/main i386 libexpat1-dev i386 2.6.2-1 [165 kB] Get: 79 http://deb.debian.org/debian unstable/main i386 libfribidi0 i386 1.0.13-3+b1 [71.8 kB] Get: 80 http://deb.debian.org/debian unstable/main i386 libgfortran5 i386 14-20240303-1 [734 kB] Get: 81 http://deb.debian.org/debian unstable/main i386 libglib2.0-0t64 i386 2.78.4-4 [1522 kB] Get: 82 http://deb.debian.org/debian unstable/main i386 libgraphite2-3 i386 1.3.14-2 [77.7 kB] Get: 83 http://deb.debian.org/debian unstable/main i386 libharfbuzz0b i386 8.3.0-2+b1 [2234 kB] Get: 84 http://deb.debian.org/debian unstable/main i386 libimagequant0 i386 2.18.0-1 [35.6 kB] Get: 85 http://deb.debian.org/debian unstable/main i386 libjbig0 i386 2.1-6.1+b1 [31.8 kB] Get: 86 http://deb.debian.org/debian unstable/main i386 libjpeg62-turbo i386 1:2.1.5-2+b2 [169 kB] Get: 87 http://deb.debian.org/debian unstable/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 88 http://deb.debian.org/debian unstable/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 89 http://deb.debian.org/debian unstable/main i386 libjs-sphinxdoc all 7.2.6-5 [150 kB] Get: 90 http://deb.debian.org/debian unstable/main i386 liblapack3 i386 3.12.0-3 [2167 kB] Get: 91 http://deb.debian.org/debian unstable/main i386 liblbfgsb0 i386 3.0+dfsg.4-1+b1 [29.1 kB] Get: 92 http://deb.debian.org/debian unstable/main i386 liblcms2-2 i386 2.14-2+b1 [165 kB] Get: 93 http://deb.debian.org/debian unstable/main i386 liblerc4 i386 4.0.0+ds-4+b1 [180 kB] Get: 94 http://deb.debian.org/debian unstable/main i386 libopenjp2-7 i386 2.5.0-2+b3 [197 kB] Get: 95 http://deb.debian.org/debian unstable/main i386 libpython3.11t64 i386 3.11.8-3 [1982 kB] Get: 96 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg-3.1 [915 kB] Get: 97 http://deb.debian.org/debian unstable/main i386 libpython3.11-dev i386 3.11.8-3 [4631 kB] Get: 98 http://deb.debian.org/debian unstable/main i386 libpython3-dev i386 3.11.8-1 [9600 B] Get: 99 http://deb.debian.org/debian unstable/main i386 libpython3.12-stdlib i386 3.12.2-4 [1889 kB] Get: 100 http://deb.debian.org/debian unstable/main i386 libpython3.12t64 i386 3.12.2-4 [2140 kB] Get: 101 http://deb.debian.org/debian unstable/main i386 libpython3.12-dev i386 3.12.2-4 [4998 kB] Get: 102 http://deb.debian.org/debian unstable/main i386 libpython3-all-dev i386 3.11.8-1 [1068 B] Get: 103 http://deb.debian.org/debian unstable/main i386 libraqm0 i386 0.10.1-1+b1 [14.7 kB] Get: 104 http://deb.debian.org/debian unstable/main i386 libsharpyuv0 i386 1.3.2-0.4+b1 [107 kB] Get: 105 http://deb.debian.org/debian unstable/main i386 libwebp7 i386 1.3.2-0.4+b1 [314 kB] Get: 106 http://deb.debian.org/debian unstable/main i386 libtiff6 i386 4.5.1+git230720-4 [338 kB] Get: 107 http://deb.debian.org/debian unstable/main i386 libwebpdemux2 i386 1.3.2-0.4+b1 [108 kB] Get: 108 http://deb.debian.org/debian unstable/main i386 libwebpmux3 i386 1.3.2-0.4+b1 [122 kB] Get: 109 http://deb.debian.org/debian unstable/main i386 python3.12 i386 3.12.2-4 [653 kB] Get: 110 http://deb.debian.org/debian unstable/main i386 python3-all i386 3.11.8-1 [1056 B] Get: 111 http://deb.debian.org/debian unstable/main i386 python3.11-dev i386 3.11.8-3 [501 kB] Get: 112 http://deb.debian.org/debian unstable/main i386 python3-dev i386 3.11.8-1 [26.1 kB] Get: 113 http://deb.debian.org/debian unstable/main i386 python3.12-dev i386 3.12.2-4 [499 kB] Get: 114 http://deb.debian.org/debian unstable/main i386 python3-all-dev i386 3.11.8-1 [1072 B] Get: 115 http://deb.debian.org/debian unstable/main i386 python3-numpy i386 1:1.24.2-2 [4879 kB] Get: 116 http://deb.debian.org/debian unstable/main i386 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 117 http://deb.debian.org/debian unstable/main i386 python3-pil i386 10.2.0-1 [526 kB] Get: 118 http://deb.debian.org/debian unstable/main i386 python3-cairo i386 1.25.1-2 [142 kB] Get: 119 http://deb.debian.org/debian unstable/main i386 python3-freetype all 2.4.0-1 [80.3 kB] Get: 120 http://deb.debian.org/debian unstable/main i386 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 121 http://deb.debian.org/debian unstable/main i386 python3-reportlab all 4.1.0-2 [674 kB] Get: 122 http://deb.debian.org/debian unstable/main i386 xml-core all 0.19 [20.1 kB] Get: 123 http://deb.debian.org/debian unstable/main i386 w3c-sgml-lib all 1.3-3 [273 kB] Get: 124 http://deb.debian.org/debian unstable/main i386 python3-biopython i386 1.83+dfsg-1 [1626 kB] Get: 125 http://deb.debian.org/debian unstable/main i386 python3-decorator all 5.1.1-5 [15.1 kB] Get: 126 http://deb.debian.org/debian unstable/main i386 python3-pyparsing all 3.1.1-1 [145 kB] Get: 127 http://deb.debian.org/debian unstable/main i386 python3-scipy i386 1.11.4-6 [19.0 MB] Get: 128 http://deb.debian.org/debian unstable/main i386 python3-zombie-imp all 0.0.2-2 [11.7 kB] Fetched 102 MB in 2s (43.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19643 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.8-3_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.8-3) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.6.2-1_i386.deb ... Unpacking libexpat1:i386 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. 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Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-3.1) ... Selecting previously unselected package libpython3.11-stdlib:i386. Preparing to unpack .../6-libpython3.11-stdlib_3.11.8-3_i386.deb ... Unpacking libpython3.11-stdlib:i386 (3.11.8-3) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.8-3_i386.deb ... Unpacking python3.11 (3.11.8-3) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20952 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_i386.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libpython3.12-minimal:i386. 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Selecting previously unselected package libglib2.0-0t64:i386. Preparing to unpack .../068-libglib2.0-0t64_2.78.4-4_i386.deb ... Unpacking libglib2.0-0t64:i386 (2.78.4-4) ... Selecting previously unselected package libgraphite2-3:i386. Preparing to unpack .../069-libgraphite2-3_1.3.14-2_i386.deb ... Unpacking libgraphite2-3:i386 (1.3.14-2) ... Selecting previously unselected package libharfbuzz0b:i386. Preparing to unpack .../070-libharfbuzz0b_8.3.0-2+b1_i386.deb ... Unpacking libharfbuzz0b:i386 (8.3.0-2+b1) ... Selecting previously unselected package libimagequant0:i386. Preparing to unpack .../071-libimagequant0_2.18.0-1_i386.deb ... Unpacking libimagequant0:i386 (2.18.0-1) ... Selecting previously unselected package libjbig0:i386. Preparing to unpack .../072-libjbig0_2.1-6.1+b1_i386.deb ... Unpacking libjbig0:i386 (2.1-6.1+b1) ... Selecting previously unselected package libjpeg62-turbo:i386. Preparing to unpack .../073-libjpeg62-turbo_1%3a2.1.5-2+b2_i386.deb ... Unpacking libjpeg62-turbo:i386 (1:2.1.5-2+b2) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../074-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../075-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../076-libjs-sphinxdoc_7.2.6-5_all.deb ... Unpacking libjs-sphinxdoc (7.2.6-5) ... Selecting previously unselected package liblapack3:i386. Preparing to unpack .../077-liblapack3_3.12.0-3_i386.deb ... Unpacking liblapack3:i386 (3.12.0-3) ... Selecting previously unselected package liblbfgsb0:i386. Preparing to unpack .../078-liblbfgsb0_3.0+dfsg.4-1+b1_i386.deb ... Unpacking liblbfgsb0:i386 (3.0+dfsg.4-1+b1) ... Selecting previously unselected package liblcms2-2:i386. 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Selecting previously unselected package libpython3-dev:i386. Preparing to unpack .../085-libpython3-dev_3.11.8-1_i386.deb ... Unpacking libpython3-dev:i386 (3.11.8-1) ... Selecting previously unselected package libpython3.12-stdlib:i386. Preparing to unpack .../086-libpython3.12-stdlib_3.12.2-4_i386.deb ... Unpacking libpython3.12-stdlib:i386 (3.12.2-4) ... Selecting previously unselected package libpython3.12t64:i386. Preparing to unpack .../087-libpython3.12t64_3.12.2-4_i386.deb ... Unpacking libpython3.12t64:i386 (3.12.2-4) ... Selecting previously unselected package libpython3.12-dev:i386. Preparing to unpack .../088-libpython3.12-dev_3.12.2-4_i386.deb ... Unpacking libpython3.12-dev:i386 (3.12.2-4) ... Selecting previously unselected package libpython3-all-dev:i386. Preparing to unpack .../089-libpython3-all-dev_3.11.8-1_i386.deb ... Unpacking libpython3-all-dev:i386 (3.11.8-1) ... Selecting previously unselected package libraqm0:i386. Preparing to unpack .../090-libraqm0_0.10.1-1+b1_i386.deb ... Unpacking libraqm0:i386 (0.10.1-1+b1) ... Selecting previously unselected package libsharpyuv0:i386. Preparing to unpack .../091-libsharpyuv0_1.3.2-0.4+b1_i386.deb ... Unpacking libsharpyuv0:i386 (1.3.2-0.4+b1) ... Selecting previously unselected package libwebp7:i386. Preparing to unpack .../092-libwebp7_1.3.2-0.4+b1_i386.deb ... Unpacking libwebp7:i386 (1.3.2-0.4+b1) ... Selecting previously unselected package libtiff6:i386. Preparing to unpack .../093-libtiff6_4.5.1+git230720-4_i386.deb ... Unpacking libtiff6:i386 (4.5.1+git230720-4) ... Selecting previously unselected package libwebpdemux2:i386. Preparing to unpack .../094-libwebpdemux2_1.3.2-0.4+b1_i386.deb ... Unpacking libwebpdemux2:i386 (1.3.2-0.4+b1) ... Selecting previously unselected package libwebpmux3:i386. Preparing to unpack .../095-libwebpmux3_1.3.2-0.4+b1_i386.deb ... Unpacking libwebpmux3:i386 (1.3.2-0.4+b1) ... Selecting previously unselected package python3.12. Preparing to unpack .../096-python3.12_3.12.2-4_i386.deb ... Unpacking python3.12 (3.12.2-4) ... Selecting previously unselected package python3-all. Preparing to unpack .../097-python3-all_3.11.8-1_i386.deb ... Unpacking python3-all (3.11.8-1) ... Selecting previously unselected package python3.11-dev. Preparing to unpack .../098-python3.11-dev_3.11.8-3_i386.deb ... Unpacking python3.11-dev (3.11.8-3) ... Selecting previously unselected package python3-dev. Preparing to unpack .../099-python3-dev_3.11.8-1_i386.deb ... Unpacking python3-dev (3.11.8-1) ... Selecting previously unselected package python3.12-dev. Preparing to unpack .../100-python3.12-dev_3.12.2-4_i386.deb ... Unpacking python3.12-dev (3.12.2-4) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../101-python3-all-dev_3.11.8-1_i386.deb ... Unpacking python3-all-dev (3.11.8-1) ... Selecting previously unselected package python3-numpy. 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Preparing to unpack .../114-python3-scipy_1.11.4-6_i386.deb ... Unpacking python3-scipy (1.11.4-6) ... Selecting previously unselected package python3-zombie-imp. Preparing to unpack .../115-python3-zombie-imp_0.0.2-2_all.deb ... Unpacking python3-zombie-imp (0.0.2-2) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:i386 (1.5.7-1+b2) ... Setting up libgraphite2-3:i386 (1.3.14-2) ... Setting up liblcms2-2:i386 (2.14-2+b1) ... Setting up libpixman-1-0:i386 (0.42.2-1+b1) ... Setting up libsharpyuv0:i386 (1.3.2-0.4+b1) ... Setting up libxau6:i386 (1:1.0.9-1) ... Setting up libicu72:i386 (72.1-4+b1) ... Setting up liblerc4:i386 (4.0.0+ds-4+b1) ... Setting up bsdextrautils (2.39.3-10) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.14.1) ... Setting up libbrotli1:i386 (1.1.0-2+b3) ... Setting up libmagic1t64:i386 (1:5.45-3) ... Setting up libpython3.12-minimal:i386 (3.12.2-4) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libdeflate0:i386 (1.19-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libjbig0:i386 (2.1-6.1+b1) ... Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Apr 18 18:20:32 UTC 2025. Universal Time is now: Fri Apr 18 18:20:32 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:i386 (1:1.1.8-1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:i386 (2.78.4-4) ... No schema files found: doing nothing. Setting up libblas3:i386 (3.12.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libexpat1-dev:i386 (2.6.2-1) ... Setting up libjpeg62-turbo:i386 (1:2.1.5-2+b2) ... Setting up libx11-data (2:1.8.7-1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:i386 (1.0.13-3+b1) ... Setting up libimagequant0:i386 (2.18.0-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:i386 (1.6.43-3) ... Setting up autopoint (0.21-14) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libgfortran5:i386 (14-20240303-1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:i386 (1.3.2-0.4+b1) ... Setting up zlib1g-dev:i386 (1:1.3.dfsg-3.1) ... Setting up sensible-utils (0.0.22) ... Setting up libtiff6:i386 (4.5.1+git230720-4) ... Setting up libuchardet0:i386 (0.0.8-1+b1) ... Setting up libopenjp2-7:i386 (2.5.0-2+b3) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libwebpmux3:i386 (1.3.2-0.4+b1) ... Setting up libbsd0:i386 (0.12.1-1) ... Setting up libelf1:i386 (0.190-1+b1) ... Setting up readline-common (8.2-3.1) ... Setting up libxml2:i386 (2.9.14+dfsg-1.3+b2) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.12-minimal (3.12.2-4) ... Setting up libxdmcp6:i386 (1:1.1.2-3) ... Setting up liblapack3:i386 (3.12.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up libxcb1:i386 (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:i386 (1.15-1) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libwebpdemux2:i386 (1.3.2-0.4+b1) ... Setting up libxcb-shm0:i386 (1.15-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libfreetype6:i386 (2.13.2+dfsg-1+b2) ... Setting up libjs-sphinxdoc (7.2.6-5) ... Setting up libreadline8t64:i386 (8.2-3.1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3+b1) ... Setting up xml-core (0.19) ... Setting up libx11-6:i386 (2:1.8.7-1) ... Setting up libharfbuzz0b:i386 (8.3.0-2+b1) ... Setting up libfontconfig1:i386 (2.15.0-1.1) ... Setting up liblbfgsb0:i386 (3.0+dfsg.4-1+b1) ... Setting up libpython3.12-stdlib:i386 (3.12.2-4) ... Setting up libxrender1:i386 (1:0.9.10-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:i386 (3.11.8-3) ... Setting up python3.12 (3.12.2-4) ... Setting up libpython3.11t64:i386 (3.11.8-3) ... Setting up libxext6:i386 (2:1.3.4-1+b1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:i386 (1.18.0-2) ... Setting up libpython3.12t64:i386 (3.12.2-4) ... Setting up libpython3.11-dev:i386 (3.11.8-3) ... Setting up libraqm0:i386 (0.10.1-1+b1) ... Setting up libpython3-stdlib:i386 (3.11.8-1) ... Setting up python3.11 (3.11.8-3) ... Setting up libpython3-dev:i386 (3.11.8-1) ... Setting up python3.11-dev (3.11.8-3) ... Setting up debhelper (13.14.1) ... Setting up python3 (3.11.8-1) ... Setting up libpython3.12-dev:i386 (3.12.2-4) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-freetype (2.4.0-1) ... Setting up python3-pil:i386 (10.2.0-1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-pyparsing (3.1.1-1) ... Setting up libpython3-all-dev:i386 (3.11.8-1) ... Setting up python3.12-dev (3.12.2-4) ... Setting up python3-lib2to3 (3.12.2-3) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.2-3) ... python3.12: can't get files for byte-compilation Setting up python3-zombie-imp (0.0.2-2) ... Setting up python3-cairo (1.25.1-2) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-all (3.11.8-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-dev (3.11.8-1) ... Setting up python3-numpy (1:1.24.2-2) ... Setting up python3-reportlab (4.1.0-2) ... Setting up dh-python (6.20240310) ... Setting up python3-all-dev (3.11.8-1) ... Setting up python3-scipy (1.11.4-6) ... Processing triggers for libc-bin (2.37-15.1) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.83+dfsg-1) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/17053/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/17053/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/prody-2.4.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../prody_2.4.1+dfsg-2_source.changes dpkg-buildpackage: info: source package prody dpkg-buildpackage: info: source version 2.4.1+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --buildsystem pybuild --with numpy3,python3 dh_auto_clean -O--buildsystem=pybuild I: pybuild base:305: python3.12 setup.py clean running clean removing '/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build' (and everything under it) 'build/bdist.linux-i686' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it I: pybuild base:305: python3.11 setup.py clean running clean removing '/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build' (and everything under it) 'build/bdist.linux-i686' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/prody-2.4.1+dfsg' rm -rf ProDy.egg-info make[1]: Leaving directory '/build/reproducible-path/prody-2.4.1+dfsg' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem pybuild --with numpy3,python3 dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:305: python3.12 setup.py config running config I: pybuild base:305: python3.11 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:305: /usr/bin/python3.12 setup.py build running build running build_py creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody copying prody/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/crossterm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/nbexclusion.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/segment.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/atomic.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/hierview.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/dihedral.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/select.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/donor.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/chain.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/subset.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/angle.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/pointer.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/improper.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/residue.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/flags.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/fields.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/bond.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/acceptor.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/atom.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/atommap.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/atomgroup.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic copying prody/atomic/selection.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/database copying prody/database/cath.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/database copying prody/database/pfam.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/database copying prody/database/quartataweb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/database copying prody/database/goa.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/database copying prody/database/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/database copying prody/database/dali.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/database copying prody/database/uniprot.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/database creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/compare.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/bbenm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/editing.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/pca.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/bildfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/nma.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/mode.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/adaptive.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/essa.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/modeset.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/nmdfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/analysis.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/gamma.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/exgnm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/heatmapper.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/entropy.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/exanm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/clustenm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/sampling.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/imanm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/plotting.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/perturb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/mechstiff.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/rtb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/anm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/gnm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/vmdfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics copying prody/dynamics/signature.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/ensemble copying prody/ensemble/functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/ensemble copying prody/ensemble/conformation.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/ensemble copying prody/ensemble/pdbensemble.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/ensemble copying prody/ensemble/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/ensemble copying prody/ensemble/ensemble.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/ensemble creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/kdtree copying prody/kdtree/kdtree.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/kdtree copying prody/kdtree/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/kdtree creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/measure copying prody/measure/contacts.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/measure copying prody/measure/measure.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/measure copying prody/measure/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/measure copying prody/measure/transform.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/measure creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/wwpdb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/compare.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/pdbfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/stride.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/fixer.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/dssp.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/localpdb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/ciffile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/header.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/emdfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/pdbclusters.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/cifheader.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/blastpdb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/starfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins copying prody/proteins/waterbridges.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/sequence copying prody/sequence/analysis.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/sequence copying prody/sequence/msafile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/sequence copying prody/sequence/msa.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/sequence copying prody/sequence/sequence.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/sequence copying prody/sequence/plotting.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/sequence copying prody/sequence/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/sequence creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/trajectory copying prody/trajectory/frame.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/trajectory copying prody/trajectory/psffile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/trajectory copying prody/trajectory/dcdfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/trajectory copying prody/trajectory/trajectory.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/trajectory copying prody/trajectory/trajfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/trajectory copying prody/trajectory/trajbase.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/trajectory copying prody/trajectory/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/trajectory creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/chromatin copying prody/chromatin/functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/chromatin copying prody/chromatin/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/chromatin copying prody/chromatin/straw.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/chromatin copying prody/chromatin/cluster.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/chromatin copying prody/chromatin/hic.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/chromatin copying prody/chromatin/norm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/chromatin creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/compounds copying prody/compounds/functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/compounds copying prody/compounds/pdbligands.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/compounds copying prody/compounds/ccd.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/compounds copying prody/compounds/bird.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/compounds copying prody/compounds/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/compounds creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/domain_decomposition copying prody/domain_decomposition/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/domain_decomposition copying prody/domain_decomposition/spectrus.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/domain_decomposition creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/misctools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/doctools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/seqtools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/legacy.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/logger.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/eigtools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/pathtools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/drawtools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/TreeConstruction.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/checkers.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/settings.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/laptools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities copying prody/utilities/catchall.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps copying prody/apps/apptools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps copying prody/apps/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_eda.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_contacts.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_select.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_align.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/nmaoptions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_pca.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_catdcd.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_blast.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_biomol.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_energy.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_anm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_clustenm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_fetch.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_gnm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/prody_apps creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_coevol.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_rankorder.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_filter.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_conserv.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_fetch.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_refine.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_occupancy.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_merge.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_search.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/apps/evol_apps creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests copying prody/tests/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/apps copying prody/tests/apps/test_prody_catdcd.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/apps copying prody/tests/apps/test_prody_examples.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/apps copying prody/tests/apps/test_prody_gnm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/apps copying prody/tests/apps/test_prody_anm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/apps copying prody/tests/apps/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/apps copying prody/tests/apps/test_prody_pca.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/apps creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/atomic copying prody/tests/atomic/test_atommap.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/atomic copying prody/tests/atomic/test_fragment.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/atomic copying prody/tests/atomic/test_atomic.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/atomic copying prody/tests/atomic/test_subset.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/atomic copying prody/tests/atomic/test_select.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/atomic copying prody/tests/atomic/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/atomic copying prody/tests/atomic/test_hierview.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/atomic creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/dynamics copying prody/tests/dynamics/test_editing.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/dynamics copying prody/tests/dynamics/test_pca.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/dynamics copying prody/tests/dynamics/test_enms.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/dynamics copying prody/tests/dynamics/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/dynamics copying prody/tests/dynamics/test_signature.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/dynamics creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/ensemble copying prody/tests/ensemble/test_pdbensemble.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/ensemble copying prody/tests/ensemble/test_functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/ensemble copying prody/tests/ensemble/test_ensemble.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/ensemble copying prody/tests/ensemble/test_conformation.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/ensemble copying prody/tests/ensemble/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/ensemble creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/kdtree copying prody/tests/kdtree/test_kdtree.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/kdtree copying prody/tests/kdtree/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/kdtree creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/measure copying prody/tests/measure/test_transform.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/measure copying prody/tests/measure/test_contacts.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/measure copying prody/tests/measure/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/measure copying prody/tests/measure/test_measure.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/measure creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins copying prody/tests/proteins/test_pdbfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins copying prody/tests/proteins/test_ciffile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins copying prody/tests/proteins/test_localpdb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins copying prody/tests/proteins/test_dssp.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins copying prody/tests/proteins/test_header.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins copying prody/tests/proteins/test_wwpdb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins copying prody/tests/proteins/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/proteins creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/sequence copying prody/tests/sequence/test_sequence.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/sequence copying prody/tests/sequence/test_msa.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/sequence copying prody/tests/sequence/test_msafile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/sequence copying prody/tests/sequence/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/sequence copying prody/tests/sequence/test_analysis.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/sequence creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/trajectory copying prody/tests/trajectory/test_frame.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/trajectory copying prody/tests/trajectory/test_dcdfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/trajectory copying prody/tests/trajectory/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/trajectory creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/utilities copying prody/tests/utilities/test_checkers.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/utilities copying prody/tests/utilities/test_misctools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/utilities copying prody/tests/utilities/test_pathtools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/utilities copying prody/tests/utilities/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/utilities creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities/datafiles copying prody/utilities/datafiles/saxs_water.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities/datafiles copying prody/utilities/datafiles/mod_res_map.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities/datafiles copying prody/tests/datafiles/pdb1r19_dssp.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1ubi_ca.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1ejg_oneatom.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb3hsy.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1tw7_step3_charmm2namd.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb2nwl-opm.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdbRTER.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1tw7_step3_charmm2namd_doubled_h36.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb3mht.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb6fpj_Bb_fixed_solv_ions.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1tw7_step3_charmm2namd_doubled_hex.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb2gb1_truncated.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1ejg.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb3o21.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb4v8r_hex.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb2k39_truncated.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb2k39_ca.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb3p3w.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1ubi.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb4v8r_h36.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/commute1ubi.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/exanm2nwl_evalues.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/anm1ubi_evalues.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pca2k39_evalues.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/hit1ubi.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/gnm1ubi_vectors.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/gnm1ubi_evalues.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_Cys_knot_sca.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pca2k39_vectors.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/exanm2nwl_vectors.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_Cys_knot_di.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/anm1ubi_vectors.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/mmcif_6zu5.cif -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/mmcif_6yfy.cif -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/gnm1ubi_kirchhoff.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pca2k39_cov.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/anm1ubi_hessian.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/rtb2gb1_project.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/exanm2nwl_hessian.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/rtb2gb1_hessian.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/dcd2k39_truncated.dcd -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/xmlSTI.xml -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_3hsyA_3o21A.fasta -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_Cys_knot.slx -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_3hsyA_3o21A_new.fasta -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_Cys_knot.fasta -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_Cys_knot.sth -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles running build_ext building 'prody.dynamics.rtbtools' extension creating build creating build/temp.linux-i686-cpython-312 creating build/temp.linux-i686-cpython-312/prody creating build/temp.linux-i686-cpython-312/prody/dynamics i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c prody/dynamics/rtbtools.c -o build/temp.linux-i686-cpython-312/prody/dynamics/rtbtools.o i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/prody/dynamics/rtbtools.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics/rtbtools.cpython-312-i386-linux-gnu.so building 'prody.dynamics.smtools' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c prody/dynamics/smtools.c -o build/temp.linux-i686-cpython-312/prody/dynamics/smtools.o i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/prody/dynamics/smtools.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics/smtools.cpython-312-i386-linux-gnu.so building 'prody.sequence.msatools' extension creating build/temp.linux-i686-cpython-312/prody/sequence i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c prody/sequence/msatools.c -o build/temp.linux-i686-cpython-312/prody/sequence/msatools.o i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/prody/sequence/msatools.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/sequence/msatools.cpython-312-i386-linux-gnu.so building 'prody.sequence.msaio' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c prody/sequence/msaio.c -o build/temp.linux-i686-cpython-312/prody/sequence/msaio.o i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/prody/sequence/msaio.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/sequence/msaio.cpython-312-i386-linux-gnu.so building 'prody.sequence.seqtools' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c prody/sequence/seqtools.c -o build/temp.linux-i686-cpython-312/prody/sequence/seqtools.o i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/prody/sequence/seqtools.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/sequence/seqtools.cpython-312-i386-linux-gnu.so building 'prody.kdtree._CKDTree' extension creating build/temp.linux-i686-cpython-312/prody/kdtree i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c prody/kdtree/KDTree.c -o build/temp.linux-i686-cpython-312/prody/kdtree/KDTree.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c prody/kdtree/KDTreemodule.c -o build/temp.linux-i686-cpython-312/prody/kdtree/KDTreemodule.o i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/prody/kdtree/KDTree.o build/temp.linux-i686-cpython-312/prody/kdtree/KDTreemodule.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/kdtree/_CKDTree.cpython-312-i386-linux-gnu.so building 'prody.proteins.ccealign' extension creating build/temp.linux-i686-cpython-312/prody/proteins creating build/temp.linux-i686-cpython-312/prody/proteins/ccealign i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iprody/utilities/tnt -I/usr/include/python3.12 -c prody/proteins/ccealign/ccealignmodule.cpp -o build/temp.linux-i686-cpython-312/prody/proteins/ccealign/ccealignmodule.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/prody/proteins/ccealign/ccealignmodule.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins/ccealign.cpython-312-i386-linux-gnu.so I: pybuild base:305: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody copying prody/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/crossterm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/nbexclusion.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/segment.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/atomic.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/hierview.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/dihedral.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/select.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/donor.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/chain.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/subset.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/angle.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/pointer.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/improper.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/residue.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/flags.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/fields.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/bond.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/acceptor.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/atom.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/atommap.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/atomgroup.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic copying prody/atomic/selection.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/atomic creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/database copying prody/database/cath.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/database copying prody/database/pfam.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/database copying prody/database/quartataweb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/database copying prody/database/goa.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/database copying prody/database/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/database copying prody/database/dali.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/database copying prody/database/uniprot.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/database creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/compare.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/bbenm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/editing.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/pca.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/bildfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/nma.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/mode.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/adaptive.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/essa.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/modeset.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/nmdfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/analysis.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/gamma.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/exgnm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/heatmapper.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/entropy.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/exanm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/clustenm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/sampling.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/imanm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/plotting.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/perturb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/mechstiff.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/rtb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/anm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/gnm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/vmdfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics copying prody/dynamics/signature.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/ensemble copying prody/ensemble/functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/ensemble copying prody/ensemble/conformation.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/ensemble copying prody/ensemble/pdbensemble.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/ensemble copying prody/ensemble/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/ensemble copying prody/ensemble/ensemble.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/ensemble creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/kdtree copying prody/kdtree/kdtree.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/kdtree copying prody/kdtree/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/kdtree creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/measure copying prody/measure/contacts.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/measure copying prody/measure/measure.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/measure copying prody/measure/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/measure copying prody/measure/transform.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/measure creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/wwpdb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/compare.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/pdbfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/stride.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/fixer.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/dssp.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/localpdb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/ciffile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/header.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/emdfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/pdbclusters.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/cifheader.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/blastpdb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/starfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins copying prody/proteins/waterbridges.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence copying prody/sequence/analysis.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence copying prody/sequence/msafile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence copying prody/sequence/msa.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence copying prody/sequence/sequence.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence copying prody/sequence/plotting.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence copying prody/sequence/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/trajectory copying prody/trajectory/frame.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/trajectory copying prody/trajectory/psffile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/trajectory copying prody/trajectory/dcdfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/trajectory copying prody/trajectory/trajectory.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/trajectory copying prody/trajectory/trajfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/trajectory copying prody/trajectory/trajbase.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/trajectory copying prody/trajectory/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/trajectory creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/chromatin copying prody/chromatin/functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/chromatin copying prody/chromatin/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/chromatin copying prody/chromatin/straw.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/chromatin copying prody/chromatin/cluster.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/chromatin copying prody/chromatin/hic.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/chromatin copying prody/chromatin/norm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/chromatin creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/compounds copying prody/compounds/functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/compounds copying prody/compounds/pdbligands.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/compounds copying prody/compounds/ccd.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/compounds copying prody/compounds/bird.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/compounds copying prody/compounds/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/compounds creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/domain_decomposition copying prody/domain_decomposition/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/domain_decomposition copying prody/domain_decomposition/spectrus.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/domain_decomposition creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/misctools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/doctools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/seqtools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/legacy.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/logger.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/eigtools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/pathtools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/drawtools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/TreeConstruction.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/checkers.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/settings.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/laptools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities copying prody/utilities/catchall.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps copying prody/apps/apptools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps copying prody/apps/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_eda.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_contacts.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_select.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_align.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/nmaoptions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_pca.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_catdcd.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_blast.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_biomol.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_energy.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_anm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_clustenm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_fetch.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps copying prody/apps/prody_apps/prody_gnm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/prody_apps creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_coevol.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_rankorder.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_filter.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_conserv.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_fetch.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_refine.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_occupancy.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_merge.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/evol_search.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps copying prody/apps/evol_apps/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/apps/evol_apps creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests copying prody/tests/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/apps copying prody/tests/apps/test_prody_catdcd.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/apps copying prody/tests/apps/test_prody_examples.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/apps copying prody/tests/apps/test_prody_gnm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/apps copying prody/tests/apps/test_prody_anm.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/apps copying prody/tests/apps/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/apps copying prody/tests/apps/test_prody_pca.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/apps creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic copying prody/tests/atomic/test_atommap.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic copying prody/tests/atomic/test_fragment.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic copying prody/tests/atomic/test_atomic.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic copying prody/tests/atomic/test_subset.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic copying prody/tests/atomic/test_select.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic copying prody/tests/atomic/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic copying prody/tests/atomic/test_hierview.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/atomic creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics copying prody/tests/dynamics/test_editing.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics copying prody/tests/dynamics/test_pca.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics copying prody/tests/dynamics/test_enms.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics copying prody/tests/dynamics/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics copying prody/tests/dynamics/test_signature.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/ensemble copying prody/tests/ensemble/test_pdbensemble.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/ensemble copying prody/tests/ensemble/test_functions.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/ensemble copying prody/tests/ensemble/test_ensemble.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/ensemble copying prody/tests/ensemble/test_conformation.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/ensemble copying prody/tests/ensemble/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/ensemble creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/kdtree copying prody/tests/kdtree/test_kdtree.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/kdtree copying prody/tests/kdtree/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/kdtree creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/measure copying prody/tests/measure/test_transform.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/measure copying prody/tests/measure/test_contacts.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/measure copying prody/tests/measure/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/measure copying prody/tests/measure/test_measure.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/measure creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins copying prody/tests/proteins/test_pdbfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins copying prody/tests/proteins/test_ciffile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins copying prody/tests/proteins/test_localpdb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins copying prody/tests/proteins/test_dssp.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins copying prody/tests/proteins/test_header.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins copying prody/tests/proteins/test_wwpdb.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins copying prody/tests/proteins/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/proteins creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/sequence copying prody/tests/sequence/test_sequence.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/sequence copying prody/tests/sequence/test_msa.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/sequence copying prody/tests/sequence/test_msafile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/sequence copying prody/tests/sequence/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/sequence copying prody/tests/sequence/test_analysis.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/sequence creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/trajectory copying prody/tests/trajectory/test_frame.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/trajectory copying prody/tests/trajectory/test_dcdfile.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/trajectory copying prody/tests/trajectory/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/trajectory creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/utilities copying prody/tests/utilities/test_checkers.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/utilities copying prody/tests/utilities/test_misctools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/utilities copying prody/tests/utilities/test_pathtools.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/utilities copying prody/tests/utilities/__init__.py -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/utilities creating /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities/datafiles copying prody/utilities/datafiles/saxs_water.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities/datafiles copying prody/utilities/datafiles/mod_res_map.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities/datafiles copying prody/tests/datafiles/pdb1r19_dssp.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1ubi_ca.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1ejg_oneatom.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb3hsy.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1tw7_step3_charmm2namd.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb2nwl-opm.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdbRTER.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1tw7_step3_charmm2namd_doubled_h36.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb3mht.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb6fpj_Bb_fixed_solv_ions.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1tw7_step3_charmm2namd_doubled_hex.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb2gb1_truncated.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1ejg.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb3o21.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb4v8r_hex.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb2k39_truncated.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb2k39_ca.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb3p3w.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb1ubi.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pdb4v8r_h36.pdb -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/commute1ubi.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/exanm2nwl_evalues.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/anm1ubi_evalues.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pca2k39_evalues.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/hit1ubi.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/gnm1ubi_vectors.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/gnm1ubi_evalues.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_Cys_knot_sca.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pca2k39_vectors.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/exanm2nwl_vectors.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_Cys_knot_di.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/anm1ubi_vectors.dat -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/mmcif_6zu5.cif -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/mmcif_6yfy.cif -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/gnm1ubi_kirchhoff.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/pca2k39_cov.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/anm1ubi_hessian.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/rtb2gb1_project.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/exanm2nwl_hessian.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/rtb2gb1_hessian.coo -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/dcd2k39_truncated.dcd -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/xmlSTI.xml -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_3hsyA_3o21A.fasta -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_Cys_knot.slx -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_3hsyA_3o21A_new.fasta -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_Cys_knot.fasta -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles copying prody/tests/datafiles/msa_Cys_knot.sth -> /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles running build_ext building 'prody.dynamics.rtbtools' extension creating build/temp.linux-i686-cpython-311 creating build/temp.linux-i686-cpython-311/prody creating build/temp.linux-i686-cpython-311/prody/dynamics i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c prody/dynamics/rtbtools.c -o build/temp.linux-i686-cpython-311/prody/dynamics/rtbtools.o i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/prody/dynamics/rtbtools.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics/rtbtools.cpython-311-i386-linux-gnu.so building 'prody.dynamics.smtools' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c prody/dynamics/smtools.c -o build/temp.linux-i686-cpython-311/prody/dynamics/smtools.o i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/prody/dynamics/smtools.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/dynamics/smtools.cpython-311-i386-linux-gnu.so building 'prody.sequence.msatools' extension creating build/temp.linux-i686-cpython-311/prody/sequence i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c prody/sequence/msatools.c -o build/temp.linux-i686-cpython-311/prody/sequence/msatools.o i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/prody/sequence/msatools.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence/msatools.cpython-311-i386-linux-gnu.so building 'prody.sequence.msaio' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c prody/sequence/msaio.c -o build/temp.linux-i686-cpython-311/prody/sequence/msaio.o i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/prody/sequence/msaio.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence/msaio.cpython-311-i386-linux-gnu.so building 'prody.sequence.seqtools' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c prody/sequence/seqtools.c -o build/temp.linux-i686-cpython-311/prody/sequence/seqtools.o i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/prody/sequence/seqtools.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence/seqtools.cpython-311-i386-linux-gnu.so building 'prody.kdtree._CKDTree' extension creating build/temp.linux-i686-cpython-311/prody/kdtree i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c prody/kdtree/KDTree.c -o build/temp.linux-i686-cpython-311/prody/kdtree/KDTree.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c prody/kdtree/KDTreemodule.c -o build/temp.linux-i686-cpython-311/prody/kdtree/KDTreemodule.o i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/prody/kdtree/KDTree.o build/temp.linux-i686-cpython-311/prody/kdtree/KDTreemodule.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/kdtree/_CKDTree.cpython-311-i386-linux-gnu.so building 'prody.proteins.ccealign' extension creating build/temp.linux-i686-cpython-311/prody/proteins creating build/temp.linux-i686-cpython-311/prody/proteins/ccealign i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iprody/utilities/tnt -I/usr/include/python3.11 -c prody/proteins/ccealign/ccealignmodule.cpp -o build/temp.linux-i686-cpython-311/prody/proteins/ccealign/ccealignmodule.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prody-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/prody/proteins/ccealign/ccealignmodule.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/proteins/ccealign.cpython-311-i386-linux-gnu.so dh_auto_test -O--buildsystem=pybuild I: pybuild base:305: cd /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build; python3.12 -m unittest discover -v /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities/doctools.py:48: SyntaxWarning: invalid escape sequence '\i' """Returns wrapped lines from :func:`textwrap.wrap` after *join*\ing them. /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic/flags.py:463: SyntaxWarning: invalid escape sequence '\ ' __doc__ += """ /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic/select.py:2: SyntaxWarning: invalid escape sequence '\|' """This module defines a class for selecting subsets of atoms. You can read /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic/select.py:719: SyntaxWarning: invalid escape sequence '\w' RE_SCHARS = re_compile('`[\w\W]*?`') /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic/select.py:738: SyntaxWarning: invalid escape sequence '\w' RE_REGEXP = re_compile('"[\w\W]*"') /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic/select.py:757: SyntaxWarning: invalid escape sequence '\d' _ = '[-+]?\d+(\.\d*)?([eE]\d+)?' /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic/select.py:758: SyntaxWarning: invalid escape sequence '\ ' RE_NRANGE = re_compile(_ + '\ *(to|:)\ *' + _) /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/atomic/select.py:761: SyntaxWarning: invalid escape sequence '\ ' pp.Optional(pp.Regex('(\ *:\ *' + _ + ')'))) /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/sequence/analysis.py:169: SyntaxWarning: invalid escape sequence '\{' """Apply one of the normalizations discussed in [MLC05]_ to *mutinfo* /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins/localpdb.py:438: SyntaxWarning: invalid escape sequence '\.' pdbext = compile('\.(pdb|ent)(\.gz)?$', IGNORECASE) /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins/localpdb.py:440: SyntaxWarning: invalid escape sequence '\.' pdbext = compile('\.(pdb|ent)\.gz$', IGNORECASE) /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins/localpdb.py:442: SyntaxWarning: invalid escape sequence '\.' pdbext = compile('\.(pdb|ent)$', IGNORECASE) /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/proteins/dssp.py:78: SyntaxWarning: invalid escape sequence '\*' """Parse DSSP data from file *dssp* into :class:`.AtomGroup` instance /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/dynamics/pca.py:59: SyntaxWarning: invalid escape sequence '\_' """Build a covariance matrix for *coordsets* using mean coordinates testANMCommand (prody.tests.apps.test_prody_anm.TestANMCommand.testANMCommand) ... skipped 'prody command not found' testAlignConcat (prody.tests.apps.test_prody_catdcd.TestCatdcdCommand.testAlignConcat) ... skipped 'prody command not found' testAlignException (prody.tests.apps.test_prody_catdcd.TestCatdcdCommand.testAlignException) ... skipped 'prody command is not found' testIOException (prody.tests.apps.test_prody_catdcd.TestCatdcdCommand.testIOException) ... skipped 'prody command is not found' testSelectConcat (prody.tests.apps.test_prody_catdcd.TestCatdcdCommand.testSelectConcat) ... skipped 'prody command not found' testSelectException (prody.tests.apps.test_prody_catdcd.TestCatdcdCommand.testSelectException) ... skipped 'prody command is not found' testSelectException2 (prody.tests.apps.test_prody_catdcd.TestCatdcdCommand.testSelectException2) ... skipped 'prody command is not found' testSimpleConcat (prody.tests.apps.test_prody_catdcd.TestCatdcdCommand.testSimpleConcat) ... skipped 'prody command not found' testCommandExample1 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample1) Test example: $ prody anm 1p38 ... skipped 'prody command not found' testCommandExample10 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample10) Test example: $ prody align 2k39 --select "backbone and resnum < 71" ... skipped 'prody command not found' testCommandExample11 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample11) Test example: $ prody align --select "resnum < 300" 1p38 1r39 1zz2 ... skipped 'prody command not found' testCommandExample12 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample12) Test example: $ prody align --select "resnum 1 to 70" 1aar 2k39 ... skipped 'prody command not found' testCommandExample13 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample13) Test example: $ prody align --select "noh heme and chain A" 1hrc 1fi7 ... skipped 'prody command not found' testCommandExample14 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample14) Test example: $ prody biomol 2bfu ... skipped 'prody command not found' testCommandExample15 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample15) Test example: $ prody select -o B11 "resname B11" 1zz2 $ prody select -o BOG "resname BOG" 1zz2 $ prody contacts -r 4.0 -t residue -s protein 1zz2 B11.pdb BOG.pdb ... skipped 'prody command not found' testCommandExample16 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample16) Test example: $ prody fetch 1mkp 1p38 ... skipped 'prody command not found' testCommandExample17 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample17) Test example: $ prody select backbone 1p38 1r39 ... skipped 'prody command not found' testCommandExample18 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample18) Test example: $ prody energy 1p38 1r39 ... skipped 'prody command not found' testCommandExample19 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample19) Test example: $ prody clustenm 1p38 ... skipped 'prody command not found' testCommandExample2 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample2) Test example: $ prody anm 1aar -s "calpha and chain A and resnum < 70" -A ... skipped 'prody command not found' testCommandExample20 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample20) Test example: $ prody clustenm 1aar -s "calpha and chain A and resnum < 70" -A ... skipped 'prody command not found' testCommandExample3 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample3) Test example: $ prody gnm 1p38 ... skipped 'prody command not found' testCommandExample4 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample4) Test example: $ prody gnm 1aar -c 7 -s "calpha and chain A and resnum < 70" -A ... skipped 'prody command not found' testCommandExample5 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample5) Test example: $ prody pca 2k39 ... skipped 'prody command not found' testCommandExample6 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample6) Test example: $ prody pca 2k39 --select "backbone and resnum < 71" -a -A ... skipped 'prody command not found' testCommandExample7 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample7) Test example: $ prody pca 2k39 ... skipped 'prody command not found' testCommandExample8 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample8) Test example: $ prody pca 2k39 --select "backbone and resnum < 71" -a -A ... skipped 'prody command not found' testCommandExample9 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample9) Test example: $ prody align 2k39 ... skipped 'prody command not found' testGNMCommand (prody.tests.apps.test_prody_gnm.TestGNMCommand.testGNMCommand) ... skipped 'prody command not found' testPCACommandDCD (prody.tests.apps.test_prody_pca.TestPCACommand.testPCACommandDCD) ... skipped 'prody command not found' testPCACommandPDB (prody.tests.apps.test_prody_pca.TestPCACommand.testPCACommandPDB) ... skipped 'prody command not found' testAtomGroup (prody.tests.atomic.test_atomic.TestAtomIterations.testAtomGroup) ... ok testAtomMap (prody.tests.atomic.test_atomic.TestAtomIterations.testAtomMap) ... ok testChain (prody.tests.atomic.test_atomic.TestAtomIterations.testChain) ... ok testResidue (prody.tests.atomic.test_atomic.TestAtomIterations.testResidue) ... ok testSelection (prody.tests.atomic.test_atomic.TestAtomIterations.testSelection) ... ok testAtom (prody.tests.atomic.test_atomic.TestPickling.testAtom) ... ok testAtomGroup (prody.tests.atomic.test_atomic.TestPickling.testAtomGroup) ... ok testSelection (prody.tests.atomic.test_atomic.TestPickling.testSelection) ... ok testSaveLoad (prody.tests.atomic.test_atomic.TestSaveLoad.testSaveLoad) ... ok testInstantiation (prody.tests.atomic.test_atommap.TestInstantiation.testInstantiation) ... ok testAllSelection (prody.tests.atomic.test_atommap.TestSelection.testAllSelection) ... ok testChainSelection (prody.tests.atomic.test_atommap.TestSelection.testChainSelection) ... ok testGetBoolArray (prody.tests.atomic.test_atommap.TestSelection.testGetBoolArray) ... ok testNameSelection (prody.tests.atomic.test_atommap.TestSelection.testNameSelection) ... ok testSplit (prody.tests.atomic.test_fragment.TestFragment.testSplit) ... ok testSplitCopy (prody.tests.atomic.test_fragment.TestFragment.testSplitCopy) ... ok testSplitNoh (prody.tests.atomic.test_fragment.TestFragment.testSplitNoh) ... ok testSplitNohCopy (prody.tests.atomic.test_fragment.TestFragment.testSplitNohCopy) ... ok testWhole (prody.tests.atomic.test_fragment.TestFragment.testWhole) ... ok testWhole2 (prody.tests.atomic.test_fragment.TestFragment.testWhole2) ... ok testWholeAll (prody.tests.atomic.test_fragment.TestFragment.testWholeAll) ... ok testWholeCopy (prody.tests.atomic.test_fragment.TestFragment.testWholeCopy) ... ok testWholeNoh (prody.tests.atomic.test_fragment.TestFragment.testWholeNoh) ... ok testWholeNohCopy (prody.tests.atomic.test_fragment.TestFragment.testWholeNohCopy) ... ok testCA (prody.tests.atomic.test_hierview.TestShuffled.testCA) ... ok testProtein (prody.tests.atomic.test_hierview.TestShuffled.testProtein) ... ok testNumResidues (prody.tests.atomic.test_hierview.TestTerRecord.testNumResidues) ... ok testResidueIndexing (prody.tests.atomic.test_hierview.TestTerRecord.testResidueIndexing) ... ok testSelectionResidueIndexing (prody.tests.atomic.test_hierview.TestTerRecord.testSelectionResidueIndexing) ... ok testSelectionResidueIndexing2 (prody.tests.atomic.test_hierview.TestTerRecord.testSelectionResidueIndexing2) ... ok testMacro1 (prody.tests.atomic.test_select.TestMacros.testMacro1) Test macro *cacb*: 'name CA CB' ... ok testMacro2 (prody.tests.atomic.test_select.TestMacros.testMacro2) Test macro *donors*: '(protein) and (name N NE NH2 ND2 NE2 ND1 OG OH NH1 SG OG1 NE2 NZ NE1 ND1 NE2)' ... ok testMacroFunctions (prody.tests.atomic.test_select.TestMacros.testMacroFunctions) ... ok testBondedtoSelection1 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection1) Test bondedto selections 'bonded to index 0' for imatinib ... ok testBondedtoSelection10 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection10) Test bondedto selections "bonded 2 to index 0" ... ok testBondedtoSelection11 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection11) Test bondedto selections 'bonded 0 to index 0' for imatinib ... ok testBondedtoSelection12 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection12) Test bondedto selections "bonded 0 to index 0" ... ok testBondedtoSelection13 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection13) Test bondedto selections 'bonded 3 to index 0' for imatinib ... ok testBondedtoSelection14 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection14) Test bondedto selections "bonded 3 to index 0" ... ok testBondedtoSelection15 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection15) Test bondedto selections 'bonded 4 to index 0' for imatinib ... ok testBondedtoSelection16 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection16) Test bondedto selections "bonded 4 to index 0" ... ok testBondedtoSelection17 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection17) Test bondedto selections 'bonded 4 to index 0' for imatinib ... ok testBondedtoSelection18 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection18) Test bondedto selections "bonded 4 to index 0" ... ok testBondedtoSelection19 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection19) Test bondedto selections 'bonded 4 to index 0' for imatinib ... ok testBondedtoSelection2 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection2) Test bondedto selections "bonded to index 0" ... ok testBondedtoSelection20 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection20) Test bondedto selections "bonded 4 to index 0" ... ok testBondedtoSelection21 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection21) Test bondedto selections 'exbonded 1 to index 0' for imatinib ... ok testBondedtoSelection22 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection22) Test bondedto selections "exbonded 1 to index 0" ... ok testBondedtoSelection23 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection23) Test bondedto selections 'exbonded 2 to index 0' for imatinib ... ok testBondedtoSelection24 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection24) Test bondedto selections "exbonded 2 to index 0" ... ok testBondedtoSelection25 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection25) Test bondedto selections 'exbonded 3 to index 0' for imatinib ... ok testBondedtoSelection26 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection26) Test bondedto selections "exbonded 3 to index 0" ... ok testBondedtoSelection27 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection27) Test bondedto selections 'bonded 20 to index 0' for imatinib ... ok testBondedtoSelection28 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection28) Test bondedto selections "bonded 20 to index 0" ... ok testBondedtoSelection29 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection29) Test bondedto selections 'bonded 20 to index 10' for imatinib ... ok testBondedtoSelection3 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection3) Test bondedto selections 'exbonded to index 0' for imatinib ... ok testBondedtoSelection30 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection30) Test bondedto selections "bonded 20 to index 10" ... ok testBondedtoSelection31 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection31) Test bondedto selections 'bonded to index 1000' for imatinib ... ok testBondedtoSelection32 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection32) Test bondedto selections "bonded to index 1000" ... ok testBondedtoSelection33 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection33) Test bondedto selections 'fragment 0' for imatinib ... ok testBondedtoSelection34 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection34) Test bondedto selections "fragment 0" ... ok testBondedtoSelection35 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection35) Test bondedto selections 'fragment 1' for imatinib ... ok testBondedtoSelection36 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection36) Test bondedto selections "fragment 1" ... ok testBondedtoSelection37 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection37) Test bondedto selections 'fragment 0 1 2' for imatinib ... ok testBondedtoSelection38 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection38) Test bondedto selections "fragment 0 1 2" ... ok testBondedtoSelection39 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection39) Test bondedto selections 'fragindex 0 1 2' for imatinib ... ok testBondedtoSelection4 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection4) Test bondedto selections "exbonded to index 0" ... ok testBondedtoSelection40 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection40) Test bondedto selections "fragindex 0 1 2" ... ok testBondedtoSelection41 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection41) Test bondedto selections 'fragindex 0:2' for imatinib ... ok testBondedtoSelection42 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection42) Test bondedto selections "fragindex 0:2" ... ok testBondedtoSelection5 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection5) Test bondedto selections 'bonded to index 67' for imatinib ... ok testBondedtoSelection6 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection6) Test bondedto selections "bonded to index 67" ... ok testBondedtoSelection7 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection7) Test bondedto selections 'exbonded to index 67' for imatinib ... ok testBondedtoSelection8 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection8) Test bondedto selections "exbonded to index 67" ... ok testBondedtoSelection9 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection9) Test bondedto selections 'bonded 2 to index 0' for imatinib ... ok testComparisonsSelection1 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection1) Test comparisons selections 'x = -51.659' for pdb3mht ... ok testComparisonsSelection10 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection10) Test comparisons selections "beta > 10" ... ok testComparisonsSelection11 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection11) Test comparisons selections 'beta < 10' for pdb3mht ... ok testComparisonsSelection12 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection12) Test comparisons selections "beta < 10" ... ok testComparisonsSelection13 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection13) Test comparisons selections 'occupancy > 0.999999' for pdb3mht ... ok testComparisonsSelection14 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection14) Test comparisons selections "occupancy > 0.999999" ... ok testComparisonsSelection15 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection15) Test comparisons selections '-10 <= x < 0' for pdb3mht ... ok testComparisonsSelection16 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection16) Test comparisons selections "-10 <= x < 0" ... ok testComparisonsSelection17 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection17) Test comparisons selections '11 > 10' for pdb3mht ... ok testComparisonsSelection18 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection18) Test comparisons selections "11 > 10" ... ok testComparisonsSelection19 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection19) Test comparisons selections 'radius > 10' for pdb3mht ... ok testComparisonsSelection2 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection2) Test comparisons selections "x = -51.659" ... ok testComparisonsSelection20 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection20) Test comparisons selections "radius > 10" ... ok testComparisonsSelection21 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection21) Test comparisons selections 'chain = A' for pdb3mht ... ok testComparisonsSelection22 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection22) Test comparisons selections "chain = A" ... ok testComparisonsSelection23 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection23) Test comparisons selections 'x x < 1' for pdb3mht ... ok testComparisonsSelection24 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection24) Test comparisons selections "x x < 1" ... ok testComparisonsSelection25 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection25) Test comparisons selections 'name < 1' for pdb3mht ... ok testComparisonsSelection26 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection26) Test comparisons selections "name < 1" ... ok testComparisonsSelection3 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection3) Test comparisons selections 'x != -51.659' for pdb3mht ... ok testComparisonsSelection4 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection4) Test comparisons selections "x != -51.659" ... ok testComparisonsSelection5 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection5) Test comparisons selections 'z >= 82.813' for pdb3mht ... ok testComparisonsSelection6 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection6) Test comparisons selections "z >= 82.813" ... ok testComparisonsSelection7 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection7) Test comparisons selections 'z < 82.813' for pdb3mht ... ok testComparisonsSelection8 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection8) Test comparisons selections "z < 82.813" ... ok testComparisonsSelection9 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection9) Test comparisons selections 'beta > 10' for pdb3mht ... ok testCompositeSelection1 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection1) Test composite selections 'chain x y z C and x 10' for pdb3mht ... ok testCompositeSelection10 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection10) Test composite selections "water and within 5 of not protein" ... ok testCompositeSelection11 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection11) Test composite selections 'backbone and sqrt((x - 25)**2 + (y - 74)**2 + (z - 13)**2) <= 500' for pdb3mht ... ok testCompositeSelection12 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection12) Test composite selections "backbone and sqrt((x - 25)**2 + (y - 74)**2 + (z - 13)**2) <= 500" ... ok testCompositeSelection13 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection13) Test composite selections '(not resname SAH) and (protein and name CA) or (nucleic and name P)' for pdb3mht ... ok testCompositeSelection14 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection14) Test composite selections "(not resname SAH) and (protein and name CA) or (nucleic and name P)" ... ok testCompositeSelection15 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection15) Test composite selections 'protein and (backbone or name H)' for pdb3mht ... ok testCompositeSelection16 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection16) Test composite selections "protein and (backbone or name H)" ... ok testCompositeSelection17 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection17) Test composite selections 'same residue as within 4 of and resname SAH' for pdb3mht ... ok testCompositeSelection18 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection18) Test composite selections "same residue as within 4 of and resname SAH" ... ok testCompositeSelection19 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection19) Test composite selections 'protein and name CA CB and same residue as ((x+21.2)**2 + (y-35.9)**2 + (z-80.0)**2)**0.5 < 10' for pdb3mht ... ok testCompositeSelection2 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection2) Test composite selections "chain x y z C and x 10" ... ok testCompositeSelection20 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection20) Test composite selections "protein and name CA CB and same residue as ((x+21.2)**2 + (y-35.9)**2 + (z-80.0)**2)**0.5 < 10" ... ok testCompositeSelection3 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection3) Test composite selections 'resnum `1` `2`' for pdb3mht ... ok testCompositeSelection4 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection4) Test composite selections "resnum `1` `2`" ... ok testCompositeSelection5 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection5) Test composite selections 'same residue as within 4 of resname SAH' for pdb3mht ... ok testCompositeSelection6 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection6) Test composite selections "same residue as within 4 of resname SAH" ... ok testCompositeSelection7 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection7) Test composite selections 'name CA and same residue as within 4 of resname SAH' for pdb3mht ... ok testCompositeSelection8 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection8) Test composite selections "name CA and same residue as within 4 of resname SAH" ... ok testCompositeSelection9 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection9) Test composite selections 'water and within 5 of not protein' for pdb3mht ... ok testDocexamplesSelection1 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection1) Test docexamples selections 'serial 1 2 3' for pdb3mht ... ok testDocexamplesSelection10 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection10) Test docexamples selections "beta 555.55" ... ok testDocexamplesSelection11 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection11) Test docexamples selections 'beta 1 to 500' for pdb3mht ... ok testDocexamplesSelection12 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection12) Test docexamples selections "beta 1 to 500" ... ok testDocexamplesSelection13 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection13) Test docexamples selections 'beta 1:500' for pdb3mht ... ok testDocexamplesSelection14 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection14) Test docexamples selections "beta 1:500" ... ok testDocexamplesSelection15 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection15) Test docexamples selections 'beta < 500' for pdb3mht ... ok testDocexamplesSelection16 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection16) Test docexamples selections "beta < 500" ... ok testDocexamplesSelection17 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection17) Test docexamples selections 'resnum 120A 120B' for pdb3mht ... ok testDocexamplesSelection18 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection18) Test docexamples selections "resnum 120A 120B" ... ok testDocexamplesSelection19 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection19) Test docexamples selections 'icode A' for pdb3mht ... ok testDocexamplesSelection2 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection2) Test docexamples selections "serial 1 2 3" ... ok testDocexamplesSelection20 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection20) Test docexamples selections "icode A" ... ok testDocexamplesSelection21 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection21) Test docexamples selections 'icode _' for pdb3mht ... ok testDocexamplesSelection22 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection22) Test docexamples selections "icode _" ... ok testDocexamplesSelection23 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection23) Test docexamples selections 'charge 1' for pdb3mht ... ok testDocexamplesSelection24 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection24) Test docexamples selections "charge 1" ... ok testDocexamplesSelection25 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection25) Test docexamples selections 'abs(charge) == 1' for pdb3mht ... ok testDocexamplesSelection26 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection26) Test docexamples selections "abs(charge) == 1" ... ok testDocexamplesSelection27 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection27) Test docexamples selections 'charge < 0' for pdb3mht ... ok testDocexamplesSelection28 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection28) Test docexamples selections "charge < 0" ... ok testDocexamplesSelection29 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection29) Test docexamples selections '0 < mass < 500' for pdb3mht ... ok testDocexamplesSelection3 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection3) Test docexamples selections 'serial 1 to 10' for pdb3mht ... ok testDocexamplesSelection30 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection30) Test docexamples selections "0 < mass < 500" ... ok testDocexamplesSelection31 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection31) Test docexamples selections 'abs(mass) <= mass <= 10' for pdb3mht ... ok testDocexamplesSelection32 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection32) Test docexamples selections "abs(mass) <= mass <= 10" ... ok testDocexamplesSelection4 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection4) Test docexamples selections "serial 1 to 10" ... ok testDocexamplesSelection5 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection5) Test docexamples selections 'serial 1:10:2' for pdb3mht ... ok testDocexamplesSelection6 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection6) Test docexamples selections "serial 1:10:2" ... ok testDocexamplesSelection7 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection7) Test docexamples selections 'serial < 10' for pdb3mht ... ok testDocexamplesSelection8 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection8) Test docexamples selections "serial < 10" ... ok testDocexamplesSelection9 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection9) Test docexamples selections 'beta 555.55' for pdb3mht ... ok testEquivalentSelection1 (prody.tests.atomic.test_select.TestSelect.testEquivalentSelection1) Test equivalent selections 'chain C' for pdb3mht ... ok testEquivalentSelection2 (prody.tests.atomic.test_select.TestSelect.testEquivalentSelection2) Test equivalent selections "chain C" ... ok testEquivalentSelection3 (prody.tests.atomic.test_select.TestSelect.testEquivalentSelection3) Test equivalent selections 'chain C' for pdb3mht ... ok testEquivalentSelection4 (prody.tests.atomic.test_select.TestSelect.testEquivalentSelection4) Test equivalent selections "chain C" ... ok testEquivalentSelection5 (prody.tests.atomic.test_select.TestSelect.testEquivalentSelection5) Test equivalent selections 'nucleic' for pdb3mht ... ok testEquivalentSelection6 (prody.tests.atomic.test_select.TestSelect.testEquivalentSelection6) Test equivalent selections "nucleic" ... ok testFlagsSelection1 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection1) Test flags selections 'protein' for gromacs ... ok testFlagsSelection10 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection10) Test flags selections "aliphatic" ... ok testFlagsSelection100 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection100) Test flags selections "bridge" ... ok testFlagsSelection101 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection101) Test flags selections 'bend' for pdb3mht ... ok testFlagsSelection102 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection102) Test flags selections "bend" ... ok testFlagsSelection103 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection103) Test flags selections 'coil' for pdb3mht ... ok testFlagsSelection104 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection104) Test flags selections "coil" ... ok testFlagsSelection11 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection11) Test flags selections 'aromatic' for pdb3mht ... ok testFlagsSelection12 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection12) Test flags selections "aromatic" ... ok testFlagsSelection13 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection13) Test flags selections 'at' for pdb3mht ... ok testFlagsSelection14 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection14) Test flags selections "at" ... ok testFlagsSelection15 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection15) Test flags selections 'basic' for pdb3mht ... ok testFlagsSelection16 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection16) Test flags selections "basic" ... ok testFlagsSelection17 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection17) Test flags selections 'buried' for pdb3mht ... ok testFlagsSelection18 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection18) Test flags selections "buried" ... ok testFlagsSelection19 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection19) Test flags selections 'cg' for pdb3mht ... ok testFlagsSelection2 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection2) Test flags selections "protein" ... ok testFlagsSelection20 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection20) Test flags selections "cg" ... ok testFlagsSelection21 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection21) Test flags selections 'charged' for pdb3mht ... ok testFlagsSelection22 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection22) Test flags selections "charged" ... ok testFlagsSelection23 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection23) Test flags selections 'cyclic' for pdb3mht ... ok testFlagsSelection24 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection24) Test flags selections "cyclic" ... ok testFlagsSelection25 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection25) Test flags selections 'heme' for pdb3mht ... ok testFlagsSelection26 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection26) Test flags selections "heme" ... ok testFlagsSelection27 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection27) Test flags selections 'hydrophobic' for pdb3mht ... ok testFlagsSelection28 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection28) Test flags selections "hydrophobic" ... ok testFlagsSelection29 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection29) Test flags selections 'ion' for pdb3mht ... ok testFlagsSelection3 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection3) Test flags selections 'all' for pdb3mht ... ok testFlagsSelection30 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection30) Test flags selections "ion" ... ok testFlagsSelection31 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection31) Test flags selections 'large' for pdb3mht ... ok testFlagsSelection32 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection32) Test flags selections "large" ... ok testFlagsSelection33 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection33) Test flags selections 'lipid' for pdb3mht ... ok testFlagsSelection34 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection34) Test flags selections "lipid" ... ok testFlagsSelection35 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection35) Test flags selections 'medium' for pdb3mht ... ok testFlagsSelection36 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection36) Test flags selections "medium" ... ok testFlagsSelection37 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection37) Test flags selections 'neutral' for pdb3mht ... ok testFlagsSelection38 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection38) Test flags selections "neutral" ... ok testFlagsSelection39 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection39) Test flags selections 'nucleic' for pdb3mht ... ok testFlagsSelection4 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection4) Test flags selections "all" ... ok testFlagsSelection40 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection40) Test flags selections "nucleic" ... ok testFlagsSelection41 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection41) Test flags selections 'nucleotide' for pdb3mht ... ok testFlagsSelection42 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection42) Test flags selections "nucleotide" ... ok testFlagsSelection43 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection43) Test flags selections 'nucleobase' for pdb3mht ... ok testFlagsSelection44 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection44) Test flags selections "nucleobase" ... ok testFlagsSelection45 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection45) Test flags selections 'nucleoside' for pdb3mht ... ok testFlagsSelection46 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection46) Test flags selections "nucleoside" ... ok testFlagsSelection47 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection47) Test flags selections 'polar' for pdb3mht ... ok testFlagsSelection48 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection48) Test flags selections "polar" ... ok testFlagsSelection49 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection49) Test flags selections 'protein' for pdb3mht ... ok testFlagsSelection5 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection5) Test flags selections 'acidic' for pdb3mht ... ok testFlagsSelection50 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection50) Test flags selections "protein" ... ok testFlagsSelection51 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection51) Test flags selections 'stdaa' for pdb3mht ... ok testFlagsSelection52 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection52) Test flags selections "stdaa" ... ok testFlagsSelection53 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection53) Test flags selections 'nonstdaa' for pdb3mht ... ok testFlagsSelection54 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection54) Test flags selections "nonstdaa" ... ok testFlagsSelection55 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection55) Test flags selections 'purine' for pdb3mht ... ok testFlagsSelection56 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection56) Test flags selections "purine" ... ok testFlagsSelection57 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection57) Test flags selections 'pyrimidine' for pdb3mht ... ok testFlagsSelection58 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection58) Test flags selections "pyrimidine" ... ok testFlagsSelection59 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection59) Test flags selections 'small' for pdb3mht ... ok testFlagsSelection6 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection6) Test flags selections "acidic" ... ok testFlagsSelection60 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection60) Test flags selections "small" ... ok testFlagsSelection61 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection61) Test flags selections 'sugar' for pdb3mht ... ok testFlagsSelection62 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection62) Test flags selections "sugar" ... ok testFlagsSelection63 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection63) Test flags selections 'surface' for pdb3mht ... ok testFlagsSelection64 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection64) Test flags selections "surface" ... ok testFlagsSelection65 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection65) Test flags selections 'water' for pdb3mht ... ok testFlagsSelection66 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection66) Test flags selections "water" ... ok testFlagsSelection67 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection67) Test flags selections 'hetero' for pdb3mht ... ok testFlagsSelection68 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection68) Test flags selections "hetero" ... ok testFlagsSelection69 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection69) Test flags selections 'hetatm' for pdb3mht ... ok testFlagsSelection7 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection7) Test flags selections 'acyclic' for pdb3mht ... ok testFlagsSelection70 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection70) Test flags selections "hetatm" ... ok testFlagsSelection71 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection71) Test flags selections 'calpha' for pdb3mht ... ok testFlagsSelection72 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection72) Test flags selections "calpha" ... ok testFlagsSelection73 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection73) Test flags selections 'backbone' for pdb3mht ... ok testFlagsSelection74 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection74) Test flags selections "backbone" ... ok testFlagsSelection75 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection75) Test flags selections 'backbonefull' for pdb3mht ... ok testFlagsSelection76 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection76) Test flags selections "backbonefull" ... ok testFlagsSelection77 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection77) Test flags selections 'sidechain' for pdb3mht ... ok testFlagsSelection78 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection78) Test flags selections "sidechain" ... ok testFlagsSelection79 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection79) Test flags selections 'carbon' for pdb3mht ... ok testFlagsSelection8 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection8) Test flags selections "acyclic" ... ok testFlagsSelection80 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection80) Test flags selections "carbon" ... ok testFlagsSelection81 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection81) Test flags selections 'hydrogen' for pdb3mht ... ok testFlagsSelection82 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection82) Test flags selections "hydrogen" ... ok testFlagsSelection83 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection83) Test flags selections 'noh' for pdb3mht ... ok testFlagsSelection84 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection84) Test flags selections "noh" ... ok testFlagsSelection85 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection85) Test flags selections 'nitrogen' for pdb3mht ... ok testFlagsSelection86 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection86) Test flags selections "nitrogen" ... ok testFlagsSelection87 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection87) Test flags selections 'oxygen' for pdb3mht ... ok testFlagsSelection88 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection88) Test flags selections "oxygen" ... ok testFlagsSelection89 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection89) Test flags selections 'sulfur' for pdb3mht ... ok testFlagsSelection9 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection9) Test flags selections 'aliphatic' for pdb3mht ... ok testFlagsSelection90 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection90) Test flags selections "sulfur" ... ok testFlagsSelection91 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection91) Test flags selections 'extended' for pdb3mht ... ok testFlagsSelection92 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection92) Test flags selections "extended" ... ok testFlagsSelection93 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection93) Test flags selections 'helix' for pdb3mht ... ok testFlagsSelection94 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection94) Test flags selections "helix" ... ok testFlagsSelection95 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection95) Test flags selections 'helix310' for pdb3mht ... ok testFlagsSelection96 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection96) Test flags selections "helix310" ... ok testFlagsSelection97 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection97) Test flags selections 'turn' for pdb3mht ... ok testFlagsSelection98 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection98) Test flags selections "turn" ... ok testFlagsSelection99 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection99) Test flags selections 'bridge' for pdb3mht ... ok testFloatSelection1 (prody.tests.atomic.test_select.TestSelect.testFloatSelection1) Test float selections 'beta 5.0 41.15 11.85' for pdb3mht ... ok testFloatSelection10 (prody.tests.atomic.test_select.TestSelect.testFloatSelection10) Test float selections "z 115.246 45.784" ... ok testFloatSelection11 (prody.tests.atomic.test_select.TestSelect.testFloatSelection11) Test float selections 'charge 0' for pdb3mht ... ok testFloatSelection12 (prody.tests.atomic.test_select.TestSelect.testFloatSelection12) Test float selections "charge 0" ... ok testFloatSelection13 (prody.tests.atomic.test_select.TestSelect.testFloatSelection13) Test float selections 'mass 1' for pdb3mht ... ok testFloatSelection14 (prody.tests.atomic.test_select.TestSelect.testFloatSelection14) Test float selections "mass 1" ... ok testFloatSelection15 (prody.tests.atomic.test_select.TestSelect.testFloatSelection15) Test float selections 'radius 0' for pdb3mht ... ok testFloatSelection16 (prody.tests.atomic.test_select.TestSelect.testFloatSelection16) Test float selections "radius 0" ... ok testFloatSelection17 (prody.tests.atomic.test_select.TestSelect.testFloatSelection17) Test float selections 'beta "1."' for pdb3mht ... ok testFloatSelection18 (prody.tests.atomic.test_select.TestSelect.testFloatSelection18) Test float selections "beta "1."" ... ok testFloatSelection19 (prody.tests.atomic.test_select.TestSelect.testFloatSelection19) Test float selections 'beta = "1."' for pdb3mht ... ok testFloatSelection2 (prody.tests.atomic.test_select.TestSelect.testFloatSelection2) Test float selections "beta 5.0 41.15 11.85" ... ok testFloatSelection20 (prody.tests.atomic.test_select.TestSelect.testFloatSelection20) Test float selections "beta = "1."" ... ok testFloatSelection3 (prody.tests.atomic.test_select.TestSelect.testFloatSelection3) Test float selections 'occupancy 1.0' for pdb3mht ... ok testFloatSelection4 (prody.tests.atomic.test_select.TestSelect.testFloatSelection4) Test float selections "occupancy 1.0" ... ok testFloatSelection5 (prody.tests.atomic.test_select.TestSelect.testFloatSelection5) Test float selections 'x 6.665' for pdb3mht ... ok testFloatSelection6 (prody.tests.atomic.test_select.TestSelect.testFloatSelection6) Test float selections "x 6.665" ... ok testFloatSelection7 (prody.tests.atomic.test_select.TestSelect.testFloatSelection7) Test float selections 'y 69.99 13.314' for pdb3mht ... ok testFloatSelection8 (prody.tests.atomic.test_select.TestSelect.testFloatSelection8) Test float selections "y 69.99 13.314" ... ok testFloatSelection9 (prody.tests.atomic.test_select.TestSelect.testFloatSelection9) Test float selections 'z 115.246 45.784' for pdb3mht ... ok testFunctionSelection1 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection1) Test function selections 'sqrt(x**2 + y**2 + z**2) < 100' for pdb3mht ... ok testFunctionSelection10 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection10) Test function selections "ceil(beta) == 10" ... ok testFunctionSelection11 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection11) Test function selections 'floor(beta) == 10' for pdb3mht ... ok testFunctionSelection12 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection12) Test function selections "floor(beta) == 10" ... ok testFunctionSelection13 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection13) Test function selections 'sq(x-5)+sq(y+4)+sq(z) > sq(100)' for pdb3mht ... ok testFunctionSelection14 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection14) Test function selections "sq(x-5)+sq(y+4)+sq(z) > sq(100)" ... ok testFunctionSelection15 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection15) Test function selections '1 > sq(occ)' for pdb3mht ... ok testFunctionSelection16 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection16) Test function selections "1 > sq(occ)" ... ok testFunctionSelection17 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection17) Test function selections 'sq(x x) > 1' for pdb3mht ... ok testFunctionSelection18 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection18) Test function selections "sq(x x) > 1" ... ok testFunctionSelection2 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection2) Test function selections "sqrt(x**2 + y**2 + z**2) < 100" ... ok testFunctionSelection3 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection3) Test function selections 'sqrt(x**2 + y**2 + z**2) == (x**2 + y**2 + z**2) ** 0.5' for pdb3mht ... ok testFunctionSelection4 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection4) Test function selections "sqrt(x**2 + y**2 + z**2) == (x**2 + y**2 + z**2) ** 0.5" ... ok testFunctionSelection5 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection5) Test function selections 'beta % 3 < 1' for pdb3mht ... ok testFunctionSelection6 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection6) Test function selections "beta % 3 < 1" ... ok testFunctionSelection7 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection7) Test function selections 'beta % 4 % 3 < 1' for pdb3mht ... ok testFunctionSelection8 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection8) Test function selections "beta % 4 % 3 < 1" ... ok testFunctionSelection9 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection9) Test function selections 'ceil(beta) == 10' for pdb3mht ... ok testIntegerSelection1 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection1) Test integer selections 'index 10 20 10000' for pdb3mht ... ok testIntegerSelection10 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection10) Test integer selections "resnum 100 105" ... ok testIntegerSelection11 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection11) Test integer selections 'resid 0' for pdb3mht ... ok testIntegerSelection12 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection12) Test integer selections "resid 0" ... ok testIntegerSelection13 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection13) Test integer selections 'resid 100 105' for pdb3mht ... ok testIntegerSelection14 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection14) Test integer selections "resid 100 105" ... ok testIntegerSelection15 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection15) Test integer selections 'resid 100 A 105' for pdb3mht ... ok testIntegerSelection16 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection16) Test integer selections "resid 100 A 105" ... ok testIntegerSelection17 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection17) Test integer selections 'fragindex 0' for pdb3mht ... ok testIntegerSelection18 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection18) Test integer selections "fragindex 0" ... ok testIntegerSelection19 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection19) Test integer selections 'fragment 0' for pdb3mht ... ok testIntegerSelection2 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection2) Test integer selections "index 10 20 10000" ... ok testIntegerSelection20 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection20) Test integer selections "fragment 0" ... ok testIntegerSelection3 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection3) Test integer selections 'serial 0' for pdb3mht ... ok testIntegerSelection4 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection4) Test integer selections "serial 0" ... ok testIntegerSelection5 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection5) Test integer selections 'serial 1 2' for pdb3mht ... ok testIntegerSelection6 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection6) Test integer selections "serial 1 2" ... ok testIntegerSelection7 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection7) Test integer selections 'resnum 0' for pdb3mht ... ok testIntegerSelection8 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection8) Test integer selections "resnum 0" ... ok testIntegerSelection9 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection9) Test integer selections 'resnum 100 105' for pdb3mht ... ok testInvalidSelection1 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection1) Test invalid selections 'chain C and and chain C' for pdb3mht ... ok testInvalidSelection10 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection10) Test invalid selections "sqr(x-5)+sqr(y+4)+sqr(z) > sqr(100)" ... ok testInvalidSelection11 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection11) Test invalid selections 'x > sq(calpha)' for pdb3mht ... ok testInvalidSelection12 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection12) Test invalid selections "x > sq(calpha)" ... ok testInvalidSelection13 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection13) Test invalid selections 'x > sq(name CA and resname ALA)' for pdb3mht ... ok testInvalidSelection14 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection14) Test invalid selections "x > sq(name CA and resname ALA)" ... ok testInvalidSelection15 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection15) Test invalid selections 'resname ALA and +1' for pdb3mht ... ok testInvalidSelection16 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection16) Test invalid selections "resname ALA and +1" ... ok testInvalidSelection2 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection2) Test invalid selections "chain C and and chain C" ... ok testInvalidSelection3 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection3) Test invalid selections 'chain C or or chain D' for pdb3mht ... ok testInvalidSelection4 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection4) Test invalid selections "chain C or or chain D" ... ok testInvalidSelection5 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection5) Test invalid selections 'chain C or not or chain D' for pdb3mht ... ok testInvalidSelection6 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection6) Test invalid selections "chain C or not or chain D" ... ok testInvalidSelection7 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection7) Test invalid selections 'chain C + 3' for pdb3mht ... ok testInvalidSelection8 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection8) Test invalid selections "chain C + 3" ... ok testInvalidSelection9 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection9) Test invalid selections 'sqr(x-5)+sqr(y+4)+sqr(z) > sqr(100)' for pdb3mht ... ok testKwargsSelection1 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection1) Test kwargs selections 'within 100 of origin' for pdb3mht ... ok testKwargsSelection10 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection10) Test kwargs selections "within 100 of none" ... ok testKwargsSelection2 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection2) Test kwargs selections "within 100 of origin" ... ok testKwargsSelection3 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection3) Test kwargs selections 'within 100 of origin' for pdb3mht ... ok testKwargsSelection4 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection4) Test kwargs selections "within 100 of origin" ... ok testKwargsSelection5 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection5) Test kwargs selections 'within 100 of origin' for pdb3mht ... ok testKwargsSelection6 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection6) Test kwargs selections "within 100 of origin" ... ok testKwargsSelection7 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection7) Test kwargs selections 'within 100 of origin' for pdb3mht ... ok testKwargsSelection8 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection8) Test kwargs selections "within 100 of origin" ... ok testKwargsSelection9 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection9) Test kwargs selections 'within 100 of none' for pdb3mht ... ok testLogicalSelection1 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection1) Test logical selections 'name or name' for pdb3mht ... ok testLogicalSelection10 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection10) Test logical selections "index 0 or index 1 " ... ok testLogicalSelection11 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection11) Test logical selections 'not not not not index 1' for pdb3mht ... ok testLogicalSelection12 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection12) Test logical selections "not not not not index 1" ... ok testLogicalSelection13 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection13) Test logical selections 'index 0 or index 1 or index 2' for pdb3mht ... ok testLogicalSelection14 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection14) Test logical selections "index 0 or index 1 or index 2" ... ok testLogicalSelection15 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection15) Test logical selections 'index 0 or index 1 or index 2 or index 4' for pdb3mht ... ok testLogicalSelection16 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection16) Test logical selections "index 0 or index 1 or index 2 or index 4" ... ok testLogicalSelection17 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection17) Test logical selections 'index 0 and index 1 ' for pdb3mht ... ok testLogicalSelection18 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection18) Test logical selections "index 0 and index 1 " ... ok testLogicalSelection19 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection19) Test logical selections 'index < 50 and index < 5' for pdb3mht ... ok testLogicalSelection2 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection2) Test logical selections "name or name" ... ok testLogicalSelection20 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection20) Test logical selections "index < 50 and index < 5" ... ok testLogicalSelection21 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection21) Test logical selections 'index < 50 and index < 25 and index < 5' for pdb3mht ... ok testLogicalSelection22 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection22) Test logical selections "index < 50 and index < 25 and index < 5" ... ok testLogicalSelection23 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection23) Test logical selections 'index < 5 and index < 25 and index < 50' for pdb3mht ... ok testLogicalSelection24 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection24) Test logical selections "index < 5 and index < 25 and index < 50" ... ok testLogicalSelection25 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection25) Test logical selections 'index 0 to 5 and index 0 to 25 and index 0 to 50' for pdb3mht ... ok testLogicalSelection26 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection26) Test logical selections "index 0 to 5 and index 0 to 25 and index 0 to 50" ... ok testLogicalSelection27 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection27) Test logical selections 'index < 5 and index < 25 and index < 50 or index < 50 or index < 5' for pdb3mht ... ok testLogicalSelection28 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection28) Test logical selections "index < 5 and index < 25 and index < 50 or index < 50 or index < 5" ... ok testLogicalSelection3 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection3) Test logical selections 'name and name' for pdb3mht ... ok testLogicalSelection4 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection4) Test logical selections "name and name" ... ok testLogicalSelection5 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection5) Test logical selections 'name CA and name CA' for pdb3mht ... ok testLogicalSelection6 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection6) Test logical selections "name CA and name CA" ... ok testLogicalSelection7 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection7) Test logical selections 'name CA or name CA' for pdb3mht ... ok testLogicalSelection8 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection8) Test logical selections "name CA or name CA" ... ok testLogicalSelection9 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection9) Test logical selections 'index 0 or index 1 ' for pdb3mht ... ok testOperationSelection1 (prody.tests.atomic.test_select.TestSelect.testOperationSelection1) Test operation selections 'x ** 2 < 10' for pdb3mht ... ok testOperationSelection10 (prody.tests.atomic.test_select.TestSelect.testOperationSelection10) Test operation selections "x**2 + y**2 + z**2 < 10000" ... ok testOperationSelection2 (prody.tests.atomic.test_select.TestSelect.testOperationSelection2) Test operation selections "x ** 2 < 10" ... ok testOperationSelection3 (prody.tests.atomic.test_select.TestSelect.testOperationSelection3) Test operation selections 'x ** 2 ** 2 ** 2 < 10' for pdb3mht ... ok testOperationSelection4 (prody.tests.atomic.test_select.TestSelect.testOperationSelection4) Test operation selections "x ** 2 ** 2 ** 2 < 10" ... ok testOperationSelection5 (prody.tests.atomic.test_select.TestSelect.testOperationSelection5) Test operation selections 'x ** (+2 ** (+2 ** +2)) < 10' for pdb3mht ... ok testOperationSelection6 (prody.tests.atomic.test_select.TestSelect.testOperationSelection6) Test operation selections "x ** (+2 ** (+2 ** +2)) < 10" ... ok testOperationSelection7 (prody.tests.atomic.test_select.TestSelect.testOperationSelection7) Test operation selections 'occupancy % 2 == 1' for pdb3mht ... ok testOperationSelection8 (prody.tests.atomic.test_select.TestSelect.testOperationSelection8) Test operation selections "occupancy % 2 == 1" ... ok testOperationSelection9 (prody.tests.atomic.test_select.TestSelect.testOperationSelection9) Test operation selections 'x**2 + y**2 + z**2 < 10000' for pdb3mht ... ok testRangeSelection1 (prody.tests.atomic.test_select.TestSelect.testRangeSelection1) Test range selections 'index 0:10' for pdb3mht ... ok testRangeSelection10 (prody.tests.atomic.test_select.TestSelect.testRangeSelection10) Test range selections "resnum 10to15" ... ok testRangeSelection11 (prody.tests.atomic.test_select.TestSelect.testRangeSelection11) Test range selections 'resnum 10:16:1' for pdb3mht ... ok testRangeSelection12 (prody.tests.atomic.test_select.TestSelect.testRangeSelection12) Test range selections "resnum 10:16:1" ... ok testRangeSelection13 (prody.tests.atomic.test_select.TestSelect.testRangeSelection13) Test range selections 'resnum `-3:16:1`' for pdb3mht ... ok testRangeSelection14 (prody.tests.atomic.test_select.TestSelect.testRangeSelection14) Test range selections "resnum `-3:16:1`" ... ok testRangeSelection15 (prody.tests.atomic.test_select.TestSelect.testRangeSelection15) Test range selections 'resid 10to15' for pdb3mht ... ok testRangeSelection16 (prody.tests.atomic.test_select.TestSelect.testRangeSelection16) Test range selections "resid 10to15" ... ok testRangeSelection17 (prody.tests.atomic.test_select.TestSelect.testRangeSelection17) Test range selections 'resid 10:16:1' for pdb3mht ... ok testRangeSelection18 (prody.tests.atomic.test_select.TestSelect.testRangeSelection18) Test range selections "resid 10:16:1" ... ok testRangeSelection19 (prody.tests.atomic.test_select.TestSelect.testRangeSelection19) Test range selections 'x `-10:20`' for pdb3mht ... ok testRangeSelection2 (prody.tests.atomic.test_select.TestSelect.testRangeSelection2) Test range selections "index 0:10" ... ok testRangeSelection20 (prody.tests.atomic.test_select.TestSelect.testRangeSelection20) Test range selections "x `-10:20`" ... ok testRangeSelection21 (prody.tests.atomic.test_select.TestSelect.testRangeSelection21) Test range selections 'x 0:20:1' for pdb3mht ... ok testRangeSelection22 (prody.tests.atomic.test_select.TestSelect.testRangeSelection22) Test range selections "x 0:20:1" ... ok testRangeSelection23 (prody.tests.atomic.test_select.TestSelect.testRangeSelection23) Test range selections 'beta 13.02:13.01' for pdb3mht ... ok testRangeSelection24 (prody.tests.atomic.test_select.TestSelect.testRangeSelection24) Test range selections "beta 13.02:13.01" ... ok testRangeSelection3 (prody.tests.atomic.test_select.TestSelect.testRangeSelection3) Test range selections 'index 0to10' for pdb3mht ... ok testRangeSelection4 (prody.tests.atomic.test_select.TestSelect.testRangeSelection4) Test range selections "index 0to10" ... ok testRangeSelection5 (prody.tests.atomic.test_select.TestSelect.testRangeSelection5) Test range selections 'serial 0:10:2' for pdb3mht ... ok testRangeSelection6 (prody.tests.atomic.test_select.TestSelect.testRangeSelection6) Test range selections "serial 0:10:2" ... ok testRangeSelection7 (prody.tests.atomic.test_select.TestSelect.testRangeSelection7) Test range selections 'serial 0:10:10' for pdb3mht ... ok testRangeSelection8 (prody.tests.atomic.test_select.TestSelect.testRangeSelection8) Test range selections "serial 0:10:10" ... ok testRangeSelection9 (prody.tests.atomic.test_select.TestSelect.testRangeSelection9) Test range selections 'resnum 10to15' for pdb3mht ... ok testRegexpSelection1 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection1) Test regexp selections 'resname "S.."' for pdb3mht ... ok testRegexpSelection10 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection10) Test regexp selections "name "C((A|B)"" ... ok testRegexpSelection2 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection2) Test regexp selections "resname "S.."" ... ok testRegexpSelection3 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection3) Test regexp selections 'name "C.*"' for pdb3mht ... ok testRegexpSelection4 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection4) Test regexp selections "name "C.*"" ... ok testRegexpSelection5 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection5) Test regexp selections 'name ".*\'"' for pdb3mht ... ok testRegexpSelection6 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection6) Test regexp selections "name ".*'"" ... ok testRegexpSelection7 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection7) Test regexp selections 'name "C(A|B)"' for pdb3mht ... ok testRegexpSelection8 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection8) Test regexp selections "name "C(A|B)"" ... ok testRegexpSelection9 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection9) Test regexp selections 'name "C((A|B)"' for pdb3mht ... ok testSameasSelection1 (prody.tests.atomic.test_select.TestSelect.testSameasSelection1) Test sameas selections 'same residue as index 0' for pdb3mht ... ok testSameasSelection10 (prody.tests.atomic.test_select.TestSelect.testSameasSelection10) Test sameas selections "same chain as chain C" ... ok testSameasSelection11 (prody.tests.atomic.test_select.TestSelect.testSameasSelection11) Test sameas selections 'same residue as chain X' for pdb3mht ... ok testSameasSelection12 (prody.tests.atomic.test_select.TestSelect.testSameasSelection12) Test sameas selections "same residue as chain X" ... ok testSameasSelection13 (prody.tests.atomic.test_select.TestSelect.testSameasSelection13) Test sameas selections 'same none as chain C' for pdb3mht ... ok testSameasSelection14 (prody.tests.atomic.test_select.TestSelect.testSameasSelection14) Test sameas selections "same none as chain C" ... ok testSameasSelection15 (prody.tests.atomic.test_select.TestSelect.testSameasSelection15) Test sameas selections 'same residue as same residue as same residue as index 0' for pdb3mht ... ok testSameasSelection16 (prody.tests.atomic.test_select.TestSelect.testSameasSelection16) Test sameas selections "same residue as same residue as same residue as index 0" ... ok testSameasSelection2 (prody.tests.atomic.test_select.TestSelect.testSameasSelection2) Test sameas selections "same residue as index 0" ... ok testSameasSelection3 (prody.tests.atomic.test_select.TestSelect.testSameasSelection3) Test sameas selections 'same chain as index 0' for pdb3mht ... ok testSameasSelection4 (prody.tests.atomic.test_select.TestSelect.testSameasSelection4) Test sameas selections "same chain as index 0" ... ok testSameasSelection5 (prody.tests.atomic.test_select.TestSelect.testSameasSelection5) Test sameas selections 'same segment as index 0' for pdb3mht ... ok testSameasSelection6 (prody.tests.atomic.test_select.TestSelect.testSameasSelection6) Test sameas selections "same segment as index 0" ... ok testSameasSelection7 (prody.tests.atomic.test_select.TestSelect.testSameasSelection7) Test sameas selections 'same residue as resname DG ALA' for pdb3mht ... ok testSameasSelection8 (prody.tests.atomic.test_select.TestSelect.testSameasSelection8) Test sameas selections "same residue as resname DG ALA" ... ok testSameasSelection9 (prody.tests.atomic.test_select.TestSelect.testSameasSelection9) Test sameas selections 'same chain as chain C' for pdb3mht ... ok testSequenceSelection1 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection1) Test sequence selections 'sequence al' for pdb3mht ... ok testSequenceSelection10 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection10) Test sequence selections "sequence FKPY" ... ok testSequenceSelection11 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection11) Test sequence selections 'sequence "SS."' for pdb3mht ... ok testSequenceSelection12 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection12) Test sequence selections "sequence "SS."" ... ok testSequenceSelection13 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection13) Test sequence selections 'sequence "S[A-Z]{2}G"' for pdb3mht ... ok testSequenceSelection14 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection14) Test sequence selections "sequence "S[A-Z]{2}G"" ... ok testSequenceSelection15 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection15) Test sequence selections 'sequence "S.S.S"' for pdb3mht ... ok testSequenceSelection16 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection16) Test sequence selections "sequence "S.S.S"" ... ok testSequenceSelection17 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection17) Test sequence selections 'sequence "."' for pdb3mht ... ok testSequenceSelection18 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection18) Test sequence selections "sequence "."" ... ok testSequenceSelection2 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection2) Test sequence selections "sequence al" ... ok testSequenceSelection3 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection3) Test sequence selections 'sequence A' for pdb3mht ... ok testSequenceSelection4 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection4) Test sequence selections "sequence A" ... ok testSequenceSelection5 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection5) Test sequence selections 'sequence MIEIK' for pdb3mht ... ok testSequenceSelection6 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection6) Test sequence selections "sequence MIEIK" ... ok testSequenceSelection7 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection7) Test sequence selections 'sequence VLNAL' for pdb3mht ... ok testSequenceSelection8 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection8) Test sequence selections "sequence VLNAL" ... ok testSequenceSelection9 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection9) Test sequence selections 'sequence FKPY' for pdb3mht ... ok testSpecialcharSelection1 (prody.tests.atomic.test_select.TestSelect.testSpecialcharSelection1) Test specialchar selections 'altloc ` `' for pdb3mht ... ok testSpecialcharSelection2 (prody.tests.atomic.test_select.TestSelect.testSpecialcharSelection2) Test specialchar selections "altloc ` `" ... ok testSpecialcharSelection3 (prody.tests.atomic.test_select.TestSelect.testSpecialcharSelection3) Test specialchar selections 'name A` `CA`' for pdb3mht ... ok testSpecialcharSelection4 (prody.tests.atomic.test_select.TestSelect.testSpecialcharSelection4) Test specialchar selections "name A` `CA`" ... ok testSpecialcharSelection5 (prody.tests.atomic.test_select.TestSelect.testSpecialcharSelection5) Test specialchar selections 'name `A``' for pdb3mht ... ok testSpecialcharSelection6 (prody.tests.atomic.test_select.TestSelect.testSpecialcharSelection6) Test specialchar selections "name `A``" ... ok testSpecialcharSelection7 (prody.tests.atomic.test_select.TestSelect.testSpecialcharSelection7) Test specialchar selections 'z `+100.291`' for pdb3mht ... ok testSpecialcharSelection8 (prody.tests.atomic.test_select.TestSelect.testSpecialcharSelection8) Test specialchar selections "z `+100.291`" ... ok testStringSelection1 (prody.tests.atomic.test_select.TestSelect.testStringSelection1) Test string selections 'name P' for pdb3mht ... ok testStringSelection10 (prody.tests.atomic.test_select.TestSelect.testStringSelection10) Test string selections "chain x" ... ok testStringSelection11 (prody.tests.atomic.test_select.TestSelect.testStringSelection11) Test string selections 'chain x y' for pdb3mht ... ok testStringSelection12 (prody.tests.atomic.test_select.TestSelect.testStringSelection12) Test string selections "chain x y" ... ok testStringSelection13 (prody.tests.atomic.test_select.TestSelect.testStringSelection13) Test string selections 'chain x y z' for pdb3mht ... ok testStringSelection14 (prody.tests.atomic.test_select.TestSelect.testStringSelection14) Test string selections "chain x y z" ... ok testStringSelection15 (prody.tests.atomic.test_select.TestSelect.testStringSelection15) Test string selections 'chain x y z C' for pdb3mht ... ok testStringSelection16 (prody.tests.atomic.test_select.TestSelect.testStringSelection16) Test string selections "chain x y z C" ... ok testStringSelection17 (prody.tests.atomic.test_select.TestSelect.testStringSelection17) Test string selections 'chain C D' for pdb3mht ... ok testStringSelection18 (prody.tests.atomic.test_select.TestSelect.testStringSelection18) Test string selections "chain C D" ... ok testStringSelection19 (prody.tests.atomic.test_select.TestSelect.testStringSelection19) Test string selections 'chain CD' for pdb3mht ... ok testStringSelection2 (prody.tests.atomic.test_select.TestSelect.testStringSelection2) Test string selections "name P" ... ok testStringSelection20 (prody.tests.atomic.test_select.TestSelect.testStringSelection20) Test string selections "chain CD" ... ok testStringSelection21 (prody.tests.atomic.test_select.TestSelect.testStringSelection21) Test string selections 'resname DG' for pdb3mht ... ok testStringSelection22 (prody.tests.atomic.test_select.TestSelect.testStringSelection22) Test string selections "resname DG" ... ok testStringSelection23 (prody.tests.atomic.test_select.TestSelect.testStringSelection23) Test string selections 'resname DG ALA' for pdb3mht ... ok testStringSelection24 (prody.tests.atomic.test_select.TestSelect.testStringSelection24) Test string selections "resname DG ALA" ... ok testStringSelection25 (prody.tests.atomic.test_select.TestSelect.testStringSelection25) Test string selections 'altloc A' for pdb3mht ... ok testStringSelection26 (prody.tests.atomic.test_select.TestSelect.testStringSelection26) Test string selections "altloc A" ... ok testStringSelection27 (prody.tests.atomic.test_select.TestSelect.testStringSelection27) Test string selections 'altloc _' for pdb3mht ... ok testStringSelection28 (prody.tests.atomic.test_select.TestSelect.testStringSelection28) Test string selections "altloc _" ... ok testStringSelection29 (prody.tests.atomic.test_select.TestSelect.testStringSelection29) Test string selections 'secondary H' for pdb3mht ... ok testStringSelection3 (prody.tests.atomic.test_select.TestSelect.testStringSelection3) Test string selections 'name P CA' for pdb3mht ... ok testStringSelection30 (prody.tests.atomic.test_select.TestSelect.testStringSelection30) Test string selections "secondary H" ... ok testStringSelection31 (prody.tests.atomic.test_select.TestSelect.testStringSelection31) Test string selections 'secondary H E' for pdb3mht ... ok testStringSelection32 (prody.tests.atomic.test_select.TestSelect.testStringSelection32) Test string selections "secondary H E" ... ok testStringSelection33 (prody.tests.atomic.test_select.TestSelect.testStringSelection33) Test string selections 'secondary _' for pdb3mht ... ok testStringSelection34 (prody.tests.atomic.test_select.TestSelect.testStringSelection34) Test string selections "secondary _" ... ok testStringSelection35 (prody.tests.atomic.test_select.TestSelect.testStringSelection35) Test string selections 'segment _' for pdb3mht ... ok testStringSelection36 (prody.tests.atomic.test_select.TestSelect.testStringSelection36) Test string selections "segment _" ... ok testStringSelection4 (prody.tests.atomic.test_select.TestSelect.testStringSelection4) Test string selections "name P CA" ... ok testStringSelection5 (prody.tests.atomic.test_select.TestSelect.testStringSelection5) Test string selections 'name `A 1`' for pdb3mht ... ok testStringSelection6 (prody.tests.atomic.test_select.TestSelect.testStringSelection6) Test string selections "name `A 1`" ... ok testStringSelection7 (prody.tests.atomic.test_select.TestSelect.testStringSelection7) Test string selections 'chain C' for pdb3mht ... ok testStringSelection8 (prody.tests.atomic.test_select.TestSelect.testStringSelection8) Test string selections "chain C" ... ok testStringSelection9 (prody.tests.atomic.test_select.TestSelect.testStringSelection9) Test string selections 'chain x' for pdb3mht ... ok testSynonymsSelection1 (prody.tests.atomic.test_select.TestSelect.testSynonymsSelection1) Test synonyms selections 'chain C' for pdb3mht ... ok testSynonymsSelection2 (prody.tests.atomic.test_select.TestSelect.testSynonymsSelection2) Test synonyms selections "chain C" ... ok testSynonymsSelection3 (prody.tests.atomic.test_select.TestSelect.testSynonymsSelection3) Test synonyms selections 'chain C D' for pdb3mht ... ok testSynonymsSelection4 (prody.tests.atomic.test_select.TestSelect.testSynonymsSelection4) Test synonyms selections "chain C D" ... ok testUnintendedSelection1 (prody.tests.atomic.test_select.TestSelect.testUnintendedSelection1) Test unintended selections 'abs beta = beta' for pdb3mht ... ok testUnintendedSelection2 (prody.tests.atomic.test_select.TestSelect.testUnintendedSelection2) Test unintended selections "abs beta = beta" ... ok testUserdataSelection1 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection1) Test userdata selections 'temp < 10' for pdb3mht ... ok testUserdataSelection10 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection10) Test userdata selections "occ" ... ok testUserdataSelection11 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection11) Test userdata selections 'occ and occupancy == 1' for pdb3mht ... ok testUserdataSelection12 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection12) Test userdata selections "occ and occupancy == 1" ... ok testUserdataSelection13 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection13) Test userdata selections 'occ and occupancy == 1 and oc10 - 9 == 1' for pdb3mht ... ok testUserdataSelection14 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection14) Test userdata selections "occ and occupancy == 1 and oc10 - 9 == 1" ... ok testUserdataSelection15 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection15) Test userdata selections 'occ and occupancy == 1 and temp < 10' for pdb3mht ... ok testUserdataSelection16 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection16) Test userdata selections "occ and occupancy == 1 and temp < 10" ... ok testUserdataSelection17 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection17) Test userdata selections 'occ > 0' for pdb3mht ... ok testUserdataSelection18 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection18) Test userdata selections "occ > 0" ... ok testUserdataSelection2 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection2) Test userdata selections "temp < 10" ... ok testUserdataSelection3 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection3) Test userdata selections 'temp < 10 and chain D' for pdb3mht ... ok testUserdataSelection4 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection4) Test userdata selections "temp < 10 and chain D" ... ok testUserdataSelection5 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection5) Test userdata selections 'oc10 - 9 == 1' for pdb3mht ... ok testUserdataSelection6 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection6) Test userdata selections "oc10 - 9 == 1" ... ok testUserdataSelection7 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection7) Test userdata selections 'temp < 10' for pdb3mht ... ok testUserdataSelection8 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection8) Test userdata selections "temp < 10" ... ok testUserdataSelection9 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection9) Test userdata selections 'occ' for pdb3mht ... ok testWithinSelection1 (prody.tests.atomic.test_select.TestSelect.testWithinSelection1) Test within selections 'within 10 of index 0' for pdb3mht ... ok testWithinSelection10 (prody.tests.atomic.test_select.TestSelect.testWithinSelection10) Test within selections "within 5 of within 5 of within 5 of index 0" ... ok testWithinSelection11 (prody.tests.atomic.test_select.TestSelect.testWithinSelection11) Test within selections 'exwithin 5 of exwithin 5 of exwithin 5 of index 0' for pdb3mht ... ok testWithinSelection12 (prody.tests.atomic.test_select.TestSelect.testWithinSelection12) Test within selections "exwithin 5 of exwithin 5 of exwithin 5 of index 0" ... ok testWithinSelection13 (prody.tests.atomic.test_select.TestSelect.testWithinSelection13) Test within selections 'within 1 of pdb' for pdb3mht ... ok testWithinSelection14 (prody.tests.atomic.test_select.TestSelect.testWithinSelection14) Test within selections "within 1 of pdb" ... ok testWithinSelection15 (prody.tests.atomic.test_select.TestSelect.testWithinSelection15) Test within selections 'exwithin 1 of pdb' for pdb3mht ... ok testWithinSelection16 (prody.tests.atomic.test_select.TestSelect.testWithinSelection16) Test within selections "exwithin 1 of pdb" ... ok testWithinSelection17 (prody.tests.atomic.test_select.TestSelect.testWithinSelection17) Test within selections 'exwithin 1 of ag' for pdb3mht ... ok testWithinSelection18 (prody.tests.atomic.test_select.TestSelect.testWithinSelection18) Test within selections "exwithin 1 of ag" ... ok testWithinSelection19 (prody.tests.atomic.test_select.TestSelect.testWithinSelection19) Test within selections 'within 100 of index 10000' for pdb3mht ... ok testWithinSelection2 (prody.tests.atomic.test_select.TestSelect.testWithinSelection2) Test within selections "within 10 of index 0" ... ok testWithinSelection20 (prody.tests.atomic.test_select.TestSelect.testWithinSelection20) Test within selections "within 100 of index 10000" ... ok testWithinSelection3 (prody.tests.atomic.test_select.TestSelect.testWithinSelection3) Test within selections 'exwithin 100 of index 0' for pdb3mht ... ok testWithinSelection4 (prody.tests.atomic.test_select.TestSelect.testWithinSelection4) Test within selections "exwithin 100 of index 0" ... ok testWithinSelection5 (prody.tests.atomic.test_select.TestSelect.testWithinSelection5) Test within selections 'exwithin 4 of resname SAH' for pdb3mht ... ok testWithinSelection6 (prody.tests.atomic.test_select.TestSelect.testWithinSelection6) Test within selections "exwithin 4 of resname SAH" ... ok testWithinSelection7 (prody.tests.atomic.test_select.TestSelect.testWithinSelection7) Test within selections '(within 4 of water) and not water' for pdb3mht ... ok testWithinSelection8 (prody.tests.atomic.test_select.TestSelect.testWithinSelection8) Test within selections "(within 4 of water) and not water" ... ok testWithinSelection9 (prody.tests.atomic.test_select.TestSelect.testWithinSelection9) Test within selections 'within 5 of within 5 of within 5 of index 0' for pdb3mht ... ok testWithout_AndSelection1 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection1) Test without_and selections 'coil protein' for pdb3mht ... ok testWithout_AndSelection10 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection10) Test without_and selections "(protein nucleic)" ... ok testWithout_AndSelection11 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection11) Test without_and selections 'noh hetero water' for pdb3mht ... ok testWithout_AndSelection12 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection12) Test without_and selections "noh hetero water" ... ok testWithout_AndSelection13 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection13) Test without_and selections 'ca occupancy > 0' for pdb3mht ... ok testWithout_AndSelection14 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection14) Test without_and selections "ca occupancy > 0" ... ok testWithout_AndSelection15 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection15) Test without_and selections 'ca occupancy - 0 > 0' for pdb3mht ... ok testWithout_AndSelection16 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection16) Test without_and selections "ca occupancy - 0 > 0" ... ok testWithout_AndSelection17 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection17) Test without_and selections 'ca occupancy - 0 > 0 + 0' for pdb3mht ... ok testWithout_AndSelection18 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection18) Test without_and selections "ca occupancy - 0 > 0 + 0" ... ok testWithout_AndSelection19 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection19) Test without_and selections 'occupancy > ca 0' for pdb3mht ... ok testWithout_AndSelection2 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection2) Test without_and selections "coil protein" ... ok testWithout_AndSelection20 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection20) Test without_and selections "occupancy > ca 0" ... ok testWithout_AndSelection21 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection21) Test without_and selections 'noh hetero (water)' for pdb3mht ... ok testWithout_AndSelection22 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection22) Test without_and selections "noh hetero (water)" ... ok testWithout_AndSelection23 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection23) Test without_and selections 'noh hetero not (water)' for pdb3mht ... ok testWithout_AndSelection24 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection24) Test without_and selections "noh hetero not (water)" ... ok testWithout_AndSelection25 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection25) Test without_and selections '(water) hetero' for pdb3mht ... ok testWithout_AndSelection26 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection26) Test without_and selections "(water) hetero" ... ok testWithout_AndSelection27 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection27) Test without_and selections 'ca abs(beta) = beta + abs(0)' for pdb3mht ... ok testWithout_AndSelection28 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection28) Test without_and selections "ca abs(beta) = beta + abs(0)" ... ok testWithout_AndSelection3 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection3) Test without_and selections 'sidechain sc protein' for pdb3mht ... ok testWithout_AndSelection4 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection4) Test without_and selections "sidechain sc protein" ... ok testWithout_AndSelection5 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection5) Test without_and selections 'bbfull bb' for pdb3mht ... ok testWithout_AndSelection6 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection6) Test without_and selections "bbfull bb" ... ok testWithout_AndSelection7 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection7) Test without_and selections '(charged basic)' for pdb3mht ... ok testWithout_AndSelection8 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection8) Test without_and selections "(charged basic)" ... ok testWithout_AndSelection9 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection9) Test without_and selections '(protein nucleic)' for pdb3mht ... ok testSetData (prody.tests.atomic.test_subset.TestUserData.testSetData) ... ok testDatafile_1ejg (prody.tests.datafiles.TestDatafiles.testDatafile_1ejg) Test presence of "pdb1ejg.pdb" ... ok testDatafile_1ubi (prody.tests.datafiles.TestDatafiles.testDatafile_1ubi) Test presence of "pdb1ubi.pdb" ... ok testDatafile_1ubi_ca (prody.tests.datafiles.TestDatafiles.testDatafile_1ubi_ca) Test presence of "pdb1ubi_ca.pdb" ... ok testDatafile_2gb1_truncated (prody.tests.datafiles.TestDatafiles.testDatafile_2gb1_truncated) Test presence of "pdb2gb1_truncated.pdb" ... ok testDatafile_2k39_ca (prody.tests.datafiles.TestDatafiles.testDatafile_2k39_ca) Test presence of "pdb2k39_ca.pdb" ... ok testDatafile_2nwl (prody.tests.datafiles.TestDatafiles.testDatafile_2nwl) Test presence of "pdb2nwl-opm.pdb" ... ok testDatafile_3hsy (prody.tests.datafiles.TestDatafiles.testDatafile_3hsy) Test presence of "pdb3hsy.pdb" ... ok testDatafile_3mht (prody.tests.datafiles.TestDatafiles.testDatafile_3mht) Test presence of "pdb3mht.pdb" ... ok testDatafile_3o21 (prody.tests.datafiles.TestDatafiles.testDatafile_3o21) Test presence of "pdb3o21.pdb" ... ok testDatafile_3p3w (prody.tests.datafiles.TestDatafiles.testDatafile_3p3w) Test presence of "pdb3p3w.pdb" ... ok testDatafile_DI (prody.tests.datafiles.TestDatafiles.testDatafile_DI) Test presence of "msa_Cys_knot_di.dat" ... ok testDatafile_Fasta (prody.tests.datafiles.TestDatafiles.testDatafile_Fasta) Test presence of "msa_Cys_knot.fasta" ... ok testDatafile_MSA (prody.tests.datafiles.TestDatafiles.testDatafile_MSA) Test presence of "msa_3hsyA_3o21A.fasta" ... ok testDatafile_MSA_MEW (prody.tests.datafiles.TestDatafiles.testDatafile_MSA_MEW) Test presence of "msa_3hsyA_3o21A_new.fasta" ... ok testDatafile_RTER (prody.tests.datafiles.TestDatafiles.testDatafile_RTER) Test presence of "pdbRTER.pdb" ... ok testDatafile_SCA (prody.tests.datafiles.TestDatafiles.testDatafile_SCA) Test presence of "msa_Cys_knot_sca.dat" ... ok testDatafile_Selex (prody.tests.datafiles.TestDatafiles.testDatafile_Selex) Test presence of "msa_Cys_knot.slx" ... ok testDatafile_Stockholm (prody.tests.datafiles.TestDatafiles.testDatafile_Stockholm) Test presence of "msa_Cys_knot.sth" ... ok testDatafile_anm1ubi_evalues (prody.tests.datafiles.TestDatafiles.testDatafile_anm1ubi_evalues) Test presence of "anm1ubi_evalues.dat" ... ok testDatafile_anm1ubi_hessian (prody.tests.datafiles.TestDatafiles.testDatafile_anm1ubi_hessian) Test presence of "anm1ubi_hessian.coo" ... ok testDatafile_anm1ubi_vectors (prody.tests.datafiles.TestDatafiles.testDatafile_anm1ubi_vectors) Test presence of "anm1ubi_vectors.dat" ... ok testDatafile_commute1ubi (prody.tests.datafiles.TestDatafiles.testDatafile_commute1ubi) Test presence of "commute1ubi.dat" ... ok testDatafile_dcd (prody.tests.datafiles.TestDatafiles.testDatafile_dcd) Test presence of "dcd2k39_truncated.dcd" ... ok testDatafile_dssp (prody.tests.datafiles.TestDatafiles.testDatafile_dssp) Test presence of "pdb1r19_dssp.pdb" ... ok testDatafile_five_digits (prody.tests.datafiles.TestDatafiles.testDatafile_five_digits) Test presence of "pdb1tw7_step3_charmm2namd.pdb" ... ok testDatafile_gnm1ubi_evalues (prody.tests.datafiles.TestDatafiles.testDatafile_gnm1ubi_evalues) Test presence of "gnm1ubi_evalues.dat" ... ok testDatafile_gnm1ubi_kirchhoff (prody.tests.datafiles.TestDatafiles.testDatafile_gnm1ubi_kirchhoff) Test presence of "gnm1ubi_kirchhoff.coo" ... ok testDatafile_gnm1ubi_vectors (prody.tests.datafiles.TestDatafiles.testDatafile_gnm1ubi_vectors) Test presence of "gnm1ubi_vectors.dat" ... ok testDatafile_gromacs (prody.tests.datafiles.TestDatafiles.testDatafile_gromacs) Test presence of "pdb6fpj_Bb_fixed_solv_ions.pdb" ... ok testDatafile_h36 (prody.tests.datafiles.TestDatafiles.testDatafile_h36) Test presence of "pdb1tw7_step3_charmm2namd_doubled_h36.pdb" ... ok testDatafile_h36_ter (prody.tests.datafiles.TestDatafiles.testDatafile_h36_ter) Test presence of "pdb4v8r_h36.pdb" ... ok testDatafile_hex (prody.tests.datafiles.TestDatafiles.testDatafile_hex) Test presence of "pdb1tw7_step3_charmm2namd_doubled_hex.pdb" ... ok testDatafile_hex_ter (prody.tests.datafiles.TestDatafiles.testDatafile_hex_ter) Test presence of "pdb4v8r_hex.pdb" ... ok testDatafile_hit1ubi (prody.tests.datafiles.TestDatafiles.testDatafile_hit1ubi) Test presence of "hit1ubi.dat" ... ok testDatafile_long_chid_cif (prody.tests.datafiles.TestDatafiles.testDatafile_long_chid_cif) Test presence of "mmcif_6zu5.cif" ... ok testDatafile_multi_model_cif (prody.tests.datafiles.TestDatafiles.testDatafile_multi_model_cif) Test presence of "mmcif_6yfy.cif" ... ok testDatafile_multi_model_truncated (prody.tests.datafiles.TestDatafiles.testDatafile_multi_model_truncated) Test presence of "pdb2k39_truncated.pdb" ... ok testDatafile_oneatom (prody.tests.datafiles.TestDatafiles.testDatafile_oneatom) Test presence of "pdb1ejg_oneatom.pdb" ... ok testDatafile_pca2k39_cov (prody.tests.datafiles.TestDatafiles.testDatafile_pca2k39_cov) Test presence of "pca2k39_cov.coo" ... ok testDatafile_pca2k39_evalues (prody.tests.datafiles.TestDatafiles.testDatafile_pca2k39_evalues) Test presence of "pca2k39_evalues.dat" ... ok testDatafile_pca2k39_vectors (prody.tests.datafiles.TestDatafiles.testDatafile_pca2k39_vectors) Test presence of "pca2k39_vectors.dat" ... ok testDatafile_rtb2gb1_hessian (prody.tests.datafiles.TestDatafiles.testDatafile_rtb2gb1_hessian) Test presence of "rtb2gb1_hessian.coo" ... ok testDatafile_rtb2gb1_project (prody.tests.datafiles.TestDatafiles.testDatafile_rtb2gb1_project) Test presence of "rtb2gb1_project.coo" ... ok testDatafile_sti (prody.tests.datafiles.TestDatafiles.testDatafile_sti) Test presence of "xmlSTI.xml" ... ok testMode1d (prody.tests.dynamics.test_editing.TestExtending.testMode1d) ... ok testMode3d (prody.tests.dynamics.test_editing.TestExtending.testMode3d) ... ok testModel1d (prody.tests.dynamics.test_editing.TestExtending.testModel1d) ... ok testModel3d (prody.tests.dynamics.test_editing.TestExtending.testModel3d) ... ok testVector1d (prody.tests.dynamics.test_editing.TestExtending.testVector1d) ... ok testVector3d (prody.tests.dynamics.test_editing.TestExtending.testVector3d) ... ok testModel3d (prody.tests.dynamics.test_editing.TestInterpolating.testModel3d) ... ok testMode1d (prody.tests.dynamics.test_editing.TestSlicing.testMode1d) ... ok testMode3d (prody.tests.dynamics.test_editing.TestSlicing.testMode3d) ... ok testModel1d (prody.tests.dynamics.test_editing.TestSlicing.testModel1d) ... ok testModel3d (prody.tests.dynamics.test_editing.TestSlicing.testModel3d) ... ok testVector1d (prody.tests.dynamics.test_editing.TestSlicing.testVector1d) ... ok testVector3d (prody.tests.dynamics.test_editing.TestSlicing.testVector3d) ... ok testBuildHessianSlow (prody.tests.dynamics.test_enms.TestANM.testBuildHessianSlow) ... ok testBuildMatrixCoordsArray (prody.tests.dynamics.test_enms.TestANM.testBuildMatrixCoordsArray) Test output when *coords* is an array. ... FAIL testBuildMatrixCoordsWrongType (prody.tests.dynamics.test_enms.TestANM.testBuildMatrixCoordsWrongType) Test response to wrong type *coords* argument. ... ok testBuildMatrixCutoffInvalidValue (prody.tests.dynamics.test_enms.TestANM.testBuildMatrixCutoffInvalidValue) Test response to wrong *cutoff* argument. ... ok testBuildMatrixCutoffWrongType (prody.tests.dynamics.test_enms.TestANM.testBuildMatrixCutoffWrongType) Test response to cutoff of wrong type. ... ok testBuildMatrixInvalidGamma (prody.tests.dynamics.test_enms.TestANM.testBuildMatrixInvalidGamma) Test response to invalid *gamma* argument. ... ok testBuildMatrixWrongCoords (prody.tests.dynamics.test_enms.TestANM.testBuildMatrixWrongCoords) Test response to wrong coords.dtype. ... ok testBuildMatrixWrongGamma (prody.tests.dynamics.test_enms.TestANM.testBuildMatrixWrongGamma) Test response to wrong *gamma* argument. ... ok testSetHessianWrongShape (prody.tests.dynamics.test_enms.TestANM.testSetHessianWrongShape) Test response to wrong shape *hessian* argument. ... ok testSetMatrixAcceptableDtype (prody.tests.dynamics.test_enms.TestANM.testSetMatrixAcceptableDtype) Test response to acceptable matrix.dtype. ... ok testSetMatrixNonSquare (prody.tests.dynamics.test_enms.TestANM.testSetMatrixNonSquare) Test response to non-square matrix. ... ok testSetMatrixWrongDim (prody.tests.dynamics.test_enms.TestANM.testSetMatrixWrongDim) Test response to wrong dim *kirchhoff* argument. ... ok testSetMatrixWrongDtype (prody.tests.dynamics.test_enms.TestANM.testSetMatrixWrongDtype) Test response to wrong matrix.dtype. ... ok testSetMatrixWrongType (prody.tests.dynamics.test_enms.TestANM.testSetMatrixWrongType) Test response to wrong matrix type argument. ... ok testEigenvalues (prody.tests.dynamics.test_enms.TestANMResults.testEigenvalues) Test eigenvalues. ... ok testEigenvectors (prody.tests.dynamics.test_enms.TestANMResults.testEigenvectors) Test eigenvectors. ... ok testGetCutoff (prody.tests.dynamics.test_enms.TestANMResults.testGetCutoff) Testing return type of :meth:`~.GNMBase.getCutoff`. ... ok testGetGamma (prody.tests.dynamics.test_enms.TestANMResults.testGetGamma) Testing return type of :meth:`~.GNMBase.getGamma`. ... ok testGetHessian (prody.tests.dynamics.test_enms.TestANMResults.testGetHessian) ... ok testHessian (prody.tests.dynamics.test_enms.TestANMResults.testHessian) Test Hessian matrix. ... ok testHessianSums (prody.tests.dynamics.test_enms.TestANMResults.testHessianSums) ... ok testHessianSymmetry (prody.tests.dynamics.test_enms.TestANMResults.testHessianSymmetry) ... ok testModeSlicing (prody.tests.dynamics.test_enms.TestANMResults.testModeSlicing) ... ok testVariances (prody.tests.dynamics.test_enms.TestANMResults.testVariances) Test variances. ... ok testEigenvalues (prody.tests.dynamics.test_enms.TestEXANMResults.testEigenvalues) Test eigenvalues. ... ok testEigenvectors (prody.tests.dynamics.test_enms.TestEXANMResults.testEigenvectors) Test eigenvectors. ... ok testGetCutoff (prody.tests.dynamics.test_enms.TestEXANMResults.testGetCutoff) Testing return type of :meth:`~.GNMBase.getCutoff`. ... ok testGetGamma (prody.tests.dynamics.test_enms.TestEXANMResults.testGetGamma) Testing return type of :meth:`~.GNMBase.getGamma`. ... ok testGetHessian (prody.tests.dynamics.test_enms.TestEXANMResults.testGetHessian) ... ok testHessian (prody.tests.dynamics.test_enms.TestEXANMResults.testHessian) Test Hessian matrix. ... ok testHessianSums (prody.tests.dynamics.test_enms.TestEXANMResults.testHessianSums) ... ok testHessianSymmetry (prody.tests.dynamics.test_enms.TestEXANMResults.testHessianSymmetry) ... FAIL testVariances (prody.tests.dynamics.test_enms.TestEXANMResults.testVariances) Test variances. ... ok testBuildMatrixCoordsArray (prody.tests.dynamics.test_enms.TestGNM.testBuildMatrixCoordsArray) Test output when *coords* is an array. ... ok testBuildMatrixCoordsWrongType (prody.tests.dynamics.test_enms.TestGNM.testBuildMatrixCoordsWrongType) Test response to wrong type *coords* argument. ... ok testBuildMatrixCutoffInvalidValue (prody.tests.dynamics.test_enms.TestGNM.testBuildMatrixCutoffInvalidValue) Test response to wrong *cutoff* argument. ... ok testBuildMatrixCutoffWrongType (prody.tests.dynamics.test_enms.TestGNM.testBuildMatrixCutoffWrongType) Test response to cutoff of wrong type. ... ok testBuildMatrixInvalidGamma (prody.tests.dynamics.test_enms.TestGNM.testBuildMatrixInvalidGamma) Test response to invalid *gamma* argument. ... ok testBuildMatrixWrongCoords (prody.tests.dynamics.test_enms.TestGNM.testBuildMatrixWrongCoords) Test response to wrong coords.dtype. ... ok testBuildMatrixWrongGamma (prody.tests.dynamics.test_enms.TestGNM.testBuildMatrixWrongGamma) Test response to wrong *gamma* argument. ... ok testSetMatrixAcceptableDtype (prody.tests.dynamics.test_enms.TestGNM.testSetMatrixAcceptableDtype) Test response to acceptable matrix.dtype. ... ok testSetMatrixNonSquare (prody.tests.dynamics.test_enms.TestGNM.testSetMatrixNonSquare) Test response to non-square matrix. ... ok testSetMatrixWrongDim (prody.tests.dynamics.test_enms.TestGNM.testSetMatrixWrongDim) Test response to wrong dim *kirchhoff* argument. ... ok testSetMatrixWrongDtype (prody.tests.dynamics.test_enms.TestGNM.testSetMatrixWrongDtype) Test response to wrong matrix.dtype. ... ok testSetMatrixWrongType (prody.tests.dynamics.test_enms.TestGNM.testSetMatrixWrongType) Test response to wrong matrix type argument. ... ok testBuildKirchoffSlow (prody.tests.dynamics.test_enms.TestGNMResults.testBuildKirchoffSlow) ... ok testCommuteTime (prody.tests.dynamics.test_enms.TestGNMResults.testCommuteTime) ... ok testEigenvalues (prody.tests.dynamics.test_enms.TestGNMResults.testEigenvalues) ... ok testEigenvectors (prody.tests.dynamics.test_enms.TestGNMResults.testEigenvectors) ... ok testGetCutoff (prody.tests.dynamics.test_enms.TestGNMResults.testGetCutoff) Testing return type of :meth:`~.GNMBase.getCutoff`. ... ok testGetGamma (prody.tests.dynamics.test_enms.TestGNMResults.testGetGamma) Testing return type of :meth:`~.GNMBase.getGamma`. ... ok testGetKirchoff (prody.tests.dynamics.test_enms.TestGNMResults.testGetKirchoff) ... ok testKirchhoff (prody.tests.dynamics.test_enms.TestGNMResults.testKirchhoff) ... ok testKirchhoffSums (prody.tests.dynamics.test_enms.TestGNMResults.testKirchhoffSums) ... ok testKirchhoffSymmetry (prody.tests.dynamics.test_enms.TestGNMResults.testKirchhoffSymmetry) ... ok testCalcModes (prody.tests.dynamics.test_enms.TestRTB.testCalcModes) ... /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/utilities/eigtools.py:43: DeprecationWarning: Keyword argument 'eigvals' is deprecated in favour of 'subset_by_index' keyword instead and will be removed in SciPy 1.12.0. values, vectors = linalg.eigh(M, turbo=turbo, eigvals=eigvals) ok testHessian (prody.tests.dynamics.test_enms.TestRTB.testHessian) ... ok testProjection (prody.tests.dynamics.test_enms.TestRTB.testProjection) ... ok testGetCutoff (prody.tests.dynamics.test_enms.testGNMBase.testGetCutoff) Testing return type of :meth:`~.GNMBase.getCutoff`. ... ok testGetGamma (prody.tests.dynamics.test_enms.testGNMBase.testGetGamma) Testing return type of :meth:`~.GNMBase.getGamma`. ... ok testBuildMatrixCoordsArray (prody.tests.dynamics.test_pca.TestPCA.testBuildMatrixCoordsArray) Test output when *coords* is an array. ... ok testBuildMatrixCoordsWrongType (prody.tests.dynamics.test_pca.TestPCA.testBuildMatrixCoordsWrongType) Test response to wrong type *coords* argument. ... ok testBuildMatrixWrongCoords (prody.tests.dynamics.test_pca.TestPCA.testBuildMatrixWrongCoords) Test response to wrong coords.dtype. ... ok testSetMatrixAcceptableDtype (prody.tests.dynamics.test_pca.TestPCA.testSetMatrixAcceptableDtype) Test response to acceptable matrix.dtype. ... ok testSetMatrixNonSquare (prody.tests.dynamics.test_pca.TestPCA.testSetMatrixNonSquare) Test response to non-square matrix. ... ok testSetMatrixWrongDim (prody.tests.dynamics.test_pca.TestPCA.testSetMatrixWrongDim) Test response to wrong dim *kirchhoff* argument. ... ok testSetMatrixWrongDtype (prody.tests.dynamics.test_pca.TestPCA.testSetMatrixWrongDtype) Test response to wrong matrix.dtype. ... ok testSetMatrixWrongType (prody.tests.dynamics.test_pca.TestPCA.testSetMatrixWrongType) Test response to wrong matrix type argument. ... ok testBuildMatrixCoordsArray (prody.tests.dynamics.test_pca.TestPCAResults.testBuildMatrixCoordsArray) Test output when *coords* is an array. ... ok testBuildMatrixCoordsWrongType (prody.tests.dynamics.test_pca.TestPCAResults.testBuildMatrixCoordsWrongType) Test response to wrong type *coords* argument. ... ok testBuildMatrixWrongCoords (prody.tests.dynamics.test_pca.TestPCAResults.testBuildMatrixWrongCoords) Test response to wrong coords.dtype. ... ok testCovariance (prody.tests.dynamics.test_pca.TestPCAResults.testCovariance) ... ok testCovarianceSymmetry (prody.tests.dynamics.test_pca.TestPCAResults.testCovarianceSymmetry) ... ok testEigenvalues (prody.tests.dynamics.test_pca.TestPCAResults.testEigenvalues) ... ok testEigenvectors (prody.tests.dynamics.test_pca.TestPCAResults.testEigenvectors) ... ok testNumModesAll (prody.tests.dynamics.test_pca.TestPCAResults.testNumModesAll) ... ok testNumModesSet (prody.tests.dynamics.test_pca.TestPCAResults.testNumModesSet) ... ok testSetMatrixAcceptableDtype (prody.tests.dynamics.test_pca.TestPCAResults.testSetMatrixAcceptableDtype) Test response to acceptable matrix.dtype. ... ok testSetMatrixNonSquare (prody.tests.dynamics.test_pca.TestPCAResults.testSetMatrixNonSquare) Test response to non-square matrix. ... ok testSetMatrixWrongDim (prody.tests.dynamics.test_pca.TestPCAResults.testSetMatrixWrongDim) Test response to wrong dim *kirchhoff* argument. ... ok testSetMatrixWrongDtype (prody.tests.dynamics.test_pca.TestPCAResults.testSetMatrixWrongDtype) Test response to wrong matrix.dtype. ... ok testSetMatrixWrongType (prody.tests.dynamics.test_pca.TestPCAResults.testSetMatrixWrongType) Test response to wrong matrix type argument. ... ok testSlicing (prody.tests.dynamics.test_signature.TestSDArray.testSlicing) ... ok testCoordinates (prody.tests.ensemble.test_conformation.TestConformation.testCoordinates) ... ok testCoordinatesForAll (prody.tests.ensemble.test_conformation.TestConformation.testCoordinatesForAll) ... ok testGetIndex (prody.tests.ensemble.test_conformation.TestConformation.testGetIndex) Test get index function. ... ok testGetNumAtoms (prody.tests.ensemble.test_conformation.TestConformation.testGetNumAtoms) Test get index function. ... ok testWeights (prody.tests.ensemble.test_conformation.TestConformation.testWeights) ... ok testCoordinates (prody.tests.ensemble.test_conformation.TestPDBConformation.testCoordinates) ... ok testCoordinatesForAll (prody.tests.ensemble.test_conformation.TestPDBConformation.testCoordinatesForAll) ... ok testGetIndex (prody.tests.ensemble.test_conformation.TestPDBConformation.testGetIndex) ... ok testGetNumAtoms (prody.tests.ensemble.test_conformation.TestPDBConformation.testGetNumAtoms) ... ok testWeights (prody.tests.ensemble.test_conformation.TestPDBConformation.testWeights) ... ok testWeightsForAll (prody.tests.ensemble.test_conformation.TestPDBConformation.testWeightsForAll) ... ok testConcatenation (prody.tests.ensemble.test_ensemble.TestEnsemble.testConcatenation) Test concatenation of ensembles without weights. ... ok testConcatenationNoweightsWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testConcatenationNoweightsWeights) Test concatenation of ensembles without and with weights. ... ok testConcatenationWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testConcatenationWeights) Test concatenation of ensembles with weights. ... ok testConcatenationWeightsNoweights (prody.tests.ensemble.test_ensemble.TestEnsemble.testConcatenationWeightsNoweights) Test concatenation of ensembles with and without weights. ... ok testDelCoordsetAll (prody.tests.ensemble.test_ensemble.TestEnsemble.testDelCoordsetAll) ... ok testDelCoordsetMiddle (prody.tests.ensemble.test_ensemble.TestEnsemble.testDelCoordsetMiddle) ... ok testGetCoordinates (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetCoordinates) Test correctness of reference coordinates. ... ok testGetCoordsets (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetCoordsets) Test correctness of all coordinates. ... ok testGetNumAtoms (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetNumAtoms) ... ok testGetNumCsets (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetNumCsets) ... ok testGetRMSDs (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetRMSDs) ... ok testGetRMSDsWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetRMSDsWeights) ... ok testGetWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetWeights) Test correctness of all weights. ... ok testIterCoordsets (prody.tests.ensemble.test_ensemble.TestEnsemble.testIterCoordsets) Test coordinate iteration. ... ok testSelection (prody.tests.ensemble.test_ensemble.TestEnsemble.testSelection) Test atom selection of ensemble. ... ok testSlicing (prody.tests.ensemble.test_ensemble.TestEnsemble.testSlicing) Test slicing operation. ... ok testSlicingCopy (prody.tests.ensemble.test_ensemble.TestEnsemble.testSlicingCopy) Test making a copy by slicing operation. ... ok testSlicingList (prody.tests.ensemble.test_ensemble.TestEnsemble.testSlicingList) Test slicing with a list. ... ok testSlicingWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testSlicingWeights) Test slicing operation with weights. ... ok testSuperpose (prody.tests.ensemble.test_ensemble.TestEnsemble.testSuperpose) ... ok testSuperposeWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testSuperposeWeights) ... ok testResults (prody.tests.ensemble.test_functions.TestBuildPDBEnsemble.testResults) ... ok testInvalidType (prody.tests.ensemble.test_functions.TestCalcOccupancies.testInvalidType) ... ok testResults (prody.tests.ensemble.test_functions.TestCalcOccupancies.testResults) ... ok testWeightsNone (prody.tests.ensemble.test_functions.TestCalcOccupancies.testWeightsNone) ... ok testResults (prody.tests.ensemble.test_functions.TestTrimPDBEnsemble.testResults) ... /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/sequence/sequence.py:52: DeprecationWarning: tostring() is deprecated. Use tobytes() instead. return self._array.tostring().decode() ok testAddCoordsets (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testAddCoordsets) ... ok testConcatenation (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testConcatenation) Test concatenation of PDB ensembles. ... ok testDelCoordsetAll (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testDelCoordsetAll) Test consequences of deleting all coordinate sets. ... ok testDelCoordsetMiddle (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testDelCoordsetMiddle) ... ok testDelCoordsetMiddleTrans (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testDelCoordsetMiddleTrans) ... ok testGetCoordinates (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testGetCoordinates) ... ok testGetCoordsets (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testGetCoordsets) ... ok testGetNumAtoms (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testGetNumAtoms) ... ok testGetNumCsets (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testGetNumCsets) ... ok testGetWeights (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testGetWeights) ... ok testIterCoordsets (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testIterCoordsets) ... ok testSlicing (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testSlicing) ... ok testSlicingCopy (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testSlicingCopy) ... ok testSlicingList (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testSlicingList) ... ok testSlicingWeights (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testSlicingWeights) ... ok testAllSearch (prody.tests.kdtree.test_kdtree.TestKDTree.testAllSearch) ... ok testSearch (prody.tests.kdtree.test_kdtree.TestKDTree.testSearch) ... ok testPairNoPBC (prody.tests.kdtree.test_kdtree.TestKDTreePBC.testPairNoPBC) ... ok testPairPBC (prody.tests.kdtree.test_kdtree.TestKDTreePBC.testPairPBC) ... ok testPointNoPBC (prody.tests.kdtree.test_kdtree.TestKDTreePBC.testPointNoPBC) ... ok testPointPBC (prody.tests.kdtree.test_kdtree.TestKDTreePBC.testPointPBC) ... ok testMINvsMAX (prody.tests.measure.test_contacts.TestContacts.testMINvsMAX) ... ok testPBCvsNONE (prody.tests.measure.test_contacts.TestContacts.testPBCvsNONE) ... ok testAtomicArgumentSwitching (prody.tests.measure.test_contacts.TestNeighbors.testAtomicArgumentSwitching) ... ok testCoordArgumentSwitching (prody.tests.measure.test_contacts.TestNeighbors.testCoordArgumentSwitching) ... ok testNoPBC (prody.tests.measure.test_contacts.TestNeighbors.testNoPBC) ... ok testPBC (prody.tests.measure.test_contacts.TestNeighbors.testPBC) ... ok testPBCAtomicArgumentSwitching (prody.tests.measure.test_contacts.TestNeighbors.testPBCAtomicArgumentSwitching) ... ok testPBCCoordArgumentSwitching (prody.tests.measure.test_contacts.TestNeighbors.testPBCCoordArgumentSwitching) ... ok testCenter (prody.tests.measure.test_measure.TestCenter.testCenter) ... ok testCenterWithWeights (prody.tests.measure.test_measure.TestCenter.testCenterWithWeights) ... ok testMultiCoordsets (prody.tests.measure.test_measure.TestCenter.testMultiCoordsets) ... ok testMultiCoordsetsWithWeights (prody.tests.measure.test_measure.TestCenter.testMultiCoordsetsWithWeights) ... ok testCTerPhi (prody.tests.measure.test_measure.TestDihedrals.testCTerPhi) ... ok testCTerPsi (prody.tests.measure.test_measure.TestDihedrals.testCTerPsi) ... ok testCalcPhi (prody.tests.measure.test_measure.TestDihedrals.testCalcPhi) ... ok testCalcPsi (prody.tests.measure.test_measure.TestDihedrals.testCalcPsi) ... ok testNTerPhi (prody.tests.measure.test_measure.TestDihedrals.testNTerPhi) ... ok testNTerPsi (prody.tests.measure.test_measure.TestDihedrals.testNTerPsi) ... ok testPBC (prody.tests.measure.test_measure.TestDistances.testPBC) ... ok testPBCSymmetry (prody.tests.measure.test_measure.TestDistances.testPBCSymmetry) ... ok testMSF (prody.tests.measure.test_measure.TestMSF.testMSF) ... /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/trajectory/dcdfile.py:273: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead xyz = fromstring(self._file.read(self._itemsize * n_floats), /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/trajectory/dcdfile.py:320: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead data = fromstring(data, self._dtype) /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/trajectory/dcdfile.py:294: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead unitcell = fromstring(self._file.read(48), dtype=np.float64) ok testMSFfloat (prody.tests.measure.test_measure.TestMSF.testMSFfloat) ... ok testByArgument (prody.tests.measure.test_transform.TestMoveAtoms.testByArgument) ... ok testToArgument (prody.tests.measure.test_transform.TestMoveAtoms.testToArgument) ... ok testTransformation (prody.tests.measure.test_transform.TestMoveAtoms.testTransformation) ... ok testWrap (prody.tests.measure.test_transform.TestWrapAtoms.testWrap) ... ok testAgArgMultiModel (prody.tests.proteins.test_ciffile.TestParseMMCIF.testAgArgMultiModel) Test number of coordinate sets when using *ag* arguments. ... ok testAgArgument (prody.tests.proteins.test_ciffile.TestParseMMCIF.testAgArgument) Test outcome of valid and invalid *ag* arguments. ... /usr/lib/python3.12/traceback.py:241: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles/mmcif_6yfy.cif' mode='rt' encoding='utf-8'> tb.tb_frame.clear() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok testChainArgument (prody.tests.proteins.test_ciffile.TestParseMMCIF.testChainArgument) Test outcome of valid and invalid *chain* arguments. ... ok testLongChainArgument (prody.tests.proteins.test_ciffile.TestParseMMCIF.testLongChainArgument) Test outcome of valid and invalid *chain* arguments. ... /usr/lib/python3.12/traceback.py:241: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles/mmcif_6zu5.cif' mode='rt' encoding='utf-8'> tb.tb_frame.clear() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok testModelArgument (prody.tests.proteins.test_ciffile.TestParseMMCIF.testModelArgument) Test outcome of valid and invalid *model* arguments. ... ok testPDBArgument (prody.tests.proteins.test_ciffile.TestParseMMCIF.testPDBArgument) Test outcome of invalid *pdb* arguments. ... ok testSubsetArgument (prody.tests.proteins.test_ciffile.TestParseMMCIF.testSubsetArgument) Test outcome of valid and invalid *subset* arguments. ... ok testTitleArgument (prody.tests.proteins.test_ciffile.TestParseMMCIF.testTitleArgument) Test outcome of *title* argument. ... ok testUsualCase (prody.tests.proteins.test_ciffile.TestParseMMCIF.testUsualCase) Test the outcome of a simple parsing scenario. ... ok testDSSPBridgePartners (prody.tests.proteins.test_dssp.TestDSSPFunctions.testDSSPBridgePartners) Check if the DSSP bridge-partners were correctly parsed and ... skipped 'dssp is not found' testHeaderContent (prody.tests.proteins.test_header.TestParsePDBHeaderOnly.testHeaderContent) ... ok testHeaderType (prody.tests.proteins.test_header.TestParsePDBHeaderOnly.testHeaderType) ... ok testCompressedArgument (prody.tests.proteins.test_localpdb.TestFetchPDB.testCompressedArgument) Test decompressing fetched PDB files. ... skipped 'Not running tests needing network access.' testFetchingMultipleFiles (prody.tests.proteins.test_localpdb.TestFetchPDB.testFetchingMultipleFiles) Test the outcome of fetching multiple PDB files. ... skipped 'Not running tests needing network access.' testFetchingSingleFile (prody.tests.proteins.test_localpdb.TestFetchPDB.testFetchingSingleFile) Test the outcome of fetching a single PDB file. ... skipped 'Not running tests needing network access.' testInvalidPDBIdentifier (prody.tests.proteins.test_localpdb.TestFetchPDB.testInvalidPDBIdentifier) Test outcome of passing invalid PDB identifiers. ... ok testAgArgMultiModel (prody.tests.proteins.test_pdbfile.TestParsePDB.testAgArgMultiModel) Test number of coordinate sets when using *ag* arguments. ... ok testAgArgSingleModel (prody.tests.proteins.test_pdbfile.TestParsePDB.testAgArgSingleModel) Test number of coordinate sets when using *ag* arguments. ... ok testAgArgument (prody.tests.proteins.test_pdbfile.TestParsePDB.testAgArgument) Test outcome of valid and invalid *ag* arguments. ... /usr/lib/python3.12/traceback.py:241: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/datafiles/pdb2k39_truncated.pdb' mode='rt' encoding='utf-8'> tb.tb_frame.clear() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok testChainArgument (prody.tests.proteins.test_pdbfile.TestParsePDB.testChainArgument) Test outcome of valid and invalid *chain* arguments. ... ok testFiveDigitResnum (prody.tests.proteins.test_pdbfile.TestParsePDB.testFiveDigitResnum) Test parsing PDB files with five digit resnums ... ok testHexResnum (prody.tests.proteins.test_pdbfile.TestParsePDB.testHexResnum) Test parsing PDB files with hexadecimal resnums ... ok testHexSerial (prody.tests.proteins.test_pdbfile.TestParsePDB.testHexSerial) Test parsing PDB files with hexadecimal serial numbers ... ok testHybrid36Resnum (prody.tests.proteins.test_pdbfile.TestParsePDB.testHybrid36Resnum) Test parsing PDB files with Hybrid36 resnums ... ok testHybrid36Serial (prody.tests.proteins.test_pdbfile.TestParsePDB.testHybrid36Serial) Test parsing PDB files with Hybrid36 serial numbers ... ok testModelArgument (prody.tests.proteins.test_pdbfile.TestParsePDB.testModelArgument) Test outcome of valid and invalid *model* arguments. ... ok testPDBArgument (prody.tests.proteins.test_pdbfile.TestParsePDB.testPDBArgument) Test outcome of invalid *pdb* arguments. ... ok testSubsetArgument (prody.tests.proteins.test_pdbfile.TestParsePDB.testSubsetArgument) Test outcome of valid and invalid *subset* arguments. ... ok testTitleArgument (prody.tests.proteins.test_pdbfile.TestParsePDB.testTitleArgument) Test outcome of *title* argument. ... ok testUsualCase (prody.tests.proteins.test_pdbfile.TestParsePDB.testUsualCase) Test the outcome of a simple parsing scenario. ... ok testAltlocA (prody.tests.proteins.test_pdbfile.TestParsePDBAltloc.testAltlocA) ... ok testAltlocB (prody.tests.proteins.test_pdbfile.TestParsePDBAltloc.testAltlocB) ... ok testAltlocC (prody.tests.proteins.test_pdbfile.TestParsePDBAltloc.testAltlocC) ... ok testAltlocNone (prody.tests.proteins.test_pdbfile.TestParsePDBAltloc.testAltlocNone) ... ok testAtomGroupContent (prody.tests.proteins.test_pdbfile.TestParsePDBHeaderAndAllModels.testAtomGroupContent) ... ok testAtomGroupType (prody.tests.proteins.test_pdbfile.TestParsePDBHeaderAndAllModels.testAtomGroupType) ... ok testModelArgument (prody.tests.proteins.test_pdbfile.TestWritePDB.testModelArgument) Test valid and invalid model arguments. ... /usr/lib/python3.12/traceback.py:241: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/test.pdb' mode='wt' encoding='utf-8'> tb.tb_frame.clear() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok testParsingOutput (prody.tests.proteins.test_pdbfile.TestWritePDB.testParsingOutput) Test if parsing output is the same as parsing original file. ... ok testWritingHex (prody.tests.proteins.test_pdbfile.TestWritePDB.testWritingHex) Test if output from writing hexadecimal is as expected. ... ok testWritingHexTer (prody.tests.proteins.test_pdbfile.TestWritePDB.testWritingHexTer) Test if output from writing hexadecimal with TER lines is as expected. ... ok testWritingHybrid36 (prody.tests.proteins.test_pdbfile.TestWritePDB.testWritingHybrid36) Test if output from writing Hybrid36 is as expected. ... ok testWritingHybrid36Ter (prody.tests.proteins.test_pdbfile.TestWritePDB.testWritingHybrid36Ter) Test if output from writing Hybrid36 with TER lines is as expected. ... ok testWritingSecstrs (prody.tests.proteins.test_pdbfile.TestWritePDB.testWritingSecstrs) Test if output from writing secstrs is as expected. ... ok testCompressed (prody.tests.proteins.test_wwpdb.TestFTP.testCompressed) ... skipped 'Not running tests needing network access.' testDecompressed (prody.tests.proteins.test_wwpdb.TestFTP.testDecompressed) ... skipped 'Not running tests needing network access.' testCompressed (prody.tests.proteins.test_wwpdb.TestHTTP.testCompressed) ... skipped 'Not running tests needing network access.' testDecompressed (prody.tests.proteins.test_wwpdb.TestHTTP.testDecompressed) ... skipped 'Not running tests needing network access.' testBuildMSAlocal (prody.tests.sequence.test_analysis.TestBuildMSA.testBuildMSAlocal) ... /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/sequence/msa.py:218: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison return all(other == self._msa) ok testResidueCount (prody.tests.sequence.test_analysis.TestCalcMSAOccupancy.testResidueCount) ... ok testResidueOccupancy (prody.tests.sequence.test_analysis.TestCalcMSAOccupancy.testResidueOccupancy) ... ok testSequenceCount (prody.tests.sequence.test_analysis.TestCalcMSAOccupancy.testSequenceCount) ... ok testSequenceOccupancy (prody.tests.sequence.test_analysis.TestCalcMSAOccupancy.testSequenceOccupancy) ... ok testMATLAB (prody.tests.sequence.test_analysis.TestCalcMeff.testMATLAB) ... ok testTwenty (prody.tests.sequence.test_analysis.TestCalcMeff.testTwenty) ... ok testTwentyReversed (prody.tests.sequence.test_analysis.TestCalcMeff.testTwentyReversed) ... ok testZero1 (prody.tests.sequence.test_analysis.TestCalcMeff.testZero1) ... ok testZero2 (prody.tests.sequence.test_analysis.TestCalcMeff.testZero2) ... ok testAmbiguity (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity) ... ok testAmbiguity2 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity2) ... ok testAmbiguity3 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity3) ... ok testAmbiguity4 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity4) ... ok testAmbiguity5 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity5) ... ok testAmbiguity6 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity6) ... ok testAmbiguity7 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity7) ... ok testInf (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testInf) ... ok testNoAmbiguity (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testNoAmbiguity) ... ok testNorm (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testNorm) ... ok testNorm2 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testNorm2) ... ok testSixSequences (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testSixSequences) ... ok testTwenty (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testTwenty) ... ok testTwentyReversed (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testTwentyReversed) ... ok testAmbiguity (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity) ... ok testAmbiguity2 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity2) ... ok testAmbiguity3 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity3) ... ok testAmbiguity4 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity4) ... ok testAmbiguity5 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity5) ... ok testAmbiguity6 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity6) ... ok testAmbiguity7 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity7) ... ok testFourSequences (prody.tests.sequence.test_analysis.TestCalcOMES.testFourSequences) ... ok testInf (prody.tests.sequence.test_analysis.TestCalcOMES.testInf) ... ok testNoAmbiguity (prody.tests.sequence.test_analysis.TestCalcOMES.testNoAmbiguity) ... ok testTwenty (prody.tests.sequence.test_analysis.TestCalcOMES.testTwenty) ... ok testTwentyReversed (prody.tests.sequence.test_analysis.TestCalcOMES.testTwentyReversed) ... ok testZero (prody.tests.sequence.test_analysis.TestCalcOMES.testZero) ... ok testMATLAB (prody.tests.sequence.test_analysis.TestCalcSCA.testMATLAB) ... ok testZero (prody.tests.sequence.test_analysis.TestCalcSCA.testZero) ... ok testAmbiguous (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testAmbiguous) ... ok testGapDividend (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testGapDividend) ... ok testSixSequences (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testSixSequences) ... ok testSmallProbability (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testSmallProbability) ... ok testTwenty (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testTwenty) ... ok testMATLAB10 (prody.tests.sequence.test_analysis.TestDirectInfo.testMATLAB10) ... /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/sequence/analysis.py:592: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. c = matrix.dot(matrix(zeros((length*q, 1), float)), /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/sequence/analysis.py:593: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. matrix(zeros((1, length*q), float))) /usr/lib/python3/dist-packages/numpy/matrixlib/defmatrix.py:69: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. return matrix(data, dtype=dtype, copy=False) ok testMATLAB8 (prody.tests.sequence.test_analysis.TestDirectInfo.testMATLAB8) ... ok testTwenty (prody.tests.sequence.test_analysis.TestDirectInfo.testTwenty) ... ok testTwentyReversed (prody.tests.sequence.test_analysis.TestDirectInfo.testTwentyReversed) ... ok testZero (prody.tests.sequence.test_analysis.TestDirectInfo.testZero) ... ok testZero1 (prody.tests.sequence.test_analysis.TestDirectInfo.testZero1) ... ok testZero2 (prody.tests.sequence.test_analysis.TestDirectInfo.testZero2) ... ok testZero3 (prody.tests.sequence.test_analysis.TestDirectInfo.testZero3) ... ok testZero4 (prody.tests.sequence.test_analysis.TestDirectInfo.testZero4) ... ok testIdentityMatrix (prody.tests.sequence.test_analysis.TestIdentity.testIdentityMatrix) ... ok testIdentityMatrixNonTurbo (prody.tests.sequence.test_analysis.TestIdentity.testIdentityMatrixNonTurbo) ... ok testUnique (prody.tests.sequence.test_analysis.TestUnique.testUnique) ... ok testUnique2 (prody.tests.sequence.test_analysis.TestUnique.testUnique2) ... ok testMerge (prody.tests.sequence.test_msa.TestMerging.testMerge) ... ok testAddition (prody.tests.sequence.test_msa.TestRefinement.testAddition) ... ok testAll (prody.tests.sequence.test_msa.TestRefinement.testAll) ... ok testColocc (prody.tests.sequence.test_msa.TestRefinement.testColocc) ... ok testExtension (prody.tests.sequence.test_msa.TestRefinement.testExtension) ... ok testLabel (prody.tests.sequence.test_msa.TestRefinement.testLabel) ... ok testRowCol (prody.tests.sequence.test_msa.TestRefinement.testRowCol) ... ok testRowocc (prody.tests.sequence.test_msa.TestRefinement.testRowocc) ... ok testSeqid (prody.tests.sequence.test_msa.TestRefinement.testSeqid) ... ok testSeqidLabel (prody.tests.sequence.test_msa.TestRefinement.testSeqidLabel) ... ok testMSAFile (prody.tests.sequence.test_msafile.TestMSAFile.testMSAFile) ... ok testWriteFasta (prody.tests.sequence.test_msafile.TestMSAFile.testWriteFasta) ... /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/sequence/sequence.py:32: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead self._seq = fromstring(one, '|S1') ok testWriteSelex (prody.tests.sequence.test_msafile.TestMSAFile.testWriteSelex) ... ok testWriteStockholm (prody.tests.sequence.test_msafile.TestMSAFile.testWriteStockholm) ... ok testArray (prody.tests.sequence.test_msafile.TestParseMSA.testArray) ... ok testIterator (prody.tests.sequence.test_msafile.TestParseMSA.testIterator) ... ok testMapping (prody.tests.sequence.test_msafile.TestParseMSA.testMapping) ... ok testFasta (prody.tests.sequence.test_msafile.TestWriteMSA.testFasta) ... ok testSelex (prody.tests.sequence.test_msafile.TestWriteMSA.testSelex) ... ok testStringConversion (prody.tests.sequence.test_sequence.TestSequence.testStringConversion) ... /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/sequence/sequence.py:36: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead self._seq = fromstring(args[0], '|S1') ok testParseDCD (prody.tests.trajectory.test_dcdfile.TestDCDFile.testParseDCD) ... ok testWrite (prody.tests.trajectory.test_dcdfile.TestDCDFile.testWrite) ... ok testWriteDCD (prody.tests.trajectory.test_dcdfile.TestDCDFile.testWriteDCD) ... ok testWriteModeAppend (prody.tests.trajectory.test_dcdfile.TestDCDFile.testWriteModeAppend) ... ok testAll (prody.tests.trajectory.test_frame.TestSuperpose.testAll) ... ok testCarbon (prody.tests.trajectory.test_frame.TestSuperpose.testCarbon) ... ok testCoords (prody.tests.utilities.test_checkers.TestCheckCoords.testCoords) ... ok testCoordset (prody.tests.utilities.test_checkers.TestCheckCoords.testCoordset) ... ok testCoordsetNatoms (prody.tests.utilities.test_checkers.TestCheckCoords.testCoordsetNatoms) ... ok testInvalidCoords (prody.tests.utilities.test_checkers.TestCheckCoords.testInvalidCoords) ... ok testCorrectMonotypeOneArg (prody.tests.utilities.test_checkers.testCheckTypes.testCorrectMonotypeOneArg) ... ok testCorrectMonotypeTwoArgs (prody.tests.utilities.test_checkers.testCheckTypes.testCorrectMonotypeTwoArgs) ... ok testCorrectMultitypeOneArg (prody.tests.utilities.test_checkers.testCheckTypes.testCorrectMultitypeOneArg) ... ok testWrongMonotypeOneArg (prody.tests.utilities.test_checkers.testCheckTypes.testWrongMonotypeOneArg) ... ok testWrongMonotypeTwoArgs (prody.tests.utilities.test_checkers.testCheckTypes.testWrongMonotypeTwoArgs) ... ok testWrongMultitypeOneArg (prody.tests.utilities.test_checkers.testCheckTypes.testWrongMultitypeOneArg) ... ok testContinuous (prody.tests.utilities.test_misctools.TestRangeString.testContinuous) ... ok testGapped (prody.tests.utilities.test_misctools.TestRangeString.testGapped) ... ok testNegative (prody.tests.utilities.test_misctools.TestRangeString.testNegative) ... ok testRepeated (prody.tests.utilities.test_misctools.TestRangeString.testRepeated) ... ok testBuffer (prody.tests.utilities.test_pathtools.TestGunzip.testBuffer) ... /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/utilities/test_pathtools.py:34: ResourceWarning: unclosed file <_io.BufferedReader name='/tmp/compressed.txt.gz'> buff = open(self.gzfn, 'rb').read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok testFile (prody.tests.utilities.test_pathtools.TestGunzip.testFile) ... /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/utilities/test_pathtools.py:29: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/compressed.txt' mode='r' encoding='utf-8'> text = open(fn).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok ====================================================================== FAIL: testBuildMatrixCoordsArray (prody.tests.dynamics.test_enms.TestANM.testBuildMatrixCoordsArray) Test output when *coords* is an array. ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/dynamics/test_enms.py", line 295, in testBuildMatrixCoordsArray assert_equal(self.getMatrix(), self.getExpected(), File "/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line 349, in assert_equal return assert_array_equal(actual, desired, err_msg, verbose) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line 985, in assert_array_equal assert_array_compare(operator.__eq__, x, y, err_msg=err_msg, File "/usr/lib/python3.12/contextlib.py", line 81, in inner return func(*args, **kwds) ^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line 862, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not equal failed to get correct matrix Mismatched elements: 3 / 51984 (0.00577%) Max absolute difference: 4.4408921e-16 Max relative difference: 7.83963072e-16 x: array([[ 6.913751, 0.021868, 0.94014 , ..., 0. , 0. , 0. ], [ 0.021868, 9.066915, -0.076779, ..., 0. , 0. ,... y: array([[ 6.913751, 0.021868, 0.94014 , ..., 0. , 0. , 0. ], [ 0.021868, 9.066915, -0.076779, ..., 0. , 0. ,... ====================================================================== FAIL: testHessianSymmetry (prody.tests.dynamics.test_enms.TestEXANMResults.testHessianSymmetry) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build/prody/tests/dynamics/test_enms.py", line 181, in testHessianSymmetry assert_equal(hessian, hessian.T, 'hessian is not symmetric') File "/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line 349, in assert_equal return assert_array_equal(actual, desired, err_msg, verbose) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line 985, in assert_array_equal assert_array_compare(operator.__eq__, x, y, err_msg=err_msg, File "/usr/lib/python3.12/contextlib.py", line 81, in inner return func(*args, **kwds) ^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line 862, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not equal hessian is not symmetric Mismatched elements: 166 / 13089924 (0.00127%) Max absolute difference: 8.8817842e-16 Max relative difference: 4.00832339e-16 x: array([[ 8.024368, 0.273151, 4.136877, ..., 0. , 0. , 0. ], [ 0.273151, 3.353604, -0.105517, ..., 0. , 0. ,... y: array([[ 8.024368, 0.273151, 4.136877, ..., 0. , 0. , 0. ], [ 0.273151, 3.353604, -0.105517, ..., 0. , 0. ,... ---------------------------------------------------------------------- Ran 971 tests in 112.069s FAILED (failures=2, skipped=39) E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.12_prody/build; python3.12 -m unittest discover -v I: pybuild base:305: cd /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build; python3.11 -m unittest discover -v testANMCommand (prody.tests.apps.test_prody_anm.TestANMCommand.testANMCommand) ... skipped 'prody command not found' testAlignConcat (prody.tests.apps.test_prody_catdcd.TestCatdcdCommand.testAlignConcat) ... skipped 'prody command not found' testAlignException (prody.tests.apps.test_prody_catdcd.TestCatdcdCommand.testAlignException) ... skipped 'prody command is not found' testIOException (prody.tests.apps.test_prody_catdcd.TestCatdcdCommand.testIOException) ... skipped 'prody command is not found' testSelectConcat (prody.tests.apps.test_prody_catdcd.TestCatdcdCommand.testSelectConcat) ... skipped 'prody command not found' testSelectException (prody.tests.apps.test_prody_catdcd.TestCatdcdCommand.testSelectException) ... skipped 'prody command is not found' testSelectException2 (prody.tests.apps.test_prody_catdcd.TestCatdcdCommand.testSelectException2) ... skipped 'prody command is not found' testSimpleConcat (prody.tests.apps.test_prody_catdcd.TestCatdcdCommand.testSimpleConcat) ... skipped 'prody command not found' testCommandExample1 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample1) Test example: $ prody anm 1p38 ... skipped 'prody command not found' testCommandExample10 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample10) Test example: $ prody align 2k39 --select "backbone and resnum < 71" ... skipped 'prody command not found' testCommandExample11 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample11) Test example: $ prody align --select "resnum < 300" 1p38 1r39 1zz2 ... skipped 'prody command not found' testCommandExample12 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample12) Test example: $ prody align --select "resnum 1 to 70" 1aar 2k39 ... skipped 'prody command not found' testCommandExample13 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample13) Test example: $ prody align --select "noh heme and chain A" 1hrc 1fi7 ... skipped 'prody command not found' testCommandExample14 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample14) Test example: $ prody biomol 2bfu ... skipped 'prody command not found' testCommandExample15 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample15) Test example: $ prody select -o B11 "resname B11" 1zz2 $ prody select -o BOG "resname BOG" 1zz2 $ prody contacts -r 4.0 -t residue -s protein 1zz2 B11.pdb BOG.pdb ... skipped 'prody command not found' testCommandExample16 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample16) Test example: $ prody fetch 1mkp 1p38 ... skipped 'prody command not found' testCommandExample17 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample17) Test example: $ prody select backbone 1p38 1r39 ... skipped 'prody command not found' testCommandExample18 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample18) Test example: $ prody energy 1p38 1r39 ... skipped 'prody command not found' testCommandExample19 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample19) Test example: $ prody clustenm 1p38 ... skipped 'prody command not found' testCommandExample2 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample2) Test example: $ prody anm 1aar -s "calpha and chain A and resnum < 70" -A ... skipped 'prody command not found' testCommandExample20 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample20) Test example: $ prody clustenm 1aar -s "calpha and chain A and resnum < 70" -A ... skipped 'prody command not found' testCommandExample3 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample3) Test example: $ prody gnm 1p38 ... skipped 'prody command not found' testCommandExample4 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample4) Test example: $ prody gnm 1aar -c 7 -s "calpha and chain A and resnum < 70" -A ... skipped 'prody command not found' testCommandExample5 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample5) Test example: $ prody pca 2k39 ... skipped 'prody command not found' testCommandExample6 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample6) Test example: $ prody pca 2k39 --select "backbone and resnum < 71" -a -A ... skipped 'prody command not found' testCommandExample7 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample7) Test example: $ prody pca 2k39 ... skipped 'prody command not found' testCommandExample8 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample8) Test example: $ prody pca 2k39 --select "backbone and resnum < 71" -a -A ... skipped 'prody command not found' testCommandExample9 (prody.tests.apps.test_prody_examples.TestCommandExamples.testCommandExample9) Test example: $ prody align 2k39 ... skipped 'prody command not found' testGNMCommand (prody.tests.apps.test_prody_gnm.TestGNMCommand.testGNMCommand) ... skipped 'prody command not found' testPCACommandDCD (prody.tests.apps.test_prody_pca.TestPCACommand.testPCACommandDCD) ... skipped 'prody command not found' testPCACommandPDB (prody.tests.apps.test_prody_pca.TestPCACommand.testPCACommandPDB) ... skipped 'prody command not found' testAtomGroup (prody.tests.atomic.test_atomic.TestAtomIterations.testAtomGroup) ... ok testAtomMap (prody.tests.atomic.test_atomic.TestAtomIterations.testAtomMap) ... ok testChain (prody.tests.atomic.test_atomic.TestAtomIterations.testChain) ... ok testResidue (prody.tests.atomic.test_atomic.TestAtomIterations.testResidue) ... ok testSelection (prody.tests.atomic.test_atomic.TestAtomIterations.testSelection) ... ok testAtom (prody.tests.atomic.test_atomic.TestPickling.testAtom) ... ok testAtomGroup (prody.tests.atomic.test_atomic.TestPickling.testAtomGroup) ... ok testSelection (prody.tests.atomic.test_atomic.TestPickling.testSelection) ... ok testSaveLoad (prody.tests.atomic.test_atomic.TestSaveLoad.testSaveLoad) ... ok testInstantiation (prody.tests.atomic.test_atommap.TestInstantiation.testInstantiation) ... ok testAllSelection (prody.tests.atomic.test_atommap.TestSelection.testAllSelection) ... ok testChainSelection (prody.tests.atomic.test_atommap.TestSelection.testChainSelection) ... ok testGetBoolArray (prody.tests.atomic.test_atommap.TestSelection.testGetBoolArray) ... ok testNameSelection (prody.tests.atomic.test_atommap.TestSelection.testNameSelection) ... ok testSplit (prody.tests.atomic.test_fragment.TestFragment.testSplit) ... ok testSplitCopy (prody.tests.atomic.test_fragment.TestFragment.testSplitCopy) ... ok testSplitNoh (prody.tests.atomic.test_fragment.TestFragment.testSplitNoh) ... ok testSplitNohCopy (prody.tests.atomic.test_fragment.TestFragment.testSplitNohCopy) ... ok testWhole (prody.tests.atomic.test_fragment.TestFragment.testWhole) ... ok testWhole2 (prody.tests.atomic.test_fragment.TestFragment.testWhole2) ... ok testWholeAll (prody.tests.atomic.test_fragment.TestFragment.testWholeAll) ... ok testWholeCopy (prody.tests.atomic.test_fragment.TestFragment.testWholeCopy) ... ok testWholeNoh (prody.tests.atomic.test_fragment.TestFragment.testWholeNoh) ... ok testWholeNohCopy (prody.tests.atomic.test_fragment.TestFragment.testWholeNohCopy) ... ok testCA (prody.tests.atomic.test_hierview.TestShuffled.testCA) ... ok testProtein (prody.tests.atomic.test_hierview.TestShuffled.testProtein) ... ok testNumResidues (prody.tests.atomic.test_hierview.TestTerRecord.testNumResidues) ... ok testResidueIndexing (prody.tests.atomic.test_hierview.TestTerRecord.testResidueIndexing) ... ok testSelectionResidueIndexing (prody.tests.atomic.test_hierview.TestTerRecord.testSelectionResidueIndexing) ... ok testSelectionResidueIndexing2 (prody.tests.atomic.test_hierview.TestTerRecord.testSelectionResidueIndexing2) ... ok testMacro1 (prody.tests.atomic.test_select.TestMacros.testMacro1) Test macro *cacb*: 'name CA CB' ... ok testMacro2 (prody.tests.atomic.test_select.TestMacros.testMacro2) Test macro *donors*: '(protein) and (name N NE NH2 ND2 NE2 ND1 OG OH NH1 SG OG1 NE2 NZ NE1 ND1 NE2)' ... ok testMacroFunctions (prody.tests.atomic.test_select.TestMacros.testMacroFunctions) ... ok testBondedtoSelection1 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection1) Test bondedto selections 'bonded to index 0' for imatinib ... ok testBondedtoSelection10 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection10) Test bondedto selections "bonded 2 to index 0" ... ok testBondedtoSelection11 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection11) Test bondedto selections 'bonded 0 to index 0' for imatinib ... ok testBondedtoSelection12 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection12) Test bondedto selections "bonded 0 to index 0" ... ok testBondedtoSelection13 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection13) Test bondedto selections 'bonded 3 to index 0' for imatinib ... ok testBondedtoSelection14 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection14) Test bondedto selections "bonded 3 to index 0" ... ok testBondedtoSelection15 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection15) Test bondedto selections 'bonded 4 to index 0' for imatinib ... ok testBondedtoSelection16 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection16) Test bondedto selections "bonded 4 to index 0" ... ok testBondedtoSelection17 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection17) Test bondedto selections 'bonded 4 to index 0' for imatinib ... ok testBondedtoSelection18 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection18) Test bondedto selections "bonded 4 to index 0" ... ok testBondedtoSelection19 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection19) Test bondedto selections 'bonded 4 to index 0' for imatinib ... ok testBondedtoSelection2 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection2) Test bondedto selections "bonded to index 0" ... ok testBondedtoSelection20 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection20) Test bondedto selections "bonded 4 to index 0" ... ok testBondedtoSelection21 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection21) Test bondedto selections 'exbonded 1 to index 0' for imatinib ... ok testBondedtoSelection22 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection22) Test bondedto selections "exbonded 1 to index 0" ... ok testBondedtoSelection23 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection23) Test bondedto selections 'exbonded 2 to index 0' for imatinib ... ok testBondedtoSelection24 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection24) Test bondedto selections "exbonded 2 to index 0" ... ok testBondedtoSelection25 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection25) Test bondedto selections 'exbonded 3 to index 0' for imatinib ... ok testBondedtoSelection26 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection26) Test bondedto selections "exbonded 3 to index 0" ... ok testBondedtoSelection27 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection27) Test bondedto selections 'bonded 20 to index 0' for imatinib ... ok testBondedtoSelection28 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection28) Test bondedto selections "bonded 20 to index 0" ... ok testBondedtoSelection29 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection29) Test bondedto selections 'bonded 20 to index 10' for imatinib ... ok testBondedtoSelection3 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection3) Test bondedto selections 'exbonded to index 0' for imatinib ... ok testBondedtoSelection30 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection30) Test bondedto selections "bonded 20 to index 10" ... ok testBondedtoSelection31 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection31) Test bondedto selections 'bonded to index 1000' for imatinib ... ok testBondedtoSelection32 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection32) Test bondedto selections "bonded to index 1000" ... ok testBondedtoSelection33 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection33) Test bondedto selections 'fragment 0' for imatinib ... ok testBondedtoSelection34 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection34) Test bondedto selections "fragment 0" ... ok testBondedtoSelection35 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection35) Test bondedto selections 'fragment 1' for imatinib ... ok testBondedtoSelection36 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection36) Test bondedto selections "fragment 1" ... ok testBondedtoSelection37 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection37) Test bondedto selections 'fragment 0 1 2' for imatinib ... ok testBondedtoSelection38 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection38) Test bondedto selections "fragment 0 1 2" ... ok testBondedtoSelection39 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection39) Test bondedto selections 'fragindex 0 1 2' for imatinib ... ok testBondedtoSelection4 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection4) Test bondedto selections "exbonded to index 0" ... ok testBondedtoSelection40 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection40) Test bondedto selections "fragindex 0 1 2" ... ok testBondedtoSelection41 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection41) Test bondedto selections 'fragindex 0:2' for imatinib ... ok testBondedtoSelection42 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection42) Test bondedto selections "fragindex 0:2" ... ok testBondedtoSelection5 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection5) Test bondedto selections 'bonded to index 67' for imatinib ... ok testBondedtoSelection6 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection6) Test bondedto selections "bonded to index 67" ... ok testBondedtoSelection7 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection7) Test bondedto selections 'exbonded to index 67' for imatinib ... ok testBondedtoSelection8 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection8) Test bondedto selections "exbonded to index 67" ... ok testBondedtoSelection9 (prody.tests.atomic.test_select.TestSelect.testBondedtoSelection9) Test bondedto selections 'bonded 2 to index 0' for imatinib ... ok testComparisonsSelection1 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection1) Test comparisons selections 'x = -51.659' for pdb3mht ... ok testComparisonsSelection10 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection10) Test comparisons selections "beta > 10" ... ok testComparisonsSelection11 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection11) Test comparisons selections 'beta < 10' for pdb3mht ... ok testComparisonsSelection12 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection12) Test comparisons selections "beta < 10" ... ok testComparisonsSelection13 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection13) Test comparisons selections 'occupancy > 0.999999' for pdb3mht ... ok testComparisonsSelection14 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection14) Test comparisons selections "occupancy > 0.999999" ... ok testComparisonsSelection15 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection15) Test comparisons selections '-10 <= x < 0' for pdb3mht ... ok testComparisonsSelection16 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection16) Test comparisons selections "-10 <= x < 0" ... ok testComparisonsSelection17 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection17) Test comparisons selections '11 > 10' for pdb3mht ... ok testComparisonsSelection18 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection18) Test comparisons selections "11 > 10" ... ok testComparisonsSelection19 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection19) Test comparisons selections 'radius > 10' for pdb3mht ... ok testComparisonsSelection2 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection2) Test comparisons selections "x = -51.659" ... ok testComparisonsSelection20 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection20) Test comparisons selections "radius > 10" ... ok testComparisonsSelection21 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection21) Test comparisons selections 'chain = A' for pdb3mht ... ok testComparisonsSelection22 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection22) Test comparisons selections "chain = A" ... ok testComparisonsSelection23 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection23) Test comparisons selections 'x x < 1' for pdb3mht ... ok testComparisonsSelection24 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection24) Test comparisons selections "x x < 1" ... ok testComparisonsSelection25 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection25) Test comparisons selections 'name < 1' for pdb3mht ... ok testComparisonsSelection26 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection26) Test comparisons selections "name < 1" ... ok testComparisonsSelection3 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection3) Test comparisons selections 'x != -51.659' for pdb3mht ... ok testComparisonsSelection4 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection4) Test comparisons selections "x != -51.659" ... ok testComparisonsSelection5 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection5) Test comparisons selections 'z >= 82.813' for pdb3mht ... ok testComparisonsSelection6 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection6) Test comparisons selections "z >= 82.813" ... ok testComparisonsSelection7 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection7) Test comparisons selections 'z < 82.813' for pdb3mht ... ok testComparisonsSelection8 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection8) Test comparisons selections "z < 82.813" ... ok testComparisonsSelection9 (prody.tests.atomic.test_select.TestSelect.testComparisonsSelection9) Test comparisons selections 'beta > 10' for pdb3mht ... ok testCompositeSelection1 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection1) Test composite selections 'chain x y z C and x 10' for pdb3mht ... ok testCompositeSelection10 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection10) Test composite selections "water and within 5 of not protein" ... ok testCompositeSelection11 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection11) Test composite selections 'backbone and sqrt((x - 25)**2 + (y - 74)**2 + (z - 13)**2) <= 500' for pdb3mht ... ok testCompositeSelection12 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection12) Test composite selections "backbone and sqrt((x - 25)**2 + (y - 74)**2 + (z - 13)**2) <= 500" ... ok testCompositeSelection13 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection13) Test composite selections '(not resname SAH) and (protein and name CA) or (nucleic and name P)' for pdb3mht ... ok testCompositeSelection14 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection14) Test composite selections "(not resname SAH) and (protein and name CA) or (nucleic and name P)" ... ok testCompositeSelection15 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection15) Test composite selections 'protein and (backbone or name H)' for pdb3mht ... ok testCompositeSelection16 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection16) Test composite selections "protein and (backbone or name H)" ... ok testCompositeSelection17 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection17) Test composite selections 'same residue as within 4 of and resname SAH' for pdb3mht ... ok testCompositeSelection18 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection18) Test composite selections "same residue as within 4 of and resname SAH" ... ok testCompositeSelection19 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection19) Test composite selections 'protein and name CA CB and same residue as ((x+21.2)**2 + (y-35.9)**2 + (z-80.0)**2)**0.5 < 10' for pdb3mht ... ok testCompositeSelection2 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection2) Test composite selections "chain x y z C and x 10" ... ok testCompositeSelection20 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection20) Test composite selections "protein and name CA CB and same residue as ((x+21.2)**2 + (y-35.9)**2 + (z-80.0)**2)**0.5 < 10" ... ok testCompositeSelection3 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection3) Test composite selections 'resnum `1` `2`' for pdb3mht ... ok testCompositeSelection4 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection4) Test composite selections "resnum `1` `2`" ... ok testCompositeSelection5 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection5) Test composite selections 'same residue as within 4 of resname SAH' for pdb3mht ... ok testCompositeSelection6 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection6) Test composite selections "same residue as within 4 of resname SAH" ... ok testCompositeSelection7 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection7) Test composite selections 'name CA and same residue as within 4 of resname SAH' for pdb3mht ... ok testCompositeSelection8 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection8) Test composite selections "name CA and same residue as within 4 of resname SAH" ... ok testCompositeSelection9 (prody.tests.atomic.test_select.TestSelect.testCompositeSelection9) Test composite selections 'water and within 5 of not protein' for pdb3mht ... ok testDocexamplesSelection1 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection1) Test docexamples selections 'serial 1 2 3' for pdb3mht ... ok testDocexamplesSelection10 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection10) Test docexamples selections "beta 555.55" ... ok testDocexamplesSelection11 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection11) Test docexamples selections 'beta 1 to 500' for pdb3mht ... ok testDocexamplesSelection12 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection12) Test docexamples selections "beta 1 to 500" ... ok testDocexamplesSelection13 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection13) Test docexamples selections 'beta 1:500' for pdb3mht ... ok testDocexamplesSelection14 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection14) Test docexamples selections "beta 1:500" ... ok testDocexamplesSelection15 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection15) Test docexamples selections 'beta < 500' for pdb3mht ... ok testDocexamplesSelection16 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection16) Test docexamples selections "beta < 500" ... ok testDocexamplesSelection17 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection17) Test docexamples selections 'resnum 120A 120B' for pdb3mht ... ok testDocexamplesSelection18 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection18) Test docexamples selections "resnum 120A 120B" ... ok testDocexamplesSelection19 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection19) Test docexamples selections 'icode A' for pdb3mht ... ok testDocexamplesSelection2 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection2) Test docexamples selections "serial 1 2 3" ... ok testDocexamplesSelection20 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection20) Test docexamples selections "icode A" ... ok testDocexamplesSelection21 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection21) Test docexamples selections 'icode _' for pdb3mht ... ok testDocexamplesSelection22 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection22) Test docexamples selections "icode _" ... ok testDocexamplesSelection23 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection23) Test docexamples selections 'charge 1' for pdb3mht ... ok testDocexamplesSelection24 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection24) Test docexamples selections "charge 1" ... ok testDocexamplesSelection25 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection25) Test docexamples selections 'abs(charge) == 1' for pdb3mht ... ok testDocexamplesSelection26 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection26) Test docexamples selections "abs(charge) == 1" ... ok testDocexamplesSelection27 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection27) Test docexamples selections 'charge < 0' for pdb3mht ... ok testDocexamplesSelection28 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection28) Test docexamples selections "charge < 0" ... ok testDocexamplesSelection29 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection29) Test docexamples selections '0 < mass < 500' for pdb3mht ... ok testDocexamplesSelection3 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection3) Test docexamples selections 'serial 1 to 10' for pdb3mht ... ok testDocexamplesSelection30 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection30) Test docexamples selections "0 < mass < 500" ... ok testDocexamplesSelection31 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection31) Test docexamples selections 'abs(mass) <= mass <= 10' for pdb3mht ... ok testDocexamplesSelection32 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection32) Test docexamples selections "abs(mass) <= mass <= 10" ... ok testDocexamplesSelection4 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection4) Test docexamples selections "serial 1 to 10" ... ok testDocexamplesSelection5 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection5) Test docexamples selections 'serial 1:10:2' for pdb3mht ... ok testDocexamplesSelection6 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection6) Test docexamples selections "serial 1:10:2" ... ok testDocexamplesSelection7 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection7) Test docexamples selections 'serial < 10' for pdb3mht ... ok testDocexamplesSelection8 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection8) Test docexamples selections "serial < 10" ... ok testDocexamplesSelection9 (prody.tests.atomic.test_select.TestSelect.testDocexamplesSelection9) Test docexamples selections 'beta 555.55' for pdb3mht ... ok testEquivalentSelection1 (prody.tests.atomic.test_select.TestSelect.testEquivalentSelection1) Test equivalent selections 'chain C' for pdb3mht ... ok testEquivalentSelection2 (prody.tests.atomic.test_select.TestSelect.testEquivalentSelection2) Test equivalent selections "chain C" ... ok testEquivalentSelection3 (prody.tests.atomic.test_select.TestSelect.testEquivalentSelection3) Test equivalent selections 'chain C' for pdb3mht ... ok testEquivalentSelection4 (prody.tests.atomic.test_select.TestSelect.testEquivalentSelection4) Test equivalent selections "chain C" ... ok testEquivalentSelection5 (prody.tests.atomic.test_select.TestSelect.testEquivalentSelection5) Test equivalent selections 'nucleic' for pdb3mht ... ok testEquivalentSelection6 (prody.tests.atomic.test_select.TestSelect.testEquivalentSelection6) Test equivalent selections "nucleic" ... ok testFlagsSelection1 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection1) Test flags selections 'protein' for gromacs ... ok testFlagsSelection10 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection10) Test flags selections "aliphatic" ... ok testFlagsSelection100 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection100) Test flags selections "bridge" ... ok testFlagsSelection101 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection101) Test flags selections 'bend' for pdb3mht ... ok testFlagsSelection102 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection102) Test flags selections "bend" ... ok testFlagsSelection103 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection103) Test flags selections 'coil' for pdb3mht ... ok testFlagsSelection104 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection104) Test flags selections "coil" ... ok testFlagsSelection11 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection11) Test flags selections 'aromatic' for pdb3mht ... ok testFlagsSelection12 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection12) Test flags selections "aromatic" ... ok testFlagsSelection13 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection13) Test flags selections 'at' for pdb3mht ... ok testFlagsSelection14 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection14) Test flags selections "at" ... ok testFlagsSelection15 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection15) Test flags selections 'basic' for pdb3mht ... ok testFlagsSelection16 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection16) Test flags selections "basic" ... ok testFlagsSelection17 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection17) Test flags selections 'buried' for pdb3mht ... ok testFlagsSelection18 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection18) Test flags selections "buried" ... ok testFlagsSelection19 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection19) Test flags selections 'cg' for pdb3mht ... ok testFlagsSelection2 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection2) Test flags selections "protein" ... ok testFlagsSelection20 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection20) Test flags selections "cg" ... ok testFlagsSelection21 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection21) Test flags selections 'charged' for pdb3mht ... ok testFlagsSelection22 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection22) Test flags selections "charged" ... ok testFlagsSelection23 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection23) Test flags selections 'cyclic' for pdb3mht ... ok testFlagsSelection24 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection24) Test flags selections "cyclic" ... ok testFlagsSelection25 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection25) Test flags selections 'heme' for pdb3mht ... ok testFlagsSelection26 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection26) Test flags selections "heme" ... ok testFlagsSelection27 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection27) Test flags selections 'hydrophobic' for pdb3mht ... ok testFlagsSelection28 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection28) Test flags selections "hydrophobic" ... ok testFlagsSelection29 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection29) Test flags selections 'ion' for pdb3mht ... ok testFlagsSelection3 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection3) Test flags selections 'all' for pdb3mht ... ok testFlagsSelection30 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection30) Test flags selections "ion" ... ok testFlagsSelection31 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection31) Test flags selections 'large' for pdb3mht ... ok testFlagsSelection32 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection32) Test flags selections "large" ... ok testFlagsSelection33 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection33) Test flags selections 'lipid' for pdb3mht ... ok testFlagsSelection34 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection34) Test flags selections "lipid" ... ok testFlagsSelection35 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection35) Test flags selections 'medium' for pdb3mht ... ok testFlagsSelection36 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection36) Test flags selections "medium" ... ok testFlagsSelection37 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection37) Test flags selections 'neutral' for pdb3mht ... ok testFlagsSelection38 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection38) Test flags selections "neutral" ... ok testFlagsSelection39 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection39) Test flags selections 'nucleic' for pdb3mht ... ok testFlagsSelection4 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection4) Test flags selections "all" ... ok testFlagsSelection40 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection40) Test flags selections "nucleic" ... ok testFlagsSelection41 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection41) Test flags selections 'nucleotide' for pdb3mht ... ok testFlagsSelection42 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection42) Test flags selections "nucleotide" ... ok testFlagsSelection43 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection43) Test flags selections 'nucleobase' for pdb3mht ... ok testFlagsSelection44 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection44) Test flags selections "nucleobase" ... ok testFlagsSelection45 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection45) Test flags selections 'nucleoside' for pdb3mht ... ok testFlagsSelection46 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection46) Test flags selections "nucleoside" ... ok testFlagsSelection47 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection47) Test flags selections 'polar' for pdb3mht ... ok testFlagsSelection48 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection48) Test flags selections "polar" ... ok testFlagsSelection49 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection49) Test flags selections 'protein' for pdb3mht ... ok testFlagsSelection5 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection5) Test flags selections 'acidic' for pdb3mht ... ok testFlagsSelection50 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection50) Test flags selections "protein" ... ok testFlagsSelection51 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection51) Test flags selections 'stdaa' for pdb3mht ... ok testFlagsSelection52 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection52) Test flags selections "stdaa" ... ok testFlagsSelection53 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection53) Test flags selections 'nonstdaa' for pdb3mht ... ok testFlagsSelection54 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection54) Test flags selections "nonstdaa" ... ok testFlagsSelection55 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection55) Test flags selections 'purine' for pdb3mht ... ok testFlagsSelection56 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection56) Test flags selections "purine" ... ok testFlagsSelection57 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection57) Test flags selections 'pyrimidine' for pdb3mht ... ok testFlagsSelection58 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection58) Test flags selections "pyrimidine" ... ok testFlagsSelection59 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection59) Test flags selections 'small' for pdb3mht ... ok testFlagsSelection6 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection6) Test flags selections "acidic" ... ok testFlagsSelection60 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection60) Test flags selections "small" ... ok testFlagsSelection61 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection61) Test flags selections 'sugar' for pdb3mht ... ok testFlagsSelection62 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection62) Test flags selections "sugar" ... ok testFlagsSelection63 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection63) Test flags selections 'surface' for pdb3mht ... ok testFlagsSelection64 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection64) Test flags selections "surface" ... ok testFlagsSelection65 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection65) Test flags selections 'water' for pdb3mht ... ok testFlagsSelection66 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection66) Test flags selections "water" ... ok testFlagsSelection67 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection67) Test flags selections 'hetero' for pdb3mht ... ok testFlagsSelection68 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection68) Test flags selections "hetero" ... ok testFlagsSelection69 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection69) Test flags selections 'hetatm' for pdb3mht ... ok testFlagsSelection7 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection7) Test flags selections 'acyclic' for pdb3mht ... ok testFlagsSelection70 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection70) Test flags selections "hetatm" ... ok testFlagsSelection71 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection71) Test flags selections 'calpha' for pdb3mht ... ok testFlagsSelection72 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection72) Test flags selections "calpha" ... ok testFlagsSelection73 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection73) Test flags selections 'backbone' for pdb3mht ... ok testFlagsSelection74 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection74) Test flags selections "backbone" ... ok testFlagsSelection75 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection75) Test flags selections 'backbonefull' for pdb3mht ... ok testFlagsSelection76 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection76) Test flags selections "backbonefull" ... ok testFlagsSelection77 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection77) Test flags selections 'sidechain' for pdb3mht ... ok testFlagsSelection78 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection78) Test flags selections "sidechain" ... ok testFlagsSelection79 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection79) Test flags selections 'carbon' for pdb3mht ... ok testFlagsSelection8 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection8) Test flags selections "acyclic" ... ok testFlagsSelection80 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection80) Test flags selections "carbon" ... ok testFlagsSelection81 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection81) Test flags selections 'hydrogen' for pdb3mht ... ok testFlagsSelection82 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection82) Test flags selections "hydrogen" ... ok testFlagsSelection83 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection83) Test flags selections 'noh' for pdb3mht ... ok testFlagsSelection84 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection84) Test flags selections "noh" ... ok testFlagsSelection85 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection85) Test flags selections 'nitrogen' for pdb3mht ... ok testFlagsSelection86 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection86) Test flags selections "nitrogen" ... ok testFlagsSelection87 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection87) Test flags selections 'oxygen' for pdb3mht ... ok testFlagsSelection88 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection88) Test flags selections "oxygen" ... ok testFlagsSelection89 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection89) Test flags selections 'sulfur' for pdb3mht ... ok testFlagsSelection9 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection9) Test flags selections 'aliphatic' for pdb3mht ... ok testFlagsSelection90 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection90) Test flags selections "sulfur" ... ok testFlagsSelection91 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection91) Test flags selections 'extended' for pdb3mht ... ok testFlagsSelection92 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection92) Test flags selections "extended" ... ok testFlagsSelection93 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection93) Test flags selections 'helix' for pdb3mht ... ok testFlagsSelection94 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection94) Test flags selections "helix" ... ok testFlagsSelection95 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection95) Test flags selections 'helix310' for pdb3mht ... ok testFlagsSelection96 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection96) Test flags selections "helix310" ... ok testFlagsSelection97 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection97) Test flags selections 'turn' for pdb3mht ... ok testFlagsSelection98 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection98) Test flags selections "turn" ... ok testFlagsSelection99 (prody.tests.atomic.test_select.TestSelect.testFlagsSelection99) Test flags selections 'bridge' for pdb3mht ... ok testFloatSelection1 (prody.tests.atomic.test_select.TestSelect.testFloatSelection1) Test float selections 'beta 5.0 41.15 11.85' for pdb3mht ... ok testFloatSelection10 (prody.tests.atomic.test_select.TestSelect.testFloatSelection10) Test float selections "z 115.246 45.784" ... ok testFloatSelection11 (prody.tests.atomic.test_select.TestSelect.testFloatSelection11) Test float selections 'charge 0' for pdb3mht ... ok testFloatSelection12 (prody.tests.atomic.test_select.TestSelect.testFloatSelection12) Test float selections "charge 0" ... ok testFloatSelection13 (prody.tests.atomic.test_select.TestSelect.testFloatSelection13) Test float selections 'mass 1' for pdb3mht ... ok testFloatSelection14 (prody.tests.atomic.test_select.TestSelect.testFloatSelection14) Test float selections "mass 1" ... ok testFloatSelection15 (prody.tests.atomic.test_select.TestSelect.testFloatSelection15) Test float selections 'radius 0' for pdb3mht ... ok testFloatSelection16 (prody.tests.atomic.test_select.TestSelect.testFloatSelection16) Test float selections "radius 0" ... ok testFloatSelection17 (prody.tests.atomic.test_select.TestSelect.testFloatSelection17) Test float selections 'beta "1."' for pdb3mht ... ok testFloatSelection18 (prody.tests.atomic.test_select.TestSelect.testFloatSelection18) Test float selections "beta "1."" ... ok testFloatSelection19 (prody.tests.atomic.test_select.TestSelect.testFloatSelection19) Test float selections 'beta = "1."' for pdb3mht ... ok testFloatSelection2 (prody.tests.atomic.test_select.TestSelect.testFloatSelection2) Test float selections "beta 5.0 41.15 11.85" ... ok testFloatSelection20 (prody.tests.atomic.test_select.TestSelect.testFloatSelection20) Test float selections "beta = "1."" ... ok testFloatSelection3 (prody.tests.atomic.test_select.TestSelect.testFloatSelection3) Test float selections 'occupancy 1.0' for pdb3mht ... ok testFloatSelection4 (prody.tests.atomic.test_select.TestSelect.testFloatSelection4) Test float selections "occupancy 1.0" ... ok testFloatSelection5 (prody.tests.atomic.test_select.TestSelect.testFloatSelection5) Test float selections 'x 6.665' for pdb3mht ... ok testFloatSelection6 (prody.tests.atomic.test_select.TestSelect.testFloatSelection6) Test float selections "x 6.665" ... ok testFloatSelection7 (prody.tests.atomic.test_select.TestSelect.testFloatSelection7) Test float selections 'y 69.99 13.314' for pdb3mht ... ok testFloatSelection8 (prody.tests.atomic.test_select.TestSelect.testFloatSelection8) Test float selections "y 69.99 13.314" ... ok testFloatSelection9 (prody.tests.atomic.test_select.TestSelect.testFloatSelection9) Test float selections 'z 115.246 45.784' for pdb3mht ... ok testFunctionSelection1 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection1) Test function selections 'sqrt(x**2 + y**2 + z**2) < 100' for pdb3mht ... ok testFunctionSelection10 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection10) Test function selections "ceil(beta) == 10" ... ok testFunctionSelection11 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection11) Test function selections 'floor(beta) == 10' for pdb3mht ... ok testFunctionSelection12 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection12) Test function selections "floor(beta) == 10" ... ok testFunctionSelection13 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection13) Test function selections 'sq(x-5)+sq(y+4)+sq(z) > sq(100)' for pdb3mht ... ok testFunctionSelection14 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection14) Test function selections "sq(x-5)+sq(y+4)+sq(z) > sq(100)" ... ok testFunctionSelection15 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection15) Test function selections '1 > sq(occ)' for pdb3mht ... ok testFunctionSelection16 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection16) Test function selections "1 > sq(occ)" ... ok testFunctionSelection17 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection17) Test function selections 'sq(x x) > 1' for pdb3mht ... ok testFunctionSelection18 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection18) Test function selections "sq(x x) > 1" ... ok testFunctionSelection2 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection2) Test function selections "sqrt(x**2 + y**2 + z**2) < 100" ... ok testFunctionSelection3 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection3) Test function selections 'sqrt(x**2 + y**2 + z**2) == (x**2 + y**2 + z**2) ** 0.5' for pdb3mht ... ok testFunctionSelection4 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection4) Test function selections "sqrt(x**2 + y**2 + z**2) == (x**2 + y**2 + z**2) ** 0.5" ... ok testFunctionSelection5 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection5) Test function selections 'beta % 3 < 1' for pdb3mht ... ok testFunctionSelection6 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection6) Test function selections "beta % 3 < 1" ... ok testFunctionSelection7 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection7) Test function selections 'beta % 4 % 3 < 1' for pdb3mht ... ok testFunctionSelection8 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection8) Test function selections "beta % 4 % 3 < 1" ... ok testFunctionSelection9 (prody.tests.atomic.test_select.TestSelect.testFunctionSelection9) Test function selections 'ceil(beta) == 10' for pdb3mht ... ok testIntegerSelection1 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection1) Test integer selections 'index 10 20 10000' for pdb3mht ... ok testIntegerSelection10 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection10) Test integer selections "resnum 100 105" ... ok testIntegerSelection11 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection11) Test integer selections 'resid 0' for pdb3mht ... ok testIntegerSelection12 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection12) Test integer selections "resid 0" ... ok testIntegerSelection13 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection13) Test integer selections 'resid 100 105' for pdb3mht ... ok testIntegerSelection14 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection14) Test integer selections "resid 100 105" ... ok testIntegerSelection15 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection15) Test integer selections 'resid 100 A 105' for pdb3mht ... ok testIntegerSelection16 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection16) Test integer selections "resid 100 A 105" ... ok testIntegerSelection17 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection17) Test integer selections 'fragindex 0' for pdb3mht ... ok testIntegerSelection18 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection18) Test integer selections "fragindex 0" ... ok testIntegerSelection19 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection19) Test integer selections 'fragment 0' for pdb3mht ... ok testIntegerSelection2 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection2) Test integer selections "index 10 20 10000" ... ok testIntegerSelection20 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection20) Test integer selections "fragment 0" ... ok testIntegerSelection3 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection3) Test integer selections 'serial 0' for pdb3mht ... ok testIntegerSelection4 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection4) Test integer selections "serial 0" ... ok testIntegerSelection5 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection5) Test integer selections 'serial 1 2' for pdb3mht ... ok testIntegerSelection6 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection6) Test integer selections "serial 1 2" ... ok testIntegerSelection7 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection7) Test integer selections 'resnum 0' for pdb3mht ... ok testIntegerSelection8 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection8) Test integer selections "resnum 0" ... ok testIntegerSelection9 (prody.tests.atomic.test_select.TestSelect.testIntegerSelection9) Test integer selections 'resnum 100 105' for pdb3mht ... ok testInvalidSelection1 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection1) Test invalid selections 'chain C and and chain C' for pdb3mht ... ok testInvalidSelection10 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection10) Test invalid selections "sqr(x-5)+sqr(y+4)+sqr(z) > sqr(100)" ... ok testInvalidSelection11 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection11) Test invalid selections 'x > sq(calpha)' for pdb3mht ... ok testInvalidSelection12 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection12) Test invalid selections "x > sq(calpha)" ... ok testInvalidSelection13 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection13) Test invalid selections 'x > sq(name CA and resname ALA)' for pdb3mht ... ok testInvalidSelection14 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection14) Test invalid selections "x > sq(name CA and resname ALA)" ... ok testInvalidSelection15 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection15) Test invalid selections 'resname ALA and +1' for pdb3mht ... ok testInvalidSelection16 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection16) Test invalid selections "resname ALA and +1" ... ok testInvalidSelection2 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection2) Test invalid selections "chain C and and chain C" ... ok testInvalidSelection3 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection3) Test invalid selections 'chain C or or chain D' for pdb3mht ... ok testInvalidSelection4 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection4) Test invalid selections "chain C or or chain D" ... ok testInvalidSelection5 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection5) Test invalid selections 'chain C or not or chain D' for pdb3mht ... ok testInvalidSelection6 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection6) Test invalid selections "chain C or not or chain D" ... ok testInvalidSelection7 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection7) Test invalid selections 'chain C + 3' for pdb3mht ... ok testInvalidSelection8 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection8) Test invalid selections "chain C + 3" ... ok testInvalidSelection9 (prody.tests.atomic.test_select.TestSelect.testInvalidSelection9) Test invalid selections 'sqr(x-5)+sqr(y+4)+sqr(z) > sqr(100)' for pdb3mht ... ok testKwargsSelection1 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection1) Test kwargs selections 'within 100 of origin' for pdb3mht ... ok testKwargsSelection10 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection10) Test kwargs selections "within 100 of none" ... ok testKwargsSelection2 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection2) Test kwargs selections "within 100 of origin" ... ok testKwargsSelection3 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection3) Test kwargs selections 'within 100 of origin' for pdb3mht ... ok testKwargsSelection4 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection4) Test kwargs selections "within 100 of origin" ... ok testKwargsSelection5 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection5) Test kwargs selections 'within 100 of origin' for pdb3mht ... ok testKwargsSelection6 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection6) Test kwargs selections "within 100 of origin" ... ok testKwargsSelection7 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection7) Test kwargs selections 'within 100 of origin' for pdb3mht ... ok testKwargsSelection8 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection8) Test kwargs selections "within 100 of origin" ... ok testKwargsSelection9 (prody.tests.atomic.test_select.TestSelect.testKwargsSelection9) Test kwargs selections 'within 100 of none' for pdb3mht ... ok testLogicalSelection1 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection1) Test logical selections 'name or name' for pdb3mht ... ok testLogicalSelection10 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection10) Test logical selections "index 0 or index 1 " ... ok testLogicalSelection11 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection11) Test logical selections 'not not not not index 1' for pdb3mht ... ok testLogicalSelection12 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection12) Test logical selections "not not not not index 1" ... ok testLogicalSelection13 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection13) Test logical selections 'index 0 or index 1 or index 2' for pdb3mht ... ok testLogicalSelection14 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection14) Test logical selections "index 0 or index 1 or index 2" ... ok testLogicalSelection15 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection15) Test logical selections 'index 0 or index 1 or index 2 or index 4' for pdb3mht ... ok testLogicalSelection16 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection16) Test logical selections "index 0 or index 1 or index 2 or index 4" ... ok testLogicalSelection17 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection17) Test logical selections 'index 0 and index 1 ' for pdb3mht ... ok testLogicalSelection18 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection18) Test logical selections "index 0 and index 1 " ... ok testLogicalSelection19 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection19) Test logical selections 'index < 50 and index < 5' for pdb3mht ... ok testLogicalSelection2 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection2) Test logical selections "name or name" ... ok testLogicalSelection20 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection20) Test logical selections "index < 50 and index < 5" ... ok testLogicalSelection21 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection21) Test logical selections 'index < 50 and index < 25 and index < 5' for pdb3mht ... ok testLogicalSelection22 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection22) Test logical selections "index < 50 and index < 25 and index < 5" ... ok testLogicalSelection23 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection23) Test logical selections 'index < 5 and index < 25 and index < 50' for pdb3mht ... ok testLogicalSelection24 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection24) Test logical selections "index < 5 and index < 25 and index < 50" ... ok testLogicalSelection25 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection25) Test logical selections 'index 0 to 5 and index 0 to 25 and index 0 to 50' for pdb3mht ... ok testLogicalSelection26 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection26) Test logical selections "index 0 to 5 and index 0 to 25 and index 0 to 50" ... ok testLogicalSelection27 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection27) Test logical selections 'index < 5 and index < 25 and index < 50 or index < 50 or index < 5' for pdb3mht ... ok testLogicalSelection28 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection28) Test logical selections "index < 5 and index < 25 and index < 50 or index < 50 or index < 5" ... ok testLogicalSelection3 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection3) Test logical selections 'name and name' for pdb3mht ... ok testLogicalSelection4 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection4) Test logical selections "name and name" ... ok testLogicalSelection5 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection5) Test logical selections 'name CA and name CA' for pdb3mht ... ok testLogicalSelection6 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection6) Test logical selections "name CA and name CA" ... ok testLogicalSelection7 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection7) Test logical selections 'name CA or name CA' for pdb3mht ... ok testLogicalSelection8 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection8) Test logical selections "name CA or name CA" ... ok testLogicalSelection9 (prody.tests.atomic.test_select.TestSelect.testLogicalSelection9) Test logical selections 'index 0 or index 1 ' for pdb3mht ... ok testOperationSelection1 (prody.tests.atomic.test_select.TestSelect.testOperationSelection1) Test operation selections 'x ** 2 < 10' for pdb3mht ... ok testOperationSelection10 (prody.tests.atomic.test_select.TestSelect.testOperationSelection10) Test operation selections "x**2 + y**2 + z**2 < 10000" ... ok testOperationSelection2 (prody.tests.atomic.test_select.TestSelect.testOperationSelection2) Test operation selections "x ** 2 < 10" ... ok testOperationSelection3 (prody.tests.atomic.test_select.TestSelect.testOperationSelection3) Test operation selections 'x ** 2 ** 2 ** 2 < 10' for pdb3mht ... ok testOperationSelection4 (prody.tests.atomic.test_select.TestSelect.testOperationSelection4) Test operation selections "x ** 2 ** 2 ** 2 < 10" ... ok testOperationSelection5 (prody.tests.atomic.test_select.TestSelect.testOperationSelection5) Test operation selections 'x ** (+2 ** (+2 ** +2)) < 10' for pdb3mht ... ok testOperationSelection6 (prody.tests.atomic.test_select.TestSelect.testOperationSelection6) Test operation selections "x ** (+2 ** (+2 ** +2)) < 10" ... ok testOperationSelection7 (prody.tests.atomic.test_select.TestSelect.testOperationSelection7) Test operation selections 'occupancy % 2 == 1' for pdb3mht ... ok testOperationSelection8 (prody.tests.atomic.test_select.TestSelect.testOperationSelection8) Test operation selections "occupancy % 2 == 1" ... ok testOperationSelection9 (prody.tests.atomic.test_select.TestSelect.testOperationSelection9) Test operation selections 'x**2 + y**2 + z**2 < 10000' for pdb3mht ... ok testRangeSelection1 (prody.tests.atomic.test_select.TestSelect.testRangeSelection1) Test range selections 'index 0:10' for pdb3mht ... ok testRangeSelection10 (prody.tests.atomic.test_select.TestSelect.testRangeSelection10) Test range selections "resnum 10to15" ... ok testRangeSelection11 (prody.tests.atomic.test_select.TestSelect.testRangeSelection11) Test range selections 'resnum 10:16:1' for pdb3mht ... ok testRangeSelection12 (prody.tests.atomic.test_select.TestSelect.testRangeSelection12) Test range selections "resnum 10:16:1" ... ok testRangeSelection13 (prody.tests.atomic.test_select.TestSelect.testRangeSelection13) Test range selections 'resnum `-3:16:1`' for pdb3mht ... ok testRangeSelection14 (prody.tests.atomic.test_select.TestSelect.testRangeSelection14) Test range selections "resnum `-3:16:1`" ... ok testRangeSelection15 (prody.tests.atomic.test_select.TestSelect.testRangeSelection15) Test range selections 'resid 10to15' for pdb3mht ... ok testRangeSelection16 (prody.tests.atomic.test_select.TestSelect.testRangeSelection16) Test range selections "resid 10to15" ... ok testRangeSelection17 (prody.tests.atomic.test_select.TestSelect.testRangeSelection17) Test range selections 'resid 10:16:1' for pdb3mht ... ok testRangeSelection18 (prody.tests.atomic.test_select.TestSelect.testRangeSelection18) Test range selections "resid 10:16:1" ... ok testRangeSelection19 (prody.tests.atomic.test_select.TestSelect.testRangeSelection19) Test range selections 'x `-10:20`' for pdb3mht ... ok testRangeSelection2 (prody.tests.atomic.test_select.TestSelect.testRangeSelection2) Test range selections "index 0:10" ... ok testRangeSelection20 (prody.tests.atomic.test_select.TestSelect.testRangeSelection20) Test range selections "x `-10:20`" ... ok testRangeSelection21 (prody.tests.atomic.test_select.TestSelect.testRangeSelection21) Test range selections 'x 0:20:1' for pdb3mht ... ok testRangeSelection22 (prody.tests.atomic.test_select.TestSelect.testRangeSelection22) Test range selections "x 0:20:1" ... ok testRangeSelection23 (prody.tests.atomic.test_select.TestSelect.testRangeSelection23) Test range selections 'beta 13.02:13.01' for pdb3mht ... ok testRangeSelection24 (prody.tests.atomic.test_select.TestSelect.testRangeSelection24) Test range selections "beta 13.02:13.01" ... ok testRangeSelection3 (prody.tests.atomic.test_select.TestSelect.testRangeSelection3) Test range selections 'index 0to10' for pdb3mht ... ok testRangeSelection4 (prody.tests.atomic.test_select.TestSelect.testRangeSelection4) Test range selections "index 0to10" ... ok testRangeSelection5 (prody.tests.atomic.test_select.TestSelect.testRangeSelection5) Test range selections 'serial 0:10:2' for pdb3mht ... ok testRangeSelection6 (prody.tests.atomic.test_select.TestSelect.testRangeSelection6) Test range selections "serial 0:10:2" ... ok testRangeSelection7 (prody.tests.atomic.test_select.TestSelect.testRangeSelection7) Test range selections 'serial 0:10:10' for pdb3mht ... ok testRangeSelection8 (prody.tests.atomic.test_select.TestSelect.testRangeSelection8) Test range selections "serial 0:10:10" ... ok testRangeSelection9 (prody.tests.atomic.test_select.TestSelect.testRangeSelection9) Test range selections 'resnum 10to15' for pdb3mht ... ok testRegexpSelection1 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection1) Test regexp selections 'resname "S.."' for pdb3mht ... ok testRegexpSelection10 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection10) Test regexp selections "name "C((A|B)"" ... ok testRegexpSelection2 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection2) Test regexp selections "resname "S.."" ... ok testRegexpSelection3 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection3) Test regexp selections 'name "C.*"' for pdb3mht ... ok testRegexpSelection4 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection4) Test regexp selections "name "C.*"" ... ok testRegexpSelection5 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection5) Test regexp selections 'name ".*\'"' for pdb3mht ... ok testRegexpSelection6 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection6) Test regexp selections "name ".*'"" ... ok testRegexpSelection7 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection7) Test regexp selections 'name "C(A|B)"' for pdb3mht ... ok testRegexpSelection8 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection8) Test regexp selections "name "C(A|B)"" ... ok testRegexpSelection9 (prody.tests.atomic.test_select.TestSelect.testRegexpSelection9) Test regexp selections 'name "C((A|B)"' for pdb3mht ... ok testSameasSelection1 (prody.tests.atomic.test_select.TestSelect.testSameasSelection1) Test sameas selections 'same residue as index 0' for pdb3mht ... ok testSameasSelection10 (prody.tests.atomic.test_select.TestSelect.testSameasSelection10) Test sameas selections "same chain as chain C" ... ok testSameasSelection11 (prody.tests.atomic.test_select.TestSelect.testSameasSelection11) Test sameas selections 'same residue as chain X' for pdb3mht ... ok testSameasSelection12 (prody.tests.atomic.test_select.TestSelect.testSameasSelection12) Test sameas selections "same residue as chain X" ... ok testSameasSelection13 (prody.tests.atomic.test_select.TestSelect.testSameasSelection13) Test sameas selections 'same none as chain C' for pdb3mht ... ok testSameasSelection14 (prody.tests.atomic.test_select.TestSelect.testSameasSelection14) Test sameas selections "same none as chain C" ... ok testSameasSelection15 (prody.tests.atomic.test_select.TestSelect.testSameasSelection15) Test sameas selections 'same residue as same residue as same residue as index 0' for pdb3mht ... ok testSameasSelection16 (prody.tests.atomic.test_select.TestSelect.testSameasSelection16) Test sameas selections "same residue as same residue as same residue as index 0" ... ok testSameasSelection2 (prody.tests.atomic.test_select.TestSelect.testSameasSelection2) Test sameas selections "same residue as index 0" ... ok testSameasSelection3 (prody.tests.atomic.test_select.TestSelect.testSameasSelection3) Test sameas selections 'same chain as index 0' for pdb3mht ... ok testSameasSelection4 (prody.tests.atomic.test_select.TestSelect.testSameasSelection4) Test sameas selections "same chain as index 0" ... ok testSameasSelection5 (prody.tests.atomic.test_select.TestSelect.testSameasSelection5) Test sameas selections 'same segment as index 0' for pdb3mht ... ok testSameasSelection6 (prody.tests.atomic.test_select.TestSelect.testSameasSelection6) Test sameas selections "same segment as index 0" ... ok testSameasSelection7 (prody.tests.atomic.test_select.TestSelect.testSameasSelection7) Test sameas selections 'same residue as resname DG ALA' for pdb3mht ... ok testSameasSelection8 (prody.tests.atomic.test_select.TestSelect.testSameasSelection8) Test sameas selections "same residue as resname DG ALA" ... ok testSameasSelection9 (prody.tests.atomic.test_select.TestSelect.testSameasSelection9) Test sameas selections 'same chain as chain C' for pdb3mht ... ok testSequenceSelection1 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection1) Test sequence selections 'sequence al' for pdb3mht ... ok testSequenceSelection10 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection10) Test sequence selections "sequence FKPY" ... ok testSequenceSelection11 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection11) Test sequence selections 'sequence "SS."' for pdb3mht ... ok testSequenceSelection12 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection12) Test sequence selections "sequence "SS."" ... ok testSequenceSelection13 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection13) Test sequence selections 'sequence "S[A-Z]{2}G"' for pdb3mht ... ok testSequenceSelection14 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection14) Test sequence selections "sequence "S[A-Z]{2}G"" ... ok testSequenceSelection15 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection15) Test sequence selections 'sequence "S.S.S"' for pdb3mht ... ok testSequenceSelection16 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection16) Test sequence selections "sequence "S.S.S"" ... ok testSequenceSelection17 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection17) Test sequence selections 'sequence "."' for pdb3mht ... ok testSequenceSelection18 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection18) Test sequence selections "sequence "."" ... ok testSequenceSelection2 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection2) Test sequence selections "sequence al" ... ok testSequenceSelection3 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection3) Test sequence selections 'sequence A' for pdb3mht ... ok testSequenceSelection4 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection4) Test sequence selections "sequence A" ... ok testSequenceSelection5 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection5) Test sequence selections 'sequence MIEIK' for pdb3mht ... ok testSequenceSelection6 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection6) Test sequence selections "sequence MIEIK" ... ok testSequenceSelection7 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection7) Test sequence selections 'sequence VLNAL' for pdb3mht ... ok testSequenceSelection8 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection8) Test sequence selections "sequence VLNAL" ... ok testSequenceSelection9 (prody.tests.atomic.test_select.TestSelect.testSequenceSelection9) Test sequence selections 'sequence FKPY' for pdb3mht ... ok testSpecialcharSelection1 (prody.tests.atomic.test_select.TestSelect.testSpecialcharSelection1) Test specialchar selections 'altloc ` `' for pdb3mht ... ok testSpecialcharSelection2 (prody.tests.atomic.test_select.TestSelect.testSpecialcharSelection2) Test specialchar selections "altloc ` `" ... ok testSpecialcharSelection3 (prody.tests.atomic.test_select.TestSelect.testSpecialcharSelection3) Test specialchar selections 'name A` `CA`' for pdb3mht ... ok testSpecialcharSelection4 (prody.tests.atomic.test_select.TestSelect.testSpecialcharSelection4) Test specialchar selections "name A` `CA`" ... ok testSpecialcharSelection5 (prody.tests.atomic.test_select.TestSelect.testSpecialcharSelection5) Test specialchar selections 'name `A``' for pdb3mht ... ok testSpecialcharSelection6 (prody.tests.atomic.test_select.TestSelect.testSpecialcharSelection6) Test specialchar selections "name `A``" ... ok testSpecialcharSelection7 (prody.tests.atomic.test_select.TestSelect.testSpecialcharSelection7) Test specialchar selections 'z `+100.291`' for pdb3mht ... ok testSpecialcharSelection8 (prody.tests.atomic.test_select.TestSelect.testSpecialcharSelection8) Test specialchar selections "z `+100.291`" ... ok testStringSelection1 (prody.tests.atomic.test_select.TestSelect.testStringSelection1) Test string selections 'name P' for pdb3mht ... ok testStringSelection10 (prody.tests.atomic.test_select.TestSelect.testStringSelection10) Test string selections "chain x" ... ok testStringSelection11 (prody.tests.atomic.test_select.TestSelect.testStringSelection11) Test string selections 'chain x y' for pdb3mht ... ok testStringSelection12 (prody.tests.atomic.test_select.TestSelect.testStringSelection12) Test string selections "chain x y" ... ok testStringSelection13 (prody.tests.atomic.test_select.TestSelect.testStringSelection13) Test string selections 'chain x y z' for pdb3mht ... ok testStringSelection14 (prody.tests.atomic.test_select.TestSelect.testStringSelection14) Test string selections "chain x y z" ... ok testStringSelection15 (prody.tests.atomic.test_select.TestSelect.testStringSelection15) Test string selections 'chain x y z C' for pdb3mht ... ok testStringSelection16 (prody.tests.atomic.test_select.TestSelect.testStringSelection16) Test string selections "chain x y z C" ... ok testStringSelection17 (prody.tests.atomic.test_select.TestSelect.testStringSelection17) Test string selections 'chain C D' for pdb3mht ... ok testStringSelection18 (prody.tests.atomic.test_select.TestSelect.testStringSelection18) Test string selections "chain C D" ... ok testStringSelection19 (prody.tests.atomic.test_select.TestSelect.testStringSelection19) Test string selections 'chain CD' for pdb3mht ... ok testStringSelection2 (prody.tests.atomic.test_select.TestSelect.testStringSelection2) Test string selections "name P" ... ok testStringSelection20 (prody.tests.atomic.test_select.TestSelect.testStringSelection20) Test string selections "chain CD" ... ok testStringSelection21 (prody.tests.atomic.test_select.TestSelect.testStringSelection21) Test string selections 'resname DG' for pdb3mht ... ok testStringSelection22 (prody.tests.atomic.test_select.TestSelect.testStringSelection22) Test string selections "resname DG" ... ok testStringSelection23 (prody.tests.atomic.test_select.TestSelect.testStringSelection23) Test string selections 'resname DG ALA' for pdb3mht ... ok testStringSelection24 (prody.tests.atomic.test_select.TestSelect.testStringSelection24) Test string selections "resname DG ALA" ... ok testStringSelection25 (prody.tests.atomic.test_select.TestSelect.testStringSelection25) Test string selections 'altloc A' for pdb3mht ... ok testStringSelection26 (prody.tests.atomic.test_select.TestSelect.testStringSelection26) Test string selections "altloc A" ... ok testStringSelection27 (prody.tests.atomic.test_select.TestSelect.testStringSelection27) Test string selections 'altloc _' for pdb3mht ... ok testStringSelection28 (prody.tests.atomic.test_select.TestSelect.testStringSelection28) Test string selections "altloc _" ... ok testStringSelection29 (prody.tests.atomic.test_select.TestSelect.testStringSelection29) Test string selections 'secondary H' for pdb3mht ... ok testStringSelection3 (prody.tests.atomic.test_select.TestSelect.testStringSelection3) Test string selections 'name P CA' for pdb3mht ... ok testStringSelection30 (prody.tests.atomic.test_select.TestSelect.testStringSelection30) Test string selections "secondary H" ... ok testStringSelection31 (prody.tests.atomic.test_select.TestSelect.testStringSelection31) Test string selections 'secondary H E' for pdb3mht ... ok testStringSelection32 (prody.tests.atomic.test_select.TestSelect.testStringSelection32) Test string selections "secondary H E" ... ok testStringSelection33 (prody.tests.atomic.test_select.TestSelect.testStringSelection33) Test string selections 'secondary _' for pdb3mht ... ok testStringSelection34 (prody.tests.atomic.test_select.TestSelect.testStringSelection34) Test string selections "secondary _" ... ok testStringSelection35 (prody.tests.atomic.test_select.TestSelect.testStringSelection35) Test string selections 'segment _' for pdb3mht ... ok testStringSelection36 (prody.tests.atomic.test_select.TestSelect.testStringSelection36) Test string selections "segment _" ... ok testStringSelection4 (prody.tests.atomic.test_select.TestSelect.testStringSelection4) Test string selections "name P CA" ... ok testStringSelection5 (prody.tests.atomic.test_select.TestSelect.testStringSelection5) Test string selections 'name `A 1`' for pdb3mht ... ok testStringSelection6 (prody.tests.atomic.test_select.TestSelect.testStringSelection6) Test string selections "name `A 1`" ... ok testStringSelection7 (prody.tests.atomic.test_select.TestSelect.testStringSelection7) Test string selections 'chain C' for pdb3mht ... ok testStringSelection8 (prody.tests.atomic.test_select.TestSelect.testStringSelection8) Test string selections "chain C" ... ok testStringSelection9 (prody.tests.atomic.test_select.TestSelect.testStringSelection9) Test string selections 'chain x' for pdb3mht ... ok testSynonymsSelection1 (prody.tests.atomic.test_select.TestSelect.testSynonymsSelection1) Test synonyms selections 'chain C' for pdb3mht ... ok testSynonymsSelection2 (prody.tests.atomic.test_select.TestSelect.testSynonymsSelection2) Test synonyms selections "chain C" ... ok testSynonymsSelection3 (prody.tests.atomic.test_select.TestSelect.testSynonymsSelection3) Test synonyms selections 'chain C D' for pdb3mht ... ok testSynonymsSelection4 (prody.tests.atomic.test_select.TestSelect.testSynonymsSelection4) Test synonyms selections "chain C D" ... ok testUnintendedSelection1 (prody.tests.atomic.test_select.TestSelect.testUnintendedSelection1) Test unintended selections 'abs beta = beta' for pdb3mht ... ok testUnintendedSelection2 (prody.tests.atomic.test_select.TestSelect.testUnintendedSelection2) Test unintended selections "abs beta = beta" ... ok testUserdataSelection1 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection1) Test userdata selections 'temp < 10' for pdb3mht ... ok testUserdataSelection10 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection10) Test userdata selections "occ" ... ok testUserdataSelection11 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection11) Test userdata selections 'occ and occupancy == 1' for pdb3mht ... ok testUserdataSelection12 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection12) Test userdata selections "occ and occupancy == 1" ... ok testUserdataSelection13 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection13) Test userdata selections 'occ and occupancy == 1 and oc10 - 9 == 1' for pdb3mht ... ok testUserdataSelection14 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection14) Test userdata selections "occ and occupancy == 1 and oc10 - 9 == 1" ... ok testUserdataSelection15 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection15) Test userdata selections 'occ and occupancy == 1 and temp < 10' for pdb3mht ... ok testUserdataSelection16 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection16) Test userdata selections "occ and occupancy == 1 and temp < 10" ... ok testUserdataSelection17 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection17) Test userdata selections 'occ > 0' for pdb3mht ... ok testUserdataSelection18 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection18) Test userdata selections "occ > 0" ... ok testUserdataSelection2 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection2) Test userdata selections "temp < 10" ... ok testUserdataSelection3 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection3) Test userdata selections 'temp < 10 and chain D' for pdb3mht ... ok testUserdataSelection4 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection4) Test userdata selections "temp < 10 and chain D" ... ok testUserdataSelection5 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection5) Test userdata selections 'oc10 - 9 == 1' for pdb3mht ... ok testUserdataSelection6 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection6) Test userdata selections "oc10 - 9 == 1" ... ok testUserdataSelection7 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection7) Test userdata selections 'temp < 10' for pdb3mht ... ok testUserdataSelection8 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection8) Test userdata selections "temp < 10" ... ok testUserdataSelection9 (prody.tests.atomic.test_select.TestSelect.testUserdataSelection9) Test userdata selections 'occ' for pdb3mht ... ok testWithinSelection1 (prody.tests.atomic.test_select.TestSelect.testWithinSelection1) Test within selections 'within 10 of index 0' for pdb3mht ... ok testWithinSelection10 (prody.tests.atomic.test_select.TestSelect.testWithinSelection10) Test within selections "within 5 of within 5 of within 5 of index 0" ... ok testWithinSelection11 (prody.tests.atomic.test_select.TestSelect.testWithinSelection11) Test within selections 'exwithin 5 of exwithin 5 of exwithin 5 of index 0' for pdb3mht ... ok testWithinSelection12 (prody.tests.atomic.test_select.TestSelect.testWithinSelection12) Test within selections "exwithin 5 of exwithin 5 of exwithin 5 of index 0" ... ok testWithinSelection13 (prody.tests.atomic.test_select.TestSelect.testWithinSelection13) Test within selections 'within 1 of pdb' for pdb3mht ... ok testWithinSelection14 (prody.tests.atomic.test_select.TestSelect.testWithinSelection14) Test within selections "within 1 of pdb" ... ok testWithinSelection15 (prody.tests.atomic.test_select.TestSelect.testWithinSelection15) Test within selections 'exwithin 1 of pdb' for pdb3mht ... ok testWithinSelection16 (prody.tests.atomic.test_select.TestSelect.testWithinSelection16) Test within selections "exwithin 1 of pdb" ... ok testWithinSelection17 (prody.tests.atomic.test_select.TestSelect.testWithinSelection17) Test within selections 'exwithin 1 of ag' for pdb3mht ... ok testWithinSelection18 (prody.tests.atomic.test_select.TestSelect.testWithinSelection18) Test within selections "exwithin 1 of ag" ... ok testWithinSelection19 (prody.tests.atomic.test_select.TestSelect.testWithinSelection19) Test within selections 'within 100 of index 10000' for pdb3mht ... ok testWithinSelection2 (prody.tests.atomic.test_select.TestSelect.testWithinSelection2) Test within selections "within 10 of index 0" ... ok testWithinSelection20 (prody.tests.atomic.test_select.TestSelect.testWithinSelection20) Test within selections "within 100 of index 10000" ... ok testWithinSelection3 (prody.tests.atomic.test_select.TestSelect.testWithinSelection3) Test within selections 'exwithin 100 of index 0' for pdb3mht ... ok testWithinSelection4 (prody.tests.atomic.test_select.TestSelect.testWithinSelection4) Test within selections "exwithin 100 of index 0" ... ok testWithinSelection5 (prody.tests.atomic.test_select.TestSelect.testWithinSelection5) Test within selections 'exwithin 4 of resname SAH' for pdb3mht ... ok testWithinSelection6 (prody.tests.atomic.test_select.TestSelect.testWithinSelection6) Test within selections "exwithin 4 of resname SAH" ... ok testWithinSelection7 (prody.tests.atomic.test_select.TestSelect.testWithinSelection7) Test within selections '(within 4 of water) and not water' for pdb3mht ... ok testWithinSelection8 (prody.tests.atomic.test_select.TestSelect.testWithinSelection8) Test within selections "(within 4 of water) and not water" ... ok testWithinSelection9 (prody.tests.atomic.test_select.TestSelect.testWithinSelection9) Test within selections 'within 5 of within 5 of within 5 of index 0' for pdb3mht ... ok testWithout_AndSelection1 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection1) Test without_and selections 'coil protein' for pdb3mht ... ok testWithout_AndSelection10 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection10) Test without_and selections "(protein nucleic)" ... ok testWithout_AndSelection11 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection11) Test without_and selections 'noh hetero water' for pdb3mht ... ok testWithout_AndSelection12 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection12) Test without_and selections "noh hetero water" ... ok testWithout_AndSelection13 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection13) Test without_and selections 'ca occupancy > 0' for pdb3mht ... ok testWithout_AndSelection14 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection14) Test without_and selections "ca occupancy > 0" ... ok testWithout_AndSelection15 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection15) Test without_and selections 'ca occupancy - 0 > 0' for pdb3mht ... ok testWithout_AndSelection16 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection16) Test without_and selections "ca occupancy - 0 > 0" ... ok testWithout_AndSelection17 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection17) Test without_and selections 'ca occupancy - 0 > 0 + 0' for pdb3mht ... ok testWithout_AndSelection18 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection18) Test without_and selections "ca occupancy - 0 > 0 + 0" ... ok testWithout_AndSelection19 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection19) Test without_and selections 'occupancy > ca 0' for pdb3mht ... ok testWithout_AndSelection2 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection2) Test without_and selections "coil protein" ... ok testWithout_AndSelection20 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection20) Test without_and selections "occupancy > ca 0" ... ok testWithout_AndSelection21 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection21) Test without_and selections 'noh hetero (water)' for pdb3mht ... ok testWithout_AndSelection22 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection22) Test without_and selections "noh hetero (water)" ... ok testWithout_AndSelection23 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection23) Test without_and selections 'noh hetero not (water)' for pdb3mht ... ok testWithout_AndSelection24 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection24) Test without_and selections "noh hetero not (water)" ... ok testWithout_AndSelection25 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection25) Test without_and selections '(water) hetero' for pdb3mht ... ok testWithout_AndSelection26 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection26) Test without_and selections "(water) hetero" ... ok testWithout_AndSelection27 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection27) Test without_and selections 'ca abs(beta) = beta + abs(0)' for pdb3mht ... ok testWithout_AndSelection28 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection28) Test without_and selections "ca abs(beta) = beta + abs(0)" ... ok testWithout_AndSelection3 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection3) Test without_and selections 'sidechain sc protein' for pdb3mht ... ok testWithout_AndSelection4 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection4) Test without_and selections "sidechain sc protein" ... ok testWithout_AndSelection5 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection5) Test without_and selections 'bbfull bb' for pdb3mht ... ok testWithout_AndSelection6 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection6) Test without_and selections "bbfull bb" ... ok testWithout_AndSelection7 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection7) Test without_and selections '(charged basic)' for pdb3mht ... ok testWithout_AndSelection8 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection8) Test without_and selections "(charged basic)" ... ok testWithout_AndSelection9 (prody.tests.atomic.test_select.TestSelect.testWithout_AndSelection9) Test without_and selections '(protein nucleic)' for pdb3mht ... ok testSetData (prody.tests.atomic.test_subset.TestUserData.testSetData) ... ok testDatafile_1ejg (prody.tests.datafiles.TestDatafiles.testDatafile_1ejg) Test presence of "pdb1ejg.pdb" ... ok testDatafile_1ubi (prody.tests.datafiles.TestDatafiles.testDatafile_1ubi) Test presence of "pdb1ubi.pdb" ... ok testDatafile_1ubi_ca (prody.tests.datafiles.TestDatafiles.testDatafile_1ubi_ca) Test presence of "pdb1ubi_ca.pdb" ... ok testDatafile_2gb1_truncated (prody.tests.datafiles.TestDatafiles.testDatafile_2gb1_truncated) Test presence of "pdb2gb1_truncated.pdb" ... ok testDatafile_2k39_ca (prody.tests.datafiles.TestDatafiles.testDatafile_2k39_ca) Test presence of "pdb2k39_ca.pdb" ... ok testDatafile_2nwl (prody.tests.datafiles.TestDatafiles.testDatafile_2nwl) Test presence of "pdb2nwl-opm.pdb" ... ok testDatafile_3hsy (prody.tests.datafiles.TestDatafiles.testDatafile_3hsy) Test presence of "pdb3hsy.pdb" ... ok testDatafile_3mht (prody.tests.datafiles.TestDatafiles.testDatafile_3mht) Test presence of "pdb3mht.pdb" ... ok testDatafile_3o21 (prody.tests.datafiles.TestDatafiles.testDatafile_3o21) Test presence of "pdb3o21.pdb" ... ok testDatafile_3p3w (prody.tests.datafiles.TestDatafiles.testDatafile_3p3w) Test presence of "pdb3p3w.pdb" ... ok testDatafile_DI (prody.tests.datafiles.TestDatafiles.testDatafile_DI) Test presence of "msa_Cys_knot_di.dat" ... ok testDatafile_Fasta (prody.tests.datafiles.TestDatafiles.testDatafile_Fasta) Test presence of "msa_Cys_knot.fasta" ... ok testDatafile_MSA (prody.tests.datafiles.TestDatafiles.testDatafile_MSA) Test presence of "msa_3hsyA_3o21A.fasta" ... ok testDatafile_MSA_MEW (prody.tests.datafiles.TestDatafiles.testDatafile_MSA_MEW) Test presence of "msa_3hsyA_3o21A_new.fasta" ... ok testDatafile_RTER (prody.tests.datafiles.TestDatafiles.testDatafile_RTER) Test presence of "pdbRTER.pdb" ... ok testDatafile_SCA (prody.tests.datafiles.TestDatafiles.testDatafile_SCA) Test presence of "msa_Cys_knot_sca.dat" ... ok testDatafile_Selex (prody.tests.datafiles.TestDatafiles.testDatafile_Selex) Test presence of "msa_Cys_knot.slx" ... ok testDatafile_Stockholm (prody.tests.datafiles.TestDatafiles.testDatafile_Stockholm) Test presence of "msa_Cys_knot.sth" ... ok testDatafile_anm1ubi_evalues (prody.tests.datafiles.TestDatafiles.testDatafile_anm1ubi_evalues) Test presence of "anm1ubi_evalues.dat" ... ok testDatafile_anm1ubi_hessian (prody.tests.datafiles.TestDatafiles.testDatafile_anm1ubi_hessian) Test presence of "anm1ubi_hessian.coo" ... ok testDatafile_anm1ubi_vectors (prody.tests.datafiles.TestDatafiles.testDatafile_anm1ubi_vectors) Test presence of "anm1ubi_vectors.dat" ... ok testDatafile_commute1ubi (prody.tests.datafiles.TestDatafiles.testDatafile_commute1ubi) Test presence of "commute1ubi.dat" ... ok testDatafile_dcd (prody.tests.datafiles.TestDatafiles.testDatafile_dcd) Test presence of "dcd2k39_truncated.dcd" ... ok testDatafile_dssp (prody.tests.datafiles.TestDatafiles.testDatafile_dssp) Test presence of "pdb1r19_dssp.pdb" ... ok testDatafile_five_digits (prody.tests.datafiles.TestDatafiles.testDatafile_five_digits) Test presence of "pdb1tw7_step3_charmm2namd.pdb" ... ok testDatafile_gnm1ubi_evalues (prody.tests.datafiles.TestDatafiles.testDatafile_gnm1ubi_evalues) Test presence of "gnm1ubi_evalues.dat" ... ok testDatafile_gnm1ubi_kirchhoff (prody.tests.datafiles.TestDatafiles.testDatafile_gnm1ubi_kirchhoff) Test presence of "gnm1ubi_kirchhoff.coo" ... ok testDatafile_gnm1ubi_vectors (prody.tests.datafiles.TestDatafiles.testDatafile_gnm1ubi_vectors) Test presence of "gnm1ubi_vectors.dat" ... ok testDatafile_gromacs (prody.tests.datafiles.TestDatafiles.testDatafile_gromacs) Test presence of "pdb6fpj_Bb_fixed_solv_ions.pdb" ... ok testDatafile_h36 (prody.tests.datafiles.TestDatafiles.testDatafile_h36) Test presence of "pdb1tw7_step3_charmm2namd_doubled_h36.pdb" ... ok testDatafile_h36_ter (prody.tests.datafiles.TestDatafiles.testDatafile_h36_ter) Test presence of "pdb4v8r_h36.pdb" ... ok testDatafile_hex (prody.tests.datafiles.TestDatafiles.testDatafile_hex) Test presence of "pdb1tw7_step3_charmm2namd_doubled_hex.pdb" ... ok testDatafile_hex_ter (prody.tests.datafiles.TestDatafiles.testDatafile_hex_ter) Test presence of "pdb4v8r_hex.pdb" ... ok testDatafile_hit1ubi (prody.tests.datafiles.TestDatafiles.testDatafile_hit1ubi) Test presence of "hit1ubi.dat" ... ok testDatafile_long_chid_cif (prody.tests.datafiles.TestDatafiles.testDatafile_long_chid_cif) Test presence of "mmcif_6zu5.cif" ... ok testDatafile_multi_model_cif (prody.tests.datafiles.TestDatafiles.testDatafile_multi_model_cif) Test presence of "mmcif_6yfy.cif" ... ok testDatafile_multi_model_truncated (prody.tests.datafiles.TestDatafiles.testDatafile_multi_model_truncated) Test presence of "pdb2k39_truncated.pdb" ... ok testDatafile_oneatom (prody.tests.datafiles.TestDatafiles.testDatafile_oneatom) Test presence of "pdb1ejg_oneatom.pdb" ... ok testDatafile_pca2k39_cov (prody.tests.datafiles.TestDatafiles.testDatafile_pca2k39_cov) Test presence of "pca2k39_cov.coo" ... ok testDatafile_pca2k39_evalues (prody.tests.datafiles.TestDatafiles.testDatafile_pca2k39_evalues) Test presence of "pca2k39_evalues.dat" ... ok testDatafile_pca2k39_vectors (prody.tests.datafiles.TestDatafiles.testDatafile_pca2k39_vectors) Test presence of "pca2k39_vectors.dat" ... ok testDatafile_rtb2gb1_hessian (prody.tests.datafiles.TestDatafiles.testDatafile_rtb2gb1_hessian) Test presence of "rtb2gb1_hessian.coo" ... ok testDatafile_rtb2gb1_project (prody.tests.datafiles.TestDatafiles.testDatafile_rtb2gb1_project) Test presence of "rtb2gb1_project.coo" ... ok testDatafile_sti (prody.tests.datafiles.TestDatafiles.testDatafile_sti) Test presence of "xmlSTI.xml" ... ok testMode1d (prody.tests.dynamics.test_editing.TestExtending.testMode1d) ... ok testMode3d (prody.tests.dynamics.test_editing.TestExtending.testMode3d) ... ok testModel1d (prody.tests.dynamics.test_editing.TestExtending.testModel1d) ... ok testModel3d (prody.tests.dynamics.test_editing.TestExtending.testModel3d) ... ok testVector1d (prody.tests.dynamics.test_editing.TestExtending.testVector1d) ... ok testVector3d (prody.tests.dynamics.test_editing.TestExtending.testVector3d) ... ok testModel3d (prody.tests.dynamics.test_editing.TestInterpolating.testModel3d) ... ok testMode1d (prody.tests.dynamics.test_editing.TestSlicing.testMode1d) ... ok testMode3d (prody.tests.dynamics.test_editing.TestSlicing.testMode3d) ... ok testModel1d (prody.tests.dynamics.test_editing.TestSlicing.testModel1d) ... ok testModel3d (prody.tests.dynamics.test_editing.TestSlicing.testModel3d) ... ok testVector1d (prody.tests.dynamics.test_editing.TestSlicing.testVector1d) ... ok testVector3d (prody.tests.dynamics.test_editing.TestSlicing.testVector3d) ... ok testBuildHessianSlow (prody.tests.dynamics.test_enms.TestANM.testBuildHessianSlow) ... ok testBuildMatrixCoordsArray (prody.tests.dynamics.test_enms.TestANM.testBuildMatrixCoordsArray) Test output when *coords* is an array. ... FAIL testBuildMatrixCoordsWrongType (prody.tests.dynamics.test_enms.TestANM.testBuildMatrixCoordsWrongType) Test response to wrong type *coords* argument. ... ok testBuildMatrixCutoffInvalidValue (prody.tests.dynamics.test_enms.TestANM.testBuildMatrixCutoffInvalidValue) Test response to wrong *cutoff* argument. ... ok testBuildMatrixCutoffWrongType (prody.tests.dynamics.test_enms.TestANM.testBuildMatrixCutoffWrongType) Test response to cutoff of wrong type. ... ok testBuildMatrixInvalidGamma (prody.tests.dynamics.test_enms.TestANM.testBuildMatrixInvalidGamma) Test response to invalid *gamma* argument. ... ok testBuildMatrixWrongCoords (prody.tests.dynamics.test_enms.TestANM.testBuildMatrixWrongCoords) Test response to wrong coords.dtype. ... ok testBuildMatrixWrongGamma (prody.tests.dynamics.test_enms.TestANM.testBuildMatrixWrongGamma) Test response to wrong *gamma* argument. ... ok testSetHessianWrongShape (prody.tests.dynamics.test_enms.TestANM.testSetHessianWrongShape) Test response to wrong shape *hessian* argument. ... ok testSetMatrixAcceptableDtype (prody.tests.dynamics.test_enms.TestANM.testSetMatrixAcceptableDtype) Test response to acceptable matrix.dtype. ... ok testSetMatrixNonSquare (prody.tests.dynamics.test_enms.TestANM.testSetMatrixNonSquare) Test response to non-square matrix. ... ok testSetMatrixWrongDim (prody.tests.dynamics.test_enms.TestANM.testSetMatrixWrongDim) Test response to wrong dim *kirchhoff* argument. ... ok testSetMatrixWrongDtype (prody.tests.dynamics.test_enms.TestANM.testSetMatrixWrongDtype) Test response to wrong matrix.dtype. ... ok testSetMatrixWrongType (prody.tests.dynamics.test_enms.TestANM.testSetMatrixWrongType) Test response to wrong matrix type argument. ... ok testEigenvalues (prody.tests.dynamics.test_enms.TestANMResults.testEigenvalues) Test eigenvalues. ... ok testEigenvectors (prody.tests.dynamics.test_enms.TestANMResults.testEigenvectors) Test eigenvectors. ... ok testGetCutoff (prody.tests.dynamics.test_enms.TestANMResults.testGetCutoff) Testing return type of :meth:`~.GNMBase.getCutoff`. ... ok testGetGamma (prody.tests.dynamics.test_enms.TestANMResults.testGetGamma) Testing return type of :meth:`~.GNMBase.getGamma`. ... ok testGetHessian (prody.tests.dynamics.test_enms.TestANMResults.testGetHessian) ... ok testHessian (prody.tests.dynamics.test_enms.TestANMResults.testHessian) Test Hessian matrix. ... ok testHessianSums (prody.tests.dynamics.test_enms.TestANMResults.testHessianSums) ... ok testHessianSymmetry (prody.tests.dynamics.test_enms.TestANMResults.testHessianSymmetry) ... ok testModeSlicing (prody.tests.dynamics.test_enms.TestANMResults.testModeSlicing) ... ok testVariances (prody.tests.dynamics.test_enms.TestANMResults.testVariances) Test variances. ... ok testEigenvalues (prody.tests.dynamics.test_enms.TestEXANMResults.testEigenvalues) Test eigenvalues. ... ok testEigenvectors (prody.tests.dynamics.test_enms.TestEXANMResults.testEigenvectors) Test eigenvectors. ... ok testGetCutoff (prody.tests.dynamics.test_enms.TestEXANMResults.testGetCutoff) Testing return type of :meth:`~.GNMBase.getCutoff`. ... ok testGetGamma (prody.tests.dynamics.test_enms.TestEXANMResults.testGetGamma) Testing return type of :meth:`~.GNMBase.getGamma`. ... ok testGetHessian (prody.tests.dynamics.test_enms.TestEXANMResults.testGetHessian) ... ok testHessian (prody.tests.dynamics.test_enms.TestEXANMResults.testHessian) Test Hessian matrix. ... ok testHessianSums (prody.tests.dynamics.test_enms.TestEXANMResults.testHessianSums) ... ok testHessianSymmetry (prody.tests.dynamics.test_enms.TestEXANMResults.testHessianSymmetry) ... ok testVariances (prody.tests.dynamics.test_enms.TestEXANMResults.testVariances) Test variances. ... ok testBuildMatrixCoordsArray (prody.tests.dynamics.test_enms.TestGNM.testBuildMatrixCoordsArray) Test output when *coords* is an array. ... ok testBuildMatrixCoordsWrongType (prody.tests.dynamics.test_enms.TestGNM.testBuildMatrixCoordsWrongType) Test response to wrong type *coords* argument. ... ok testBuildMatrixCutoffInvalidValue (prody.tests.dynamics.test_enms.TestGNM.testBuildMatrixCutoffInvalidValue) Test response to wrong *cutoff* argument. ... ok testBuildMatrixCutoffWrongType (prody.tests.dynamics.test_enms.TestGNM.testBuildMatrixCutoffWrongType) Test response to cutoff of wrong type. ... ok testBuildMatrixInvalidGamma (prody.tests.dynamics.test_enms.TestGNM.testBuildMatrixInvalidGamma) Test response to invalid *gamma* argument. ... ok testBuildMatrixWrongCoords (prody.tests.dynamics.test_enms.TestGNM.testBuildMatrixWrongCoords) Test response to wrong coords.dtype. ... ok testBuildMatrixWrongGamma (prody.tests.dynamics.test_enms.TestGNM.testBuildMatrixWrongGamma) Test response to wrong *gamma* argument. ... ok testSetMatrixAcceptableDtype (prody.tests.dynamics.test_enms.TestGNM.testSetMatrixAcceptableDtype) Test response to acceptable matrix.dtype. ... ok testSetMatrixNonSquare (prody.tests.dynamics.test_enms.TestGNM.testSetMatrixNonSquare) Test response to non-square matrix. ... ok testSetMatrixWrongDim (prody.tests.dynamics.test_enms.TestGNM.testSetMatrixWrongDim) Test response to wrong dim *kirchhoff* argument. ... ok testSetMatrixWrongDtype (prody.tests.dynamics.test_enms.TestGNM.testSetMatrixWrongDtype) Test response to wrong matrix.dtype. ... ok testSetMatrixWrongType (prody.tests.dynamics.test_enms.TestGNM.testSetMatrixWrongType) Test response to wrong matrix type argument. ... ok testBuildKirchoffSlow (prody.tests.dynamics.test_enms.TestGNMResults.testBuildKirchoffSlow) ... ok testCommuteTime (prody.tests.dynamics.test_enms.TestGNMResults.testCommuteTime) ... ok testEigenvalues (prody.tests.dynamics.test_enms.TestGNMResults.testEigenvalues) ... ok testEigenvectors (prody.tests.dynamics.test_enms.TestGNMResults.testEigenvectors) ... ok testGetCutoff (prody.tests.dynamics.test_enms.TestGNMResults.testGetCutoff) Testing return type of :meth:`~.GNMBase.getCutoff`. ... ok testGetGamma (prody.tests.dynamics.test_enms.TestGNMResults.testGetGamma) Testing return type of :meth:`~.GNMBase.getGamma`. ... ok testGetKirchoff (prody.tests.dynamics.test_enms.TestGNMResults.testGetKirchoff) ... ok testKirchhoff (prody.tests.dynamics.test_enms.TestGNMResults.testKirchhoff) ... ok testKirchhoffSums (prody.tests.dynamics.test_enms.TestGNMResults.testKirchhoffSums) ... ok testKirchhoffSymmetry (prody.tests.dynamics.test_enms.TestGNMResults.testKirchhoffSymmetry) ... ok testCalcModes (prody.tests.dynamics.test_enms.TestRTB.testCalcModes) ... /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/utilities/eigtools.py:43: DeprecationWarning: Keyword argument 'eigvals' is deprecated in favour of 'subset_by_index' keyword instead and will be removed in SciPy 1.12.0. values, vectors = linalg.eigh(M, turbo=turbo, eigvals=eigvals) ok testHessian (prody.tests.dynamics.test_enms.TestRTB.testHessian) ... ok testProjection (prody.tests.dynamics.test_enms.TestRTB.testProjection) ... ok testGetCutoff (prody.tests.dynamics.test_enms.testGNMBase.testGetCutoff) Testing return type of :meth:`~.GNMBase.getCutoff`. ... ok testGetGamma (prody.tests.dynamics.test_enms.testGNMBase.testGetGamma) Testing return type of :meth:`~.GNMBase.getGamma`. ... ok testBuildMatrixCoordsArray (prody.tests.dynamics.test_pca.TestPCA.testBuildMatrixCoordsArray) Test output when *coords* is an array. ... ok testBuildMatrixCoordsWrongType (prody.tests.dynamics.test_pca.TestPCA.testBuildMatrixCoordsWrongType) Test response to wrong type *coords* argument. ... ok testBuildMatrixWrongCoords (prody.tests.dynamics.test_pca.TestPCA.testBuildMatrixWrongCoords) Test response to wrong coords.dtype. ... ok testSetMatrixAcceptableDtype (prody.tests.dynamics.test_pca.TestPCA.testSetMatrixAcceptableDtype) Test response to acceptable matrix.dtype. ... ok testSetMatrixNonSquare (prody.tests.dynamics.test_pca.TestPCA.testSetMatrixNonSquare) Test response to non-square matrix. ... ok testSetMatrixWrongDim (prody.tests.dynamics.test_pca.TestPCA.testSetMatrixWrongDim) Test response to wrong dim *kirchhoff* argument. ... ok testSetMatrixWrongDtype (prody.tests.dynamics.test_pca.TestPCA.testSetMatrixWrongDtype) Test response to wrong matrix.dtype. ... ok testSetMatrixWrongType (prody.tests.dynamics.test_pca.TestPCA.testSetMatrixWrongType) Test response to wrong matrix type argument. ... ok testBuildMatrixCoordsArray (prody.tests.dynamics.test_pca.TestPCAResults.testBuildMatrixCoordsArray) Test output when *coords* is an array. ... ok testBuildMatrixCoordsWrongType (prody.tests.dynamics.test_pca.TestPCAResults.testBuildMatrixCoordsWrongType) Test response to wrong type *coords* argument. ... ok testBuildMatrixWrongCoords (prody.tests.dynamics.test_pca.TestPCAResults.testBuildMatrixWrongCoords) Test response to wrong coords.dtype. ... ok testCovariance (prody.tests.dynamics.test_pca.TestPCAResults.testCovariance) ... ok testCovarianceSymmetry (prody.tests.dynamics.test_pca.TestPCAResults.testCovarianceSymmetry) ... ok testEigenvalues (prody.tests.dynamics.test_pca.TestPCAResults.testEigenvalues) ... ok testEigenvectors (prody.tests.dynamics.test_pca.TestPCAResults.testEigenvectors) ... ok testNumModesAll (prody.tests.dynamics.test_pca.TestPCAResults.testNumModesAll) ... ok testNumModesSet (prody.tests.dynamics.test_pca.TestPCAResults.testNumModesSet) ... ok testSetMatrixAcceptableDtype (prody.tests.dynamics.test_pca.TestPCAResults.testSetMatrixAcceptableDtype) Test response to acceptable matrix.dtype. ... ok testSetMatrixNonSquare (prody.tests.dynamics.test_pca.TestPCAResults.testSetMatrixNonSquare) Test response to non-square matrix. ... ok testSetMatrixWrongDim (prody.tests.dynamics.test_pca.TestPCAResults.testSetMatrixWrongDim) Test response to wrong dim *kirchhoff* argument. ... ok testSetMatrixWrongDtype (prody.tests.dynamics.test_pca.TestPCAResults.testSetMatrixWrongDtype) Test response to wrong matrix.dtype. ... ok testSetMatrixWrongType (prody.tests.dynamics.test_pca.TestPCAResults.testSetMatrixWrongType) Test response to wrong matrix type argument. ... ok testSlicing (prody.tests.dynamics.test_signature.TestSDArray.testSlicing) ... ok testCoordinates (prody.tests.ensemble.test_conformation.TestConformation.testCoordinates) ... ok testCoordinatesForAll (prody.tests.ensemble.test_conformation.TestConformation.testCoordinatesForAll) ... ok testGetIndex (prody.tests.ensemble.test_conformation.TestConformation.testGetIndex) Test get index function. ... ok testGetNumAtoms (prody.tests.ensemble.test_conformation.TestConformation.testGetNumAtoms) Test get index function. ... ok testWeights (prody.tests.ensemble.test_conformation.TestConformation.testWeights) ... ok testCoordinates (prody.tests.ensemble.test_conformation.TestPDBConformation.testCoordinates) ... ok testCoordinatesForAll (prody.tests.ensemble.test_conformation.TestPDBConformation.testCoordinatesForAll) ... ok testGetIndex (prody.tests.ensemble.test_conformation.TestPDBConformation.testGetIndex) ... ok testGetNumAtoms (prody.tests.ensemble.test_conformation.TestPDBConformation.testGetNumAtoms) ... ok testWeights (prody.tests.ensemble.test_conformation.TestPDBConformation.testWeights) ... ok testWeightsForAll (prody.tests.ensemble.test_conformation.TestPDBConformation.testWeightsForAll) ... ok testConcatenation (prody.tests.ensemble.test_ensemble.TestEnsemble.testConcatenation) Test concatenation of ensembles without weights. ... ok testConcatenationNoweightsWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testConcatenationNoweightsWeights) Test concatenation of ensembles without and with weights. ... ok testConcatenationWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testConcatenationWeights) Test concatenation of ensembles with weights. ... ok testConcatenationWeightsNoweights (prody.tests.ensemble.test_ensemble.TestEnsemble.testConcatenationWeightsNoweights) Test concatenation of ensembles with and without weights. ... ok testDelCoordsetAll (prody.tests.ensemble.test_ensemble.TestEnsemble.testDelCoordsetAll) ... ok testDelCoordsetMiddle (prody.tests.ensemble.test_ensemble.TestEnsemble.testDelCoordsetMiddle) ... ok testGetCoordinates (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetCoordinates) Test correctness of reference coordinates. ... ok testGetCoordsets (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetCoordsets) Test correctness of all coordinates. ... ok testGetNumAtoms (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetNumAtoms) ... ok testGetNumCsets (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetNumCsets) ... ok testGetRMSDs (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetRMSDs) ... ok testGetRMSDsWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetRMSDsWeights) ... ok testGetWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testGetWeights) Test correctness of all weights. ... ok testIterCoordsets (prody.tests.ensemble.test_ensemble.TestEnsemble.testIterCoordsets) Test coordinate iteration. ... ok testSelection (prody.tests.ensemble.test_ensemble.TestEnsemble.testSelection) Test atom selection of ensemble. ... ok testSlicing (prody.tests.ensemble.test_ensemble.TestEnsemble.testSlicing) Test slicing operation. ... ok testSlicingCopy (prody.tests.ensemble.test_ensemble.TestEnsemble.testSlicingCopy) Test making a copy by slicing operation. ... ok testSlicingList (prody.tests.ensemble.test_ensemble.TestEnsemble.testSlicingList) Test slicing with a list. ... ok testSlicingWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testSlicingWeights) Test slicing operation with weights. ... ok testSuperpose (prody.tests.ensemble.test_ensemble.TestEnsemble.testSuperpose) ... ok testSuperposeWeights (prody.tests.ensemble.test_ensemble.TestEnsemble.testSuperposeWeights) ... ok testResults (prody.tests.ensemble.test_functions.TestBuildPDBEnsemble.testResults) ... ok testInvalidType (prody.tests.ensemble.test_functions.TestCalcOccupancies.testInvalidType) ... ok testResults (prody.tests.ensemble.test_functions.TestCalcOccupancies.testResults) ... ok testWeightsNone (prody.tests.ensemble.test_functions.TestCalcOccupancies.testWeightsNone) ... ok testResults (prody.tests.ensemble.test_functions.TestTrimPDBEnsemble.testResults) ... /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence/sequence.py:52: DeprecationWarning: tostring() is deprecated. Use tobytes() instead. return self._array.tostring().decode() ok testAddCoordsets (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testAddCoordsets) ... ok testConcatenation (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testConcatenation) Test concatenation of PDB ensembles. ... ok testDelCoordsetAll (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testDelCoordsetAll) Test consequences of deleting all coordinate sets. ... ok testDelCoordsetMiddle (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testDelCoordsetMiddle) ... ok testDelCoordsetMiddleTrans (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testDelCoordsetMiddleTrans) ... ok testGetCoordinates (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testGetCoordinates) ... ok testGetCoordsets (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testGetCoordsets) ... ok testGetNumAtoms (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testGetNumAtoms) ... ok testGetNumCsets (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testGetNumCsets) ... ok testGetWeights (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testGetWeights) ... ok testIterCoordsets (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testIterCoordsets) ... ok testSlicing (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testSlicing) ... ok testSlicingCopy (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testSlicingCopy) ... ok testSlicingList (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testSlicingList) ... ok testSlicingWeights (prody.tests.ensemble.test_pdbensemble.TestPDBEnsemble.testSlicingWeights) ... ok testAllSearch (prody.tests.kdtree.test_kdtree.TestKDTree.testAllSearch) ... ok testSearch (prody.tests.kdtree.test_kdtree.TestKDTree.testSearch) ... ok testPairNoPBC (prody.tests.kdtree.test_kdtree.TestKDTreePBC.testPairNoPBC) ... ok testPairPBC (prody.tests.kdtree.test_kdtree.TestKDTreePBC.testPairPBC) ... ok testPointNoPBC (prody.tests.kdtree.test_kdtree.TestKDTreePBC.testPointNoPBC) ... ok testPointPBC (prody.tests.kdtree.test_kdtree.TestKDTreePBC.testPointPBC) ... ok testMINvsMAX (prody.tests.measure.test_contacts.TestContacts.testMINvsMAX) ... ok testPBCvsNONE (prody.tests.measure.test_contacts.TestContacts.testPBCvsNONE) ... ok testAtomicArgumentSwitching (prody.tests.measure.test_contacts.TestNeighbors.testAtomicArgumentSwitching) ... ok testCoordArgumentSwitching (prody.tests.measure.test_contacts.TestNeighbors.testCoordArgumentSwitching) ... ok testNoPBC (prody.tests.measure.test_contacts.TestNeighbors.testNoPBC) ... ok testPBC (prody.tests.measure.test_contacts.TestNeighbors.testPBC) ... ok testPBCAtomicArgumentSwitching (prody.tests.measure.test_contacts.TestNeighbors.testPBCAtomicArgumentSwitching) ... ok testPBCCoordArgumentSwitching (prody.tests.measure.test_contacts.TestNeighbors.testPBCCoordArgumentSwitching) ... ok testCenter (prody.tests.measure.test_measure.TestCenter.testCenter) ... ok testCenterWithWeights (prody.tests.measure.test_measure.TestCenter.testCenterWithWeights) ... ok testMultiCoordsets (prody.tests.measure.test_measure.TestCenter.testMultiCoordsets) ... ok testMultiCoordsetsWithWeights (prody.tests.measure.test_measure.TestCenter.testMultiCoordsetsWithWeights) ... ok testCTerPhi (prody.tests.measure.test_measure.TestDihedrals.testCTerPhi) ... ok testCTerPsi (prody.tests.measure.test_measure.TestDihedrals.testCTerPsi) ... ok testCalcPhi (prody.tests.measure.test_measure.TestDihedrals.testCalcPhi) ... ok testCalcPsi (prody.tests.measure.test_measure.TestDihedrals.testCalcPsi) ... ok testNTerPhi (prody.tests.measure.test_measure.TestDihedrals.testNTerPhi) ... ok testNTerPsi (prody.tests.measure.test_measure.TestDihedrals.testNTerPsi) ... ok testPBC (prody.tests.measure.test_measure.TestDistances.testPBC) ... ok testPBCSymmetry (prody.tests.measure.test_measure.TestDistances.testPBCSymmetry) ... ok testMSF (prody.tests.measure.test_measure.TestMSF.testMSF) ... /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/trajectory/dcdfile.py:273: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead xyz = fromstring(self._file.read(self._itemsize * n_floats), /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/trajectory/dcdfile.py:320: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead data = fromstring(data, self._dtype) /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/trajectory/dcdfile.py:294: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead unitcell = fromstring(self._file.read(48), dtype=np.float64) ok testMSFfloat (prody.tests.measure.test_measure.TestMSF.testMSFfloat) ... ok testByArgument (prody.tests.measure.test_transform.TestMoveAtoms.testByArgument) ... ok testToArgument (prody.tests.measure.test_transform.TestMoveAtoms.testToArgument) ... ok testTransformation (prody.tests.measure.test_transform.TestMoveAtoms.testTransformation) ... ok testWrap (prody.tests.measure.test_transform.TestWrapAtoms.testWrap) ... ok testAgArgMultiModel (prody.tests.proteins.test_ciffile.TestParseMMCIF.testAgArgMultiModel) Test number of coordinate sets when using *ag* arguments. ... ok testAgArgument (prody.tests.proteins.test_ciffile.TestParseMMCIF.testAgArgument) Test outcome of valid and invalid *ag* arguments. ... /usr/lib/python3.11/traceback.py:237: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles/mmcif_6yfy.cif' mode='rt' encoding='utf-8'> tb.tb_frame.clear() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok testChainArgument (prody.tests.proteins.test_ciffile.TestParseMMCIF.testChainArgument) Test outcome of valid and invalid *chain* arguments. ... ok testLongChainArgument (prody.tests.proteins.test_ciffile.TestParseMMCIF.testLongChainArgument) Test outcome of valid and invalid *chain* arguments. ... /usr/lib/python3.11/traceback.py:237: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles/mmcif_6zu5.cif' mode='rt' encoding='utf-8'> tb.tb_frame.clear() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok testModelArgument (prody.tests.proteins.test_ciffile.TestParseMMCIF.testModelArgument) Test outcome of valid and invalid *model* arguments. ... ok testPDBArgument (prody.tests.proteins.test_ciffile.TestParseMMCIF.testPDBArgument) Test outcome of invalid *pdb* arguments. ... ok testSubsetArgument (prody.tests.proteins.test_ciffile.TestParseMMCIF.testSubsetArgument) Test outcome of valid and invalid *subset* arguments. ... ok testTitleArgument (prody.tests.proteins.test_ciffile.TestParseMMCIF.testTitleArgument) Test outcome of *title* argument. ... ok testUsualCase (prody.tests.proteins.test_ciffile.TestParseMMCIF.testUsualCase) Test the outcome of a simple parsing scenario. ... ok testDSSPBridgePartners (prody.tests.proteins.test_dssp.TestDSSPFunctions.testDSSPBridgePartners) Check if the DSSP bridge-partners were correctly parsed and ... skipped 'dssp is not found' testHeaderContent (prody.tests.proteins.test_header.TestParsePDBHeaderOnly.testHeaderContent) ... ok testHeaderType (prody.tests.proteins.test_header.TestParsePDBHeaderOnly.testHeaderType) ... ok testCompressedArgument (prody.tests.proteins.test_localpdb.TestFetchPDB.testCompressedArgument) Test decompressing fetched PDB files. ... skipped 'Not running tests needing network access.' testFetchingMultipleFiles (prody.tests.proteins.test_localpdb.TestFetchPDB.testFetchingMultipleFiles) Test the outcome of fetching multiple PDB files. ... skipped 'Not running tests needing network access.' testFetchingSingleFile (prody.tests.proteins.test_localpdb.TestFetchPDB.testFetchingSingleFile) Test the outcome of fetching a single PDB file. ... skipped 'Not running tests needing network access.' testInvalidPDBIdentifier (prody.tests.proteins.test_localpdb.TestFetchPDB.testInvalidPDBIdentifier) Test outcome of passing invalid PDB identifiers. ... ok testAgArgMultiModel (prody.tests.proteins.test_pdbfile.TestParsePDB.testAgArgMultiModel) Test number of coordinate sets when using *ag* arguments. ... ok testAgArgSingleModel (prody.tests.proteins.test_pdbfile.TestParsePDB.testAgArgSingleModel) Test number of coordinate sets when using *ag* arguments. ... ok testAgArgument (prody.tests.proteins.test_pdbfile.TestParsePDB.testAgArgument) Test outcome of valid and invalid *ag* arguments. ... /usr/lib/python3.11/traceback.py:237: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/datafiles/pdb2k39_truncated.pdb' mode='rt' encoding='utf-8'> tb.tb_frame.clear() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok testChainArgument (prody.tests.proteins.test_pdbfile.TestParsePDB.testChainArgument) Test outcome of valid and invalid *chain* arguments. ... ok testFiveDigitResnum (prody.tests.proteins.test_pdbfile.TestParsePDB.testFiveDigitResnum) Test parsing PDB files with five digit resnums ... ok testHexResnum (prody.tests.proteins.test_pdbfile.TestParsePDB.testHexResnum) Test parsing PDB files with hexadecimal resnums ... ok testHexSerial (prody.tests.proteins.test_pdbfile.TestParsePDB.testHexSerial) Test parsing PDB files with hexadecimal serial numbers ... ok testHybrid36Resnum (prody.tests.proteins.test_pdbfile.TestParsePDB.testHybrid36Resnum) Test parsing PDB files with Hybrid36 resnums ... ok testHybrid36Serial (prody.tests.proteins.test_pdbfile.TestParsePDB.testHybrid36Serial) Test parsing PDB files with Hybrid36 serial numbers ... ok testModelArgument (prody.tests.proteins.test_pdbfile.TestParsePDB.testModelArgument) Test outcome of valid and invalid *model* arguments. ... ok testPDBArgument (prody.tests.proteins.test_pdbfile.TestParsePDB.testPDBArgument) Test outcome of invalid *pdb* arguments. ... ok testSubsetArgument (prody.tests.proteins.test_pdbfile.TestParsePDB.testSubsetArgument) Test outcome of valid and invalid *subset* arguments. ... ok testTitleArgument (prody.tests.proteins.test_pdbfile.TestParsePDB.testTitleArgument) Test outcome of *title* argument. ... ok testUsualCase (prody.tests.proteins.test_pdbfile.TestParsePDB.testUsualCase) Test the outcome of a simple parsing scenario. ... ok testAltlocA (prody.tests.proteins.test_pdbfile.TestParsePDBAltloc.testAltlocA) ... ok testAltlocB (prody.tests.proteins.test_pdbfile.TestParsePDBAltloc.testAltlocB) ... ok testAltlocC (prody.tests.proteins.test_pdbfile.TestParsePDBAltloc.testAltlocC) ... ok testAltlocNone (prody.tests.proteins.test_pdbfile.TestParsePDBAltloc.testAltlocNone) ... ok testAtomGroupContent (prody.tests.proteins.test_pdbfile.TestParsePDBHeaderAndAllModels.testAtomGroupContent) ... ok testAtomGroupType (prody.tests.proteins.test_pdbfile.TestParsePDBHeaderAndAllModels.testAtomGroupType) ... ok testModelArgument (prody.tests.proteins.test_pdbfile.TestWritePDB.testModelArgument) Test valid and invalid model arguments. ... /usr/lib/python3.11/traceback.py:237: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/test.pdb' mode='wt' encoding='utf-8'> tb.tb_frame.clear() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok testParsingOutput (prody.tests.proteins.test_pdbfile.TestWritePDB.testParsingOutput) Test if parsing output is the same as parsing original file. ... ok testWritingHex (prody.tests.proteins.test_pdbfile.TestWritePDB.testWritingHex) Test if output from writing hexadecimal is as expected. ... ok testWritingHexTer (prody.tests.proteins.test_pdbfile.TestWritePDB.testWritingHexTer) Test if output from writing hexadecimal with TER lines is as expected. ... ok testWritingHybrid36 (prody.tests.proteins.test_pdbfile.TestWritePDB.testWritingHybrid36) Test if output from writing Hybrid36 is as expected. ... ok testWritingHybrid36Ter (prody.tests.proteins.test_pdbfile.TestWritePDB.testWritingHybrid36Ter) Test if output from writing Hybrid36 with TER lines is as expected. ... ok testWritingSecstrs (prody.tests.proteins.test_pdbfile.TestWritePDB.testWritingSecstrs) Test if output from writing secstrs is as expected. ... ok testCompressed (prody.tests.proteins.test_wwpdb.TestFTP.testCompressed) ... skipped 'Not running tests needing network access.' testDecompressed (prody.tests.proteins.test_wwpdb.TestFTP.testDecompressed) ... skipped 'Not running tests needing network access.' testCompressed (prody.tests.proteins.test_wwpdb.TestHTTP.testCompressed) ... skipped 'Not running tests needing network access.' testDecompressed (prody.tests.proteins.test_wwpdb.TestHTTP.testDecompressed) ... skipped 'Not running tests needing network access.' testBuildMSAlocal (prody.tests.sequence.test_analysis.TestBuildMSA.testBuildMSAlocal) ... /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence/msa.py:218: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison return all(other == self._msa) ok testResidueCount (prody.tests.sequence.test_analysis.TestCalcMSAOccupancy.testResidueCount) ... ok testResidueOccupancy (prody.tests.sequence.test_analysis.TestCalcMSAOccupancy.testResidueOccupancy) ... ok testSequenceCount (prody.tests.sequence.test_analysis.TestCalcMSAOccupancy.testSequenceCount) ... ok testSequenceOccupancy (prody.tests.sequence.test_analysis.TestCalcMSAOccupancy.testSequenceOccupancy) ... ok testMATLAB (prody.tests.sequence.test_analysis.TestCalcMeff.testMATLAB) ... ok testTwenty (prody.tests.sequence.test_analysis.TestCalcMeff.testTwenty) ... ok testTwentyReversed (prody.tests.sequence.test_analysis.TestCalcMeff.testTwentyReversed) ... ok testZero1 (prody.tests.sequence.test_analysis.TestCalcMeff.testZero1) ... ok testZero2 (prody.tests.sequence.test_analysis.TestCalcMeff.testZero2) ... ok testAmbiguity (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity) ... ok testAmbiguity2 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity2) ... ok testAmbiguity3 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity3) ... ok testAmbiguity4 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity4) ... ok testAmbiguity5 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity5) ... ok testAmbiguity6 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity6) ... ok testAmbiguity7 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testAmbiguity7) ... ok testInf (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testInf) ... ok testNoAmbiguity (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testNoAmbiguity) ... ok testNorm (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testNorm) ... ok testNorm2 (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testNorm2) ... ok testSixSequences (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testSixSequences) ... ok testTwenty (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testTwenty) ... ok testTwentyReversed (prody.tests.sequence.test_analysis.TestCalcMutualInfo.testTwentyReversed) ... ok testAmbiguity (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity) ... ok testAmbiguity2 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity2) ... ok testAmbiguity3 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity3) ... ok testAmbiguity4 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity4) ... ok testAmbiguity5 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity5) ... ok testAmbiguity6 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity6) ... ok testAmbiguity7 (prody.tests.sequence.test_analysis.TestCalcOMES.testAmbiguity7) ... ok testFourSequences (prody.tests.sequence.test_analysis.TestCalcOMES.testFourSequences) ... ok testInf (prody.tests.sequence.test_analysis.TestCalcOMES.testInf) ... ok testNoAmbiguity (prody.tests.sequence.test_analysis.TestCalcOMES.testNoAmbiguity) ... ok testTwenty (prody.tests.sequence.test_analysis.TestCalcOMES.testTwenty) ... ok testTwentyReversed (prody.tests.sequence.test_analysis.TestCalcOMES.testTwentyReversed) ... ok testZero (prody.tests.sequence.test_analysis.TestCalcOMES.testZero) ... ok testMATLAB (prody.tests.sequence.test_analysis.TestCalcSCA.testMATLAB) ... ok testZero (prody.tests.sequence.test_analysis.TestCalcSCA.testZero) ... ok testAmbiguous (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testAmbiguous) ... ok testGapDividend (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testGapDividend) ... ok testSixSequences (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testSixSequences) ... ok testSmallProbability (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testSmallProbability) ... ok testTwenty (prody.tests.sequence.test_analysis.TestCalcShannonEntropy.testTwenty) ... ok testMATLAB10 (prody.tests.sequence.test_analysis.TestDirectInfo.testMATLAB10) ... /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence/analysis.py:592: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. c = matrix.dot(matrix(zeros((length*q, 1), float)), /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence/analysis.py:593: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. matrix(zeros((1, length*q), float))) /usr/lib/python3/dist-packages/numpy/matrixlib/defmatrix.py:69: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. return matrix(data, dtype=dtype, copy=False) ok testMATLAB8 (prody.tests.sequence.test_analysis.TestDirectInfo.testMATLAB8) ... ok testTwenty (prody.tests.sequence.test_analysis.TestDirectInfo.testTwenty) ... ok testTwentyReversed (prody.tests.sequence.test_analysis.TestDirectInfo.testTwentyReversed) ... ok testZero (prody.tests.sequence.test_analysis.TestDirectInfo.testZero) ... ok testZero1 (prody.tests.sequence.test_analysis.TestDirectInfo.testZero1) ... ok testZero2 (prody.tests.sequence.test_analysis.TestDirectInfo.testZero2) ... ok testZero3 (prody.tests.sequence.test_analysis.TestDirectInfo.testZero3) ... ok testZero4 (prody.tests.sequence.test_analysis.TestDirectInfo.testZero4) ... ok testIdentityMatrix (prody.tests.sequence.test_analysis.TestIdentity.testIdentityMatrix) ... ok testIdentityMatrixNonTurbo (prody.tests.sequence.test_analysis.TestIdentity.testIdentityMatrixNonTurbo) ... ok testUnique (prody.tests.sequence.test_analysis.TestUnique.testUnique) ... ok testUnique2 (prody.tests.sequence.test_analysis.TestUnique.testUnique2) ... ok testMerge (prody.tests.sequence.test_msa.TestMerging.testMerge) ... ok testAddition (prody.tests.sequence.test_msa.TestRefinement.testAddition) ... ok testAll (prody.tests.sequence.test_msa.TestRefinement.testAll) ... ok testColocc (prody.tests.sequence.test_msa.TestRefinement.testColocc) ... ok testExtension (prody.tests.sequence.test_msa.TestRefinement.testExtension) ... ok testLabel (prody.tests.sequence.test_msa.TestRefinement.testLabel) ... ok testRowCol (prody.tests.sequence.test_msa.TestRefinement.testRowCol) ... ok testRowocc (prody.tests.sequence.test_msa.TestRefinement.testRowocc) ... ok testSeqid (prody.tests.sequence.test_msa.TestRefinement.testSeqid) ... ok testSeqidLabel (prody.tests.sequence.test_msa.TestRefinement.testSeqidLabel) ... ok testMSAFile (prody.tests.sequence.test_msafile.TestMSAFile.testMSAFile) ... ok testWriteFasta (prody.tests.sequence.test_msafile.TestMSAFile.testWriteFasta) ... /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence/sequence.py:32: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead self._seq = fromstring(one, '|S1') ok testWriteSelex (prody.tests.sequence.test_msafile.TestMSAFile.testWriteSelex) ... ok testWriteStockholm (prody.tests.sequence.test_msafile.TestMSAFile.testWriteStockholm) ... ok testArray (prody.tests.sequence.test_msafile.TestParseMSA.testArray) ... ok testIterator (prody.tests.sequence.test_msafile.TestParseMSA.testIterator) ... ok testMapping (prody.tests.sequence.test_msafile.TestParseMSA.testMapping) ... ok testFasta (prody.tests.sequence.test_msafile.TestWriteMSA.testFasta) ... ok testSelex (prody.tests.sequence.test_msafile.TestWriteMSA.testSelex) ... ok testStringConversion (prody.tests.sequence.test_sequence.TestSequence.testStringConversion) ... /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/sequence/sequence.py:36: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead self._seq = fromstring(args[0], '|S1') ok testParseDCD (prody.tests.trajectory.test_dcdfile.TestDCDFile.testParseDCD) ... ok testWrite (prody.tests.trajectory.test_dcdfile.TestDCDFile.testWrite) ... ok testWriteDCD (prody.tests.trajectory.test_dcdfile.TestDCDFile.testWriteDCD) ... ok testWriteModeAppend (prody.tests.trajectory.test_dcdfile.TestDCDFile.testWriteModeAppend) ... ok testAll (prody.tests.trajectory.test_frame.TestSuperpose.testAll) ... ok testCarbon (prody.tests.trajectory.test_frame.TestSuperpose.testCarbon) ... ok testCoords (prody.tests.utilities.test_checkers.TestCheckCoords.testCoords) ... ok testCoordset (prody.tests.utilities.test_checkers.TestCheckCoords.testCoordset) ... ok testCoordsetNatoms (prody.tests.utilities.test_checkers.TestCheckCoords.testCoordsetNatoms) ... ok testInvalidCoords (prody.tests.utilities.test_checkers.TestCheckCoords.testInvalidCoords) ... ok testCorrectMonotypeOneArg (prody.tests.utilities.test_checkers.testCheckTypes.testCorrectMonotypeOneArg) ... ok testCorrectMonotypeTwoArgs (prody.tests.utilities.test_checkers.testCheckTypes.testCorrectMonotypeTwoArgs) ... ok testCorrectMultitypeOneArg (prody.tests.utilities.test_checkers.testCheckTypes.testCorrectMultitypeOneArg) ... ok testWrongMonotypeOneArg (prody.tests.utilities.test_checkers.testCheckTypes.testWrongMonotypeOneArg) ... ok testWrongMonotypeTwoArgs (prody.tests.utilities.test_checkers.testCheckTypes.testWrongMonotypeTwoArgs) ... ok testWrongMultitypeOneArg (prody.tests.utilities.test_checkers.testCheckTypes.testWrongMultitypeOneArg) ... ok testContinuous (prody.tests.utilities.test_misctools.TestRangeString.testContinuous) ... ok testGapped (prody.tests.utilities.test_misctools.TestRangeString.testGapped) ... ok testNegative (prody.tests.utilities.test_misctools.TestRangeString.testNegative) ... ok testRepeated (prody.tests.utilities.test_misctools.TestRangeString.testRepeated) ... ok testBuffer (prody.tests.utilities.test_pathtools.TestGunzip.testBuffer) ... /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/utilities/test_pathtools.py:34: ResourceWarning: unclosed file <_io.BufferedReader name='/tmp/compressed.txt.gz'> buff = open(self.gzfn, 'rb').read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok testFile (prody.tests.utilities.test_pathtools.TestGunzip.testFile) ... /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/utilities/test_pathtools.py:29: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/compressed.txt' mode='r' encoding='utf-8'> text = open(fn).read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok ====================================================================== FAIL: testBuildMatrixCoordsArray (prody.tests.dynamics.test_enms.TestANM.testBuildMatrixCoordsArray) Test output when *coords* is an array. ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build/prody/tests/dynamics/test_enms.py", line 295, in testBuildMatrixCoordsArray assert_equal(self.getMatrix(), self.getExpected(), File "/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line 349, in assert_equal return assert_array_equal(actual, desired, err_msg, verbose) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line 985, in assert_array_equal assert_array_compare(operator.__eq__, x, y, err_msg=err_msg, File "/usr/lib/python3.11/contextlib.py", line 81, in inner return func(*args, **kwds) ^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/numpy/testing/_private/utils.py", line 862, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not equal failed to get correct matrix Mismatched elements: 3 / 51984 (0.00577%) Max absolute difference: 4.4408921e-16 Max relative difference: 7.83963072e-16 x: array([[ 6.913751, 0.021868, 0.94014 , ..., 0. , 0. , 0. ], [ 0.021868, 9.066915, -0.076779, ..., 0. , 0. ,... y: array([[ 6.913751, 0.021868, 0.94014 , ..., 0. , 0. , 0. ], [ 0.021868, 9.066915, -0.076779, ..., 0. , 0. ,... ---------------------------------------------------------------------- Ran 971 tests in 112.788s FAILED (failures=1, skipped=39) E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /build/reproducible-path/prody-2.4.1+dfsg/.pybuild/cpython3_3.11_prody/build; python3.11 -m unittest discover -v dh_auto_test: error: pybuild --test -i python{version} -p "3.12 3.11" returned exit code 13 make: *** [debian/rules:6: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: user script /srv/workspace/pbuilder/17053/tmp/hooks/C01_cleanup starting debug output: disk usage on i-capture-the-hostname at Fri Apr 18 18:27:59 UTC 2025 Filesystem Size Used Avail Use% Mounted on tmpfs 3.9G 0 3.9G 0% /dev/shm I: user script /srv/workspace/pbuilder/17053/tmp/hooks/C01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/17053 and its subdirectories