/usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.dvp7jCFsyn/cdk_1.2.10-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.dvp7jCFsyn/cdk_1.2.10-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.dvp7jCFsyn/cdk_1.2.10-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.dvp7jCFsyn/b1/cdk_1.2.10-7_i386.changes /srv/reproducible-results/rbuild-debian/tmp.dvp7jCFsyn/b2/cdk_1.2.10-7

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1	·096fd~~206a~~e~~c32ab8c~~3~~6ee~~8a~~f7991~~5~~ca2~~·478~~698~~0·java·optional·libcdk-java_1.2.10-7_all.deb	1	·6ed88f2e74e7061347983a8ed12569d9·4787120·java·optional·libcdk-java_1.2.10-7_all.deb


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1	-rw-r--r--···0········0········0········4·2018-03-30·20:15:48.000000·debian-binary	1	-rw-r--r--···0········0········0········4·2018-03-30·20:15:48.000000·debian-binary
2	-rw-r--r--···0········0········0·····1848·2018-03-30·20:15:48.000000·control.tar.xz	2	-rw-r--r--···0········0········0·····1848·2018-03-30·20:15:48.000000·control.tar.xz
3	-rw-r--r--···0········0········0··478~~494~~0·2018-03-30·20:15:48.000000·data.tar.xz	3	-rw-r--r--···0········0········0··4785080·2018-03-30·20:15:48.000000·data.tar.xz

+org/openscience/cdk/tools/DataFeatures.java
+org/openscience/cdk/annotations/TestClass.java
+org/openscience/cdk/annotations/TestMethod.java
+org/openscience/cdk/annotations/TestClass.java
+org/openscience/cdk/tools/DataFeatures.java


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5	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2018-03-30·20:15:48.000000·./usr/share/doc/libcdk-java/	5	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2018-03-30·20:15:48.000000·./usr/share/doc/libcdk-java/
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7	-rw-r--r--···0·root·········(0)·root·········(0)······198·2018-03-30·19:54:21.000000·./usr/share/doc/libcdk-java/TODO.Debian	7	-rw-r--r--···0·root·········(0)·root·········(0)······198·2018-03-30·19:54:21.000000·./usr/share/doc/libcdk-java/TODO.Debian
8	-rw-r--r--···0·root·········(0)·root·········(0)·····4231·2018-03-30·20:15:48.000000·./usr/share/doc/libcdk-java/changelog.Debian.gz	8	-rw-r--r--···0·root·········(0)·root·········(0)·····4231·2018-03-30·20:15:48.000000·./usr/share/doc/libcdk-java/changelog.Debian.gz
9	-rw-r--r--···0·root·········(0)·root·········(0)·····1151·2018-03-30·20:14:47.000000·./usr/share/doc/libcdk-java/copyright	9	-rw-r--r--···0·root·········(0)·root·········(0)·····1151·2018-03-30·20:14:47.000000·./usr/share/doc/libcdk-java/copyright
10	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2018-03-30·20:15:48.000000·./usr/share/java/	10	drwxr-xr-x···0·root·········(0)·root·········(0)········0·2018-03-30·20:15:48.000000·./usr/share/java/
11	-rw-r--r--···0·root·········(0)·root·········(0)·····2680·2018-03-30·20:15:48.000000·./usr/share/java/cdk-annotation-1.2.10.jar	11	-rw-r--r--···0·root·········(0)·root·········(0)·····2680·2018-03-30·20:15:48.000000·./usr/share/java/cdk-annotation-1.2.10.jar
12	-rw-r--r--···0·root·········(0)·root·········(0)····16879·2018-03-30·20:15:48.000000·./usr/share/java/cdk-atomtype-1.2.10.jar	12	-rw-r--r--···0·root·········(0)·root·········(0)····16878·2018-03-30·20:15:48.000000·./usr/share/java/cdk-atomtype-1.2.10.jar
13	-rw-r--r--···0·root·········(0)·root·········(0)··2292397·2018-03-30·20:15:48.000000·./usr/share/java/cdk-builder3d-1.2.10.jar	13	-rw-r--r--···0·root·········(0)·root·········(0)··2292395·2018-03-30·20:15:48.000000·./usr/share/java/cdk-builder3d-1.2.10.jar
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15	-rw-r--r--···0·root·········(0)·root·········(0)····34987·2018-03-30·20:15:48.000000·./usr/share/java/cdk-charges-1.2.10.jar	15	-rw-r--r--···0·root·········(0)·root·········(0)····34983·2018-03-30·20:15:48.000000·./usr/share/java/cdk-charges-1.2.10.jar
16	-rw-r--r--···0·root·········(0)·root·········(0)·····4292·2018-03-30·20:15:48.000000·./usr/share/java/cdk-control-1.2.10.jar	16	-rw-r--r--···0·root·········(0)·root·········(0)·····4289·2018-03-30·20:15:48.000000·./usr/share/java/cdk-control-1.2.10.jar
17	-rw-r--r--···0·root·········(0)·root·········(0)···157900·2018-03-30·20:15:48.000000·./usr/share/java/cdk-core-1.2.10.jar	17	-rw-r--r--···0·root·········(0)·root·········(0)···157907·2018-03-30·20:15:48.000000·./usr/share/java/cdk-core-1.2.10.jar
18	-rw-r--r--···0·root·········(0)·root·········(0)···107898·2018-03-30·20:15:48.000000·./usr/share/java/cdk-data-1.2.10.jar	18	-rw-r--r--···0·root·········(0)·root·········(0)···107898·2018-03-30·20:15:48.000000·./usr/share/java/cdk-data-1.2.10.jar
19	-rw-r--r--···0·root·········(0)·root·········(0)····18015·2018-03-30·20:15:48.000000·./usr/share/java/cdk-dict-1.2.10.jar	19	-rw-r--r--···0·root·········(0)·root·········(0)····18017·2018-03-30·20:15:48.000000·./usr/share/java/cdk-dict-1.2.10.jar
20	-rw-r--r--···0·root·········(0)·root·········(0)····28942·2018-03-30·20:15:48.000000·./usr/share/java/cdk-diff-1.2.10.jar	20	-rw-r--r--···0·root·········(0)·root·········(0)····28943·2018-03-30·20:15:48.000000·./usr/share/java/cdk-diff-1.2.10.jar
21	-rw-r--r--···0·root·········(0)·root·········(0)···266983·2018-03-30·20:15:48.000000·./usr/share/java/cdk-extra-1.2.10.jar	21	-rw-r--r--···0·root·········(0)·root·········(0)···266982·2018-03-30·20:15:48.000000·./usr/share/java/cdk-extra-1.2.10.jar
22	-rw-r--r--···0·root·········(0)·root·········(0)····15315·2018-03-30·20:15:48.000000·./usr/share/java/cdk-fingerprint-1.2.10.jar	22	-rw-r--r--···0·root·········(0)·root·········(0)····15314·2018-03-30·20:15:48.000000·./usr/share/java/cdk-fingerprint-1.2.10.jar
23	-rw-r--r--···0·root·········(0)·root·········(0)···165391·2018-03-30·20:15:48.000000·./usr/share/java/cdk-forcefield-1.2.10.jar	23	-rw-r--r--···0·root·········(0)·root·········(0)···165388·2018-03-30·20:15:48.000000·./usr/share/java/cdk-forcefield-1.2.10.jar
24	-rw-r--r--···0·root·········(0)·root·········(0)····56661·2018-03-30·20:15:48.000000·./usr/share/java/cdk-formula-1.2.10.jar	24	-rw-r--r--···0·root·········(0)·root·········(0)····56659·2018-03-30·20:15:48.000000·./usr/share/java/cdk-formula-1.2.10.jar
25	-rw-r--r--···0·root·········(0)·root·········(0)····26725·2018-03-30·20:15:48.000000·./usr/share/java/cdk-interfaces-1.2.10.jar	25	-rw-r--r--···0·root·········(0)·root·········(0)····26723·2018-03-30·20:15:48.000000·./usr/share/java/cdk-interfaces-1.2.10.jar
26	-rw-r--r--···0·root·········(0)·root·········(0)···515787·2018-03-30·20:15:48.000000·./usr/share/java/cdk-io-1.2.10.jar	26	-rw-r--r--···0·root·········(0)·root·········(0)···515774·2018-03-30·20:15:48.000000·./usr/share/java/cdk-io-1.2.10.jar
27	-rw-r--r--···0·root·········(0)·root·········(0)···105632·2018-03-30·20:15:48.000000·./usr/share/java/cdk-ioformats-1.2.10.jar	27	-rw-r--r--···0·root·········(0)·root·········(0)···105608·2018-03-30·20:15:48.000000·./usr/share/java/cdk-ioformats-1.2.10.jar
28	-rw-r--r--···0·root·········(0)·root·········(0)·····6625·2018-03-30·20:15:48.000000·./usr/share/java/cdk-ionpot-1.2.10.jar	28	-rw-r--r--···0·root·········(0)·root·········(0)·····6625·2018-03-30·20:15:48.000000·./usr/share/java/cdk-ionpot-1.2.10.jar
29	-rw-r--r--···0·root·········(0)·root·········(0)····18461·2018-03-30·20:15:48.000000·./usr/share/java/cdk-isomorphism-1.2.10.jar	29	-rw-r--r--···0·root·········(0)·root·········(0)····18455·2018-03-30·20:15:48.000000·./usr/share/java/cdk-isomorphism-1.2.10.jar
30	-rw-r--r--···0·root·········(0)·root·········(0)·····1900·2018-03-30·20:15:48.000000·./usr/share/java/cdk-libiocml-1.2.10.jar	30	-rw-r--r--···0·root·········(0)·root·········(0)·····1903·2018-03-30·20:15:48.000000·./usr/share/java/cdk-libiocml-1.2.10.jar
31	-rw-r--r--···0·root·········(0)·root·········(0)·····6919·2018-03-30·20:15:48.000000·./usr/share/java/cdk-libiomd-1.2.10.jar	31	-rw-r--r--···0·root·········(0)·root·········(0)·····6917·2018-03-30·20:15:48.000000·./usr/share/java/cdk-libiomd-1.2.10.jar
32	-rw-r--r--···0·root·········(0)·root·········(0)····31229·2018-03-30·20:15:48.000000·./usr/share/java/cdk-nonotify-1.2.10.jar	32	-rw-r--r--···0·root·········(0)·root·········(0)····31231·2018-03-30·20:15:48.000000·./usr/share/java/cdk-nonotify-1.2.10.jar
33	-rw-r--r--···0·root·········(0)·root·········(0)····20275·2018-03-30·20:15:48.000000·./usr/share/java/cdk-pcore-1.2.10.jar	33	-rw-r--r--···0·root·········(0)·root·········(0)····20272·2018-03-30·20:15:48.000000·./usr/share/java/cdk-pcore-1.2.10.jar
34	-rw-r--r--···0·root·········(0)·root·········(0)····17753·2018-03-30·20:15:48.000000·./usr/share/java/cdk-pdb-1.2.10.jar	34	-rw-r--r--···0·root·········(0)·root·········(0)····17754·2018-03-30·20:15:48.000000·./usr/share/java/cdk-pdb-1.2.10.jar
35	-rw-r--r--···0·root·········(0)·root·········(0)····40165·2018-03-30·20:15:48.000000·./usr/share/java/cdk-qm-1.2.10.jar	35	-rw-r--r--···0·root·········(0)·root·········(0)····40166·2018-03-30·20:15:48.000000·./usr/share/java/cdk-qm-1.2.10.jar
36	-rw-r--r--···0·root·········(0)·root·········(0)····54287·2018-03-30·20:15:48.000000·./usr/share/java/cdk-qsar-1.2.10.jar	36	-rw-r--r--···0·root·········(0)·root·········(0)····54290·2018-03-30·20:15:48.000000·./usr/share/java/cdk-qsar-1.2.10.jar
37	-rw-r--r--···0·root·········(0)·root·········(0)···107151·2018-03-30·20:15:48.000000·./usr/share/java/cdk-qsaratomic-1.2.10.jar	37	-rw-r--r--···0·root·········(0)·root·········(0)···107156·2018-03-30·20:15:48.000000·./usr/share/java/cdk-qsaratomic-1.2.10.jar
38	-rw-r--r--···0·root·········(0)·root·········(0)····16472·2018-03-30·20:15:48.000000·./usr/share/java/cdk-qsarbond-1.2.10.jar	38	-rw-r--r--···0·root·········(0)·root·········(0)····16471·2018-03-30·20:15:48.000000·./usr/share/java/cdk-qsarbond-1.2.10.jar
39	-rw-r--r--···0·root·········(0)·root·········(0)·····9858·2018-03-30·20:15:48.000000·./usr/share/java/cdk-qsarionpot-1.2.10.jar	39	-rw-r--r--···0·root·········(0)·root·········(0)·····9858·2018-03-30·20:15:48.000000·./usr/share/java/cdk-qsarionpot-1.2.10.jar
40	-rw-r--r--···0·root·········(0)·root·········(0)···193147·2018-03-30·20:15:48.000000·./usr/share/java/cdk-qsarmolecular-1.2.10.jar	40	-rw-r--r--···0·root·········(0)·root·········(0)···193141·2018-03-30·20:15:48.000000·./usr/share/java/cdk-qsarmolecular-1.2.10.jar
41	-rw-r--r--···0·root·········(0)·root·········(0)·····8329·2018-03-30·20:15:48.000000·./usr/share/java/cdk-qsarprotein-1.2.10.jar	41	-rw-r--r--···0·root·········(0)·root·········(0)·····8329·2018-03-30·20:15:48.000000·./usr/share/java/cdk-qsarprotein-1.2.10.jar
42	-rw-r--r--···0·root·········(0)·root·········(0)···153616·2018-03-30·20:15:48.000000·./usr/share/java/cdk-reaction-1.2.10.jar	42	-rw-r--r--···0·root·········(0)·root·········(0)···153618·2018-03-30·20:15:48.000000·./usr/share/java/cdk-reaction-1.2.10.jar
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44	-rw-r--r--···0·root·········(0)·root·········(0)····43103·2018-03-30·20:15:48.000000·./usr/share/java/cdk-sdg-1.2.10.jar	44	-rw-r--r--···0·root·········(0)·root·········(0)····43102·2018-03-30·20:15:48.000000·./usr/share/java/cdk-sdg-1.2.10.jar
45	-rw-r--r--···0·root·········(0)·root·········(0)···126441·2018-03-30·20:15:48.000000·./usr/share/java/cdk-smarts-1.2.10.jar	45	-rw-r--r--···0·root·········(0)·root·········(0)···126448·2018-03-30·20:15:48.000000·./usr/share/java/cdk-smarts-1.2.10.jar
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48	-rw-r--r--···0·root·········(0)·root·········(0)····17860·2018-03-30·20:15:48.000000·./usr/share/java/cdk-structgen-1.2.10.jar	48	-rw-r--r--···0·root·········(0)·root·········(0)····17853·2018-03-30·20:15:48.000000·./usr/share/java/cdk-structgen-1.2.10.jar
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51	lrwxrwxrwx···0·root·········(0)·root·········(0)········0·2018-03-30·20:15:48.000000·./usr/share/java/cdk-atomtype.jar·->·cdk-atomtype-1.2.10.jar	51	lrwxrwxrwx···0·root·········(0)·root·········(0)········0·2018-03-30·20:15:48.000000·./usr/share/java/cdk-atomtype.jar·->·cdk-atomtype-1.2.10.jar
52	lrwxrwxrwx···0·root·········(0)·root·········(0)········0·2018-03-30·20:15:48.000000·./usr/share/java/cdk-builder3d.jar·->·cdk-builder3d-1.2.10.jar	52	lrwxrwxrwx···0·root·········(0)·root·········(0)········0·2018-03-30·20:15:48.000000·./usr/share/java/cdk-builder3d.jar·->·cdk-builder3d-1.2.10.jar
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Offset 87, 15 lines modified		Offset 87, 15 lines modified
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88	··minimum·software·version·required·to·extract:···1.0	88	··minimum·software·version·required·to·extract:···1.0
89	··compression·method:·····························deflated	89	··compression·method:·····························deflated
90	··compression·sub-type·(deflation):···············normal	90	··compression·sub-type·(deflation):···············normal
91	··file·security·status:···························not·encrypted	91	··file·security·status:···························not·encrypted
92	··extended·local·header:··························no	92	··extended·local·header:··························no
93	··file·last·modified·on·(DOS·date/time):··········2018·Mar·30·20:15:48	93	··file·last·modified·on·(DOS·date/time):··········2018·Mar·30·20:15:48
94	··32-bit·CRC·value·(hex):·························a~~be485d1~~	94	··32-bit·CRC·value·(hex):·························a9f19e29
95	··compressed·size:································76·bytes	95	··compressed·size:································76·bytes
96	··uncompressed·size:······························139·bytes	96	··uncompressed·size:······························139·bytes
97	··length·of·filename:·····························20·characters	97	··length·of·filename:·····························20·characters
98	··length·of·extra·field:··························0·bytes	98	··length·of·extra·field:··························0·bytes
99	··length·of·file·comment:·························0·characters	99	··length·of·file·comment:·························0·characters
100	··disk·number·on·which·file·begins:···············disk·1	100	··disk·number·on·which·file·begins:···············disk·1
101	··apparent·file·type:·····························binary	101	··apparent·file·type:·····························binary


Offset 1, 8 lines modified		Offset 1, 8 lines modified
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Offset 1, 4 lines modified		Offset 1, 4 lines modified
1	org/openscience/cdk/config/atomtypes/OWLAtomTypeMappingHandler.java
2	org/openscience/cdk/config/atomtypes/OWLAtomTypeMappingReader.java
3	org/openscience/cdk/atomtype/SybylAtomTypeMatcher.java	1	org/openscience/cdk/atomtype/SybylAtomTypeMatcher.java
4	org/openscience/cdk/atomtype/mapper/AtomTypeMapper.java	2	org/openscience/cdk/atomtype/mapper/AtomTypeMapper.java
		3	org/openscience/cdk/config/atomtypes/OWLAtomTypeMappingHandler.java
		4	org/openscience/cdk/config/atomtypes/OWLAtomTypeMappingReader.java


Offset 1, 8 lines modified		Offset 1, 8 lines modified
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17	drwxr-xr-x··2.0·unx········0·b-·stor·18-Mar-30·20:15·org/openscience/cdk/qsar/	17	drwxr-xr-x··2.0·unx········0·b-·stor·18-Mar-30·20:15·org/openscience/cdk/qsar/
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20	-rw-r--r--··2.0·unx·····5244·b-·defN·18-Mar-30·20:15·org/openscience/cdk/qsar/descriptors/atomic/PartialTChargeMMFF94Descriptor.class	20	-rw-r--r--··2.0·unx·····5244·b-·defN·18-Mar-30·20:15·org/openscience/cdk/qsar/descriptors/atomic/PartialTChargeMMFF94Descriptor.class
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Offset 1, 5 lines modified		Offset 1, 5 lines modified
1	org/openscience/cdk/qsar/descriptors/atomic/PartialTChargeMMFF94Descriptor.java	1	org/openscience/cdk/qsar/descriptors/atomic/PartialTChargeMMFF94Descriptor.java
2	org/openscience/cdk/modeling/builder3d/TemplateHandler3D.java
3	org/openscience/cdk/modeling/builder3d/ModelBuilder3D.java	2	org/openscience/cdk/modeling/builder3d/ModelBuilder3D.java
4	org/openscience/cdk/modeling/builder3d/~~Atom~~Te~~trahedr~~al~~Lig~~andPlacer3D.java	3	org/openscience/cdk/modeling/builder3d/TemplateHandler3D.java
5	org/openscience/cdk/modeling/builder3d/AtomPlacer3D.java	4	org/openscience/cdk/modeling/builder3d/AtomPlacer3D.java
		5	org/openscience/cdk/modeling/builder3d/AtomTetrahedralLigandPlacer3D.java


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1	org/openscience/cdk/charges/IChargeCalculator.java	1	org/openscience/cdk/charges/IChargeCalculator.java
2	org/openscience/cdk/charges/AtomTypeCharges.java
3	org/openscience/cdk/charges/Electronegativity.java	2	org/openscience/cdk/charges/Electronegativity.java
		3	org/openscience/cdk/charges/InductivePartialCharges.java
		4	org/openscience/cdk/charges/GasteigerMarsiliPartialCharges.java
4	org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java	5	org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java
5	org/openscience/cdk/charges/StabilizationCharges.java	6	org/openscience/cdk/charges/StabilizationCharges.java
6	org/openscience/cdk/charges/~~Indu~~ctiveParti~~alCharges~~.java	7	org/openscience/cdk/charges/PiElectronegativity.java
7	org/openscience/cdk/charges/IElectronicPropertyCalculator.java	8	org/openscience/cdk/charges/IElectronicPropertyCalculator.java
8	org/openscience/cdk/charges/Gast~~eigerMarsiliPartial~~Charges.java	9	org/openscience/cdk/charges/AtomTypeCharges.java
9	org/openscience/cdk/charges/Polarizability.java	10	org/openscience/cdk/charges/Polarizability.java
10	org/openscience/cdk/charges/PiElectronegativity.java


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1	org/openscience/cdk/controller/IMouseEventRelay.java
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Offset 1, 25 lines modified		Offset 1, 25 lines modified
		1	org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
		2	org/openscience/cdk/atomtype/IAtomTypeMatcher.java
		3	org/openscience/cdk/atomtype/IAtomTypeGuesser.java
1	org/openscience/cdk/fingerprint/IFingerprinter.java	4	org/openscience/cdk/fingerprint/IFingerprinter.java
2	org/openscience/cdk/~~exception/~~CDK~~Exception~~.java	5	org/openscience/cdk/CDKConstants.java
3	org/openscience/cdk/~~exceptio~~n~~/NoSuchAt~~o~~mExce~~ption.java	6	org/openscience/cdk/tools/manipulator/BondManipulator.java
4	org/openscience/cdk/~~excep~~tio~~n/N~~oSu~~chAt~~o~~mTypeExcepti~~on.java	7	org/openscience/cdk/tools/LoggingTool.java
5	org/openscience/cdk/config/AtomTypeFactory.java
6	org/openscience/cdk/config/IsotopeFactory.java
7	org/openscience/cdk/config/atomtypes/AtomTypeHandler.java	8	org/openscience/cdk/config/atomtypes/AtomTypeHandler.java
8	org/openscience/cdk/config/atomtypes/OWLAtomTypeHandler.java
9	org/openscience/cdk/config/atomtypes/AtomTypeReader.java
10	org/openscience/cdk/config/atomtypes/OWLAtomTypeReader.java	9	org/openscience/cdk/config/atomtypes/OWLAtomTypeReader.java
11	org/openscience/cdk/config/isotopes/IsotopeReader.java	10	org/openscience/cdk/config/atomtypes/AtomTypeReader.java
12	org/openscience/cdk/config/isotopes/~~Iso~~topeHandler.java	11	org/openscience/cdk/config/atomtypes/OWLAtomTypeHandler.java
13	org/openscience/cdk/config/CDKBasedAtomTypeConfigurator.java	12	org/openscience/cdk/config/CDKBasedAtomTypeConfigurator.java
		13	org/openscience/cdk/config/OWLBasedAtomTypeConfigurator.java
		14	org/openscience/cdk/config/IsotopeFactory.java
		15	org/openscience/cdk/config/isotopes/IsotopeHandler.java
		16	org/openscience/cdk/config/isotopes/IsotopeReader.java
14	org/openscience/cdk/config/TXTBasedAtomTypeConfigurator.java	17	org/openscience/cdk/config/TXTBasedAtomTypeConfigurator.java
		18	org/openscience/cdk/config/AtomTypeFactory.java
15	org/openscience/cdk/config/IAtomTypeConfigurator.java	19	org/openscience/cdk/config/IAtomTypeConfigurator.java
16	org/openscience/cdk/config/OWLBasedAtomTypeConfigurator.java
17	org/openscience/cdk/tools/manipulator/BondManipulator.java
18	org/openscience/cdk/tools/LoggingTool.java
19	org/openscience/cdk/atomtype/IAtomTypeGuesser.java
20	org/openscience/cdk/atomtype/IAtomTypeMatcher.java
21	org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
22	org/openscience/cdk/graph/matrix/AdjacencyMatrix.java
23	org/openscience/cdk/graph/PathTools.java	20	org/openscience/cdk/graph/PathTools.java
24	org/openscience/cdk/graph/SpanningTree.java	21	org/openscience/cdk/graph/SpanningTree.java
25	org/openscience/cdk/~~CDKCons~~tants.java	22	org/openscience/cdk/graph/matrix/AdjacencyMatrix.java
		23	org/openscience/cdk/exception/NoSuchAtomTypeException.java
		24	org/openscience/cdk/exception/NoSuchAtomException.java
		25	org/openscience/cdk/exception/CDKException.java


Offset 1, 41 lines modified		Offset 1, 41 lines modified
1	org/openscience/cdk/DefaultChemObjectBuilder.java
2	org/openscience/cdk/AtomParity.java
3	org/openscience/cdk/Molecule.java
4	org/openscience/cdk/ChemFile.java
5	org/openscience/cdk/Reaction.java
6	org/openscience/cdk/MoleculeSet.java
7	org/openscience/cdk/formula/MolecularFormulaSet.java
8	org/openscience/cdk/formula/MolecularFormula.java
9	org/openscience/cdk/formula/AdductFormula.java
10	org/openscience/cdk/Ring.java	1	org/openscience/cdk/Ring.java
11	org/openscience/cdk/~~PseudoAtom~~.java	2	org/openscience/cdk/Mapping.java
		3	org/openscience/cdk/AtomType.java
		4	org/openscience/cdk/AtomContainer.java
		5	org/openscience/cdk/ChemModel.java
12	org/openscience/cdk/Strand.java	6	org/openscience/cdk/Strand.java
13	org/openscience/cdk/SingleElectron.java
14	org/openscience/cdk/event/ChemObjectChangeEvent.java	7	org/openscience/cdk/event/ChemObjectChangeEvent.java
15	org/openscience/cdk/~~Electron~~C~~onta~~iner.java	8	org/openscience/cdk/ChemFile.java
16	org/openscience/cdk/Fr~~agm~~ent~~Atom~~.java	9	org/openscience/cdk/Molecule.java
17	org/openscience/cdk/LonePair.java
18	org/openscience/cdk/protein/data/PDBPolymer.java
19	org/openscience/cdk/protein/data/PDBAtom.java
20	org/openscience/cdk/protein/data/PDBMonomer.java
21	org/openscience/cdk/protein/data/PDBStructure.java
22	org/openscience/cdk/AtomContainerSet.java
23	org/openscience/cdk/Atom.java
24	org/openscience/cdk/AminoAcid.java
25	org/openscience/cdk/BioPolymer.java	10	org/openscience/cdk/BioPolymer.java
26	org/openscience/cdk/Monomer.java	11	org/openscience/cdk/Monomer.java
27	org/openscience/cdk/Element.java	12	org/openscience/cdk/ElectronContainer.java
28	org/openscience/cdk/ReactionSet.java
29	org/openscience/cdk/ReactionScheme.java	13	org/openscience/cdk/ReactionScheme.java
		14	org/openscience/cdk/formula/MolecularFormula.java
		15	org/openscience/cdk/formula/AdductFormula.java
		16	org/openscience/cdk/formula/MolecularFormulaSet.java
30	org/openscience/cdk/Crystal.java	17	org/openscience/cdk/Crystal.java
		18	org/openscience/cdk/Atom.java
		19	org/openscience/cdk/AtomParity.java


Offset 1, 8 lines modified		Offset 1, 8 lines modified
1	org/openscience/cdk/dict/OWLFile.java
2	org/openscience/cdk/dict/OWLReact.java
3	org/openscience/cdk/dict/CDKDictionaryReferences.java
4	org/openscience/cdk/dict/Dictionary.java	1	org/openscience/cdk/dict/Dictionary.java
5	org/openscience/cdk/dict/DictionaryDatabase.java
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7	org/openscience/cdk/dict/DictionaryHandler.java
8	org/openscience/cdk/dict/EntryReact.java	3	org/openscience/cdk/dict/EntryReact.java
		4	org/openscience/cdk/dict/OWLFile.java
		5	org/openscience/cdk/dict/DictionaryDatabase.java
		6	org/openscience/cdk/dict/DictionaryHandler.java
		7	org/openscience/cdk/dict/OWLReact.java
		8	org/openscience/cdk/dict/CDKDictionaryReferences.java


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1	org/openscience/cdk/tools/diff/AtomContainerDiff.java
2	org/openscience/cdk/tools/diff/IsotopeDiff.java
3	org/openscience/cdk/tools/diff/LonePairDiff.java
4	org/openscience/cdk/tools/diff/SingleElectronDiff.java	1	org/openscience/cdk/tools/diff/SingleElectronDiff.java
		2	org/openscience/cdk/tools/diff/AtomDiff.java
5	org/openscience/cdk/tools/diff/AtomTypeDiff.java	3	org/openscience/cdk/tools/diff/AtomTypeDiff.java
6	org/openscience/cdk/tools/diff/~~Electro~~nContainerDiff.java	4	org/openscience/cdk/tools/diff/IsotopeDiff.java
		5	org/openscience/cdk/tools/diff/AtomContainerDiff.java
		6	org/openscience/cdk/tools/diff/ChemObjectDiff.java
		7	org/openscience/cdk/tools/diff/ElementDiff.java
		8	org/openscience/cdk/tools/diff/LonePairDiff.java
7	org/openscience/cdk/tools/diff/BondDiff.java	9	org/openscience/cdk/tools/diff/BondDiff.java
8	org/openscience/cdk/tools/diff/tree/IntegerDifference.java
9	org/openscience/cdk/tools/diff/tree/DoubleDifference.java
10	org/openscience/cdk/tools/diff/tree/AtomTypeHybridizationDifference.java
11	org/openscience/cdk/tools/diff/tree/BooleanDifference.java
12	org/openscience/cdk/tools/diff/tree/Point3dDifference.java
13	org/openscience/cdk/tools/diff/tree/StringDifference.java	10	org/openscience/cdk/tools/diff/tree/StringDifference.java
14	org/openscience/cdk/tools/diff/tree/BondOrderDifference.java	11	org/openscience/cdk/tools/diff/tree/BondOrderDifference.java
		12	org/openscience/cdk/tools/diff/tree/AtomTypeHybridizationDifference.java
		13	org/openscience/cdk/tools/diff/tree/BooleanArrayDifference.java
15	org/openscience/cdk/tools/diff/tree/AbstractDifferenceList.java	14	org/openscience/cdk/tools/diff/tree/AbstractDifferenceList.java
16	org/openscience/cdk/tools/diff/tree/Ch~~emO~~bjectDifference.java	15	org/openscience/cdk/tools/diff/tree/DoubleDifference.java
		16	org/openscience/cdk/tools/diff/tree/IntegerDifference.java
17	org/openscience/cdk/tools/diff/tree/IDifference.java	17	org/openscience/cdk/tools/diff/tree/IDifference.java
18	org/openscience/cdk/tools/diff/tree/Point2dDifference.java	18	org/openscience/cdk/tools/diff/tree/Point2dDifference.java
19	org/openscience/cdk/tools/diff/tree/IDifferenceList.java	19	org/openscience/cdk/tools/diff/tree/IDifferenceList.java
20	org/openscience/cdk/tools/diff/tree/Boolean~~Array~~Difference.java	20	org/openscience/cdk/tools/diff/tree/BooleanDifference.java
21	org/openscience/cdk/tools/diff/tree/AbstractDifference.java	21	org/openscience/cdk/tools/diff/tree/AbstractDifference.java
22	org/openscience/cdk/tools/diff/ElementDiff.java	22	org/openscience/cdk/tools/diff/tree/ChemObjectDifference.java
23	org/openscience/cdk/tools/diff/AtomDiff.java	23	org/openscience/cdk/tools/diff/tree/Point3dDifference.java
24	org/openscience/cdk/tools/diff/Che~~mObjec~~tDiff.java	24	org/openscience/cdk/tools/diff/ElectronContainerDiff.java


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120	-rw-r--r--··2.0·unx·····2176·b-·defN·18-Mar-30·20:15·org/openscience/cdk/validate/CDKValidator.class	120	-rw-r--r--··2.0·unx·····2176·b-·defN·18-Mar-30·20:15·org/openscience/cdk/validate/CDKValidator.class
121	-rw-r--r--··2.0·unx·····3916·b-·defN·18-Mar-30·20:15·org/openscience/cdk/validate/DictionaryValidator.class	121	-rw-r--r--··2.0·unx·····3916·b-·defN·18-Mar-30·20:15·org/openscience/cdk/validate/DictionaryValidator.class
122	-rw-r--r--··2.0·unx·····1588·b-·defN·18-Mar-30·20:15·org/openscience/cdk/validate/Geometry3DValidator.class	122	-rw-r--r--··2.0·unx·····1588·b-·defN·18-Mar-30·20:15·org/openscience/cdk/validate/Geometry3DValidator.class
123	-rw-r--r--··2.0·unx·····2098·b-·defN·18-Mar-30·20:15·org/openscience/cdk/validate/IValidator.class	123	-rw-r--r--··2.0·unx·····2098·b-·defN·18-Mar-30·20:15·org/openscience/cdk/validate/IValidator.class
124	-rw-r--r--··2.0·unx·····2339·b-·defN·18-Mar-30·20:15·org/openscience/cdk/validate/ValidationReport.class	124	-rw-r--r--··2.0·unx·····2339·b-·defN·18-Mar-30·20:15·org/openscience/cdk/validate/ValidationReport.class
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126	-rw-r--r--··2.0·unx····11581·b-·defN·18-Mar-30·20:15·org/openscience/cdk/validate/ValidatorEngine.class	126	-rw-r--r--··2.0·unx····11581·b-·defN·18-Mar-30·20:15·org/openscience/cdk/validate/ValidatorEngine.class
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Offset 1, 79 lines modified		Offset 1, 79 lines modified
1	org/openscience/cdk/io/INChIPlainTextReader.java
2	org/openscience/cdk/io/inchi/INChIContentProcessorTool.java
3	org/openscience/cdk/io/inchi/INChIHandler.java
4	org/openscience/cdk/io/CrystClustWriter.java
5	org/openscience/cdk/io/INChIReader.java
6	org/openscience/cdk/io/ShelXWriter.java
7	org/openscience/cdk/io/GamessReader.java
8	org/openscience/cdk/io/CrystClustReader.java
9	org/openscience/cdk/io/ZMatrixReader.java
10	org/openscience/cdk/io/VASPReader.java
11	org/openscience/cdk/io/iterator/IteratingMDLConformerReader.java
12	org/openscience/cdk/structgen/RandomGenerator.java
13	org/openscience/cdk/exception/IncorrectUseOfCDKCoreClassError.java
14	org/openscience/cdk/validate/DictionaryValidator.java
15	org/openscience/cdk/validate/Geometry3DValidator.java
16	org/openscience/cdk/validate/ValidationTest.java	1	org/openscience/cdk/validate/ValidationTest.java
17	org/openscience/cdk/validate/~~CDK~~Validator.java	2	org/openscience/cdk/validate/Geometry3DValidator.java
18	org/openscience/cdk/validate/ValidationReport.java
19	org/openscience/cdk/validate/ValidatorEngine.java	3	org/openscience/cdk/validate/ValidatorEngine.java
20	org/openscience/cdk/validate/IValidator.java	4	org/openscience/cdk/validate/CDKValidator.java
21	org/openscience/cdk/validate/BasicValidator.java	5	org/openscience/cdk/validate/BasicValidator.java
22	org/openscience/cdk/validate/AbstractValidator.java	6	org/openscience/cdk/validate/AbstractValidator.java
		7	org/openscience/cdk/validate/DictionaryValidator.java
		8	org/openscience/cdk/validate/ValidationReport.java
		9	org/openscience/cdk/validate/IValidator.java
		10	org/openscience/cdk/atomtype/MM2AtomTypeMatcher.java
		11	org/openscience/cdk/atomtype/MMFF94AtomTypeMatcher.java
23	org/openscience/cdk/Vibration.java	12	org/openscience/cdk/Vibration.java
24	org/openscience/cdk/~~prote~~in~~/Pro~~te~~inPocketFind~~er.java	13	org/openscience/cdk/index/CASNumber.java
25	org/openscience/cdk/En~~zymeRes~~idue~~Locato~~r.java	14	org/openscience/cdk/ringsearch/FiguerasSSSRFinder.java
26	org/openscience/cdk/co~~nfig/~~Elemen~~tPTFac~~t~~ory~~.java	15	org/openscience/cdk/PeriodicTableElement.java
27	org/openscience/cdk/config/Elements.java
28	org/openscience/cdk/config/elements/ElementPTHandler.java
29	org/openscience/cdk/config/elements/ElementPTReader.java
30	org/openscience/cdk/geometry/RDFCalculator.java
31	org/openscience/cdk/geometry/AtomTools.java
32	org/openscience/cdk/geometry/IRDFWeightFunction.java
33	org/openscience/cdk/geometry/surface/NumericalSurface.java
34	org/openscience/cdk/geometry/surface/Tessellate.java
35	org/openscience/cdk/geometry/surface/Triangle.java
36	org/openscience/cdk/geometry/surface/NeighborList.java
37	org/openscience/cdk/geometry/alignment/KabschAlignment.java	16	org/openscience/cdk/geometry/alignment/KabschAlignment.java
38	org/openscience/cdk/geometry/Projector.java	17	org/openscience/cdk/geometry/Projector.java
39	org/openscience/cdk/Per~~iodicT~~able~~Elemen~~t.java	18	org/openscience/cdk/geometry/surface/NeighborList.java
40	org/openscience/cdk/~~ind~~ex/~~CASNumbe~~r.java	19	org/openscience/cdk/geometry/surface/Triangle.java
41	org/openscience/cdk/t~~ool~~s/~~SwissArmyKni~~fe.java	20	org/openscience/cdk/geometry/surface/NumericalSurface.java
		21	org/openscience/cdk/geometry/surface/Tessellate.java
		22	org/openscience/cdk/geometry/RDFCalculator.java
		23	org/openscience/cdk/geometry/IRDFWeightFunction.java
		24	org/openscience/cdk/geometry/AtomTools.java
		25	org/openscience/cdk/modeling/forcefield/ForceFieldTools.java
		26	org/openscience/cdk/iupac/parser/Token.java
		27	org/openscience/cdk/iupac/parser/AttachedGroup.java
		28	org/openscience/cdk/iupac/parser/TokenMgrError.java
		29	org/openscience/cdk/iupac/parser/MoleculeBuilder.java
		30	org/openscience/cdk/iupac/parser/ParseException.java
		31	org/openscience/cdk/iupac/parser/NomParser.java
		32	org/openscience/cdk/iupac/parser/NomParserConstants.java
		33	org/openscience/cdk/iupac/parser/NomParserTokenManager.java
		34	org/openscience/cdk/iupac/parser/SimpleCharStream.java
		35	org/openscience/cdk/EnzymeResidueLocator.java
42	org/openscience/cdk/tools/BremserOneSphereHOSECodePredictor.java	36	org/openscience/cdk/tools/BremserOneSphereHOSECodePredictor.java
43	org/openscience/cdk/tools/PeriodicTable.java
44	org/openscience/cdk/tools/DeAromatizationTool.java
45	org/openscience/cdk/tools/GridGenerator.java
46	org/openscience/cdk/tools/DataFeaturesTool.java
47	org/openscience/cdk/tools/features/MoleculeFeaturesTool.java	37	org/openscience/cdk/tools/features/MoleculeFeaturesTool.java
48	org/openscience/cdk/tools/~~GenerateF~~r~~agments~~.java	38	org/openscience/cdk/tools/SwissArmyKnife.java
49	org/openscience/cdk/tools/HOSECodeAnalyser.java	39	org/openscience/cdk/tools/HOSECodeAnalyser.java
50	org/openscience/cdk/tools/CD~~KUtili~~ties.java	40	org/openscience/cdk/tools/DataFeaturesTool.java
51	org/openscience/cdk/tools/~~AtomTyp~~e~~Tools~~.java	41	org/openscience/cdk/tools/GridGenerator.java
52	org/openscience/cdk/tools/FixedSizeStack.java	42	org/openscience/cdk/tools/FixedSizeStack.java
		43	org/openscience/cdk/tools/PeriodicTable.java
		44	org/openscience/cdk/tools/AtomTypeTools.java
		45	org/openscience/cdk/tools/CDKUtilities.java
		46	org/openscience/cdk/tools/GenerateFragments.java
		47	org/openscience/cdk/tools/DeAromatizationTool.java
		48	org/openscience/cdk/PhysicalConstants.java
		49	org/openscience/cdk/structgen/RandomGenerator.java
53	org/openscience/cdk/Association.java	50	org/openscience/cdk/Association.java
54	org/openscience/cdk/atomtype~~/MMFF94At~~o~~mTypeMatch~~er.java	51	org/openscience/cdk/templates/saturatedhydrocarbons/IsoAlkanes.java
55	org/openscience/cdk/atom~~typ~~e~~/M~~M2A~~tomTyp~~eMatcher.java	52	org/openscience/cdk/templates/MoleculeFactory.java
56	org/openscience/cdk/~~gra~~p~~h/~~matrix/To~~pologi~~c~~alMatrix~~.java	53	org/openscience/cdk/protein/ProteinPocketFinder.java
57	org/openscience/cdk/~~graph/Atom~~Contai~~nerP~~erm~~utor~~.java	54	org/openscience/cdk/config/Elements.java
58	org/openscience/cdk/~~graph~~/~~Ato~~mCont~~ain~~e~~rAtomPermuto~~r.java	55	org/openscience/cdk/config/elements/ElementPTHandler.java
		56	org/openscience/cdk/config/elements/ElementPTReader.java
		57	org/openscience/cdk/config/ElementPTFactory.java
59	org/openscience/cdk/graph/invariant/GIMatrix.java	58	org/openscience/cdk/graph/invariant/GIMatrix.java
60	org/openscience/cdk/graph/invariant/HuLuIndexTool.java	59	org/openscience/cdk/graph/invariant/HuLuIndexTool.java
61	org/openscience/cdk/graph/invariant/exception/BadMatrixFormatException.java
62	org/openscience/cdk/graph/invariant/exception/IndexOutOfBoundsException.java	60	org/openscience/cdk/graph/invariant/exception/IndexOutOfBoundsException.java
		61	org/openscience/cdk/graph/invariant/exception/BadMatrixFormatException.java
63	org/openscience/cdk/graph/invariant/exception/MatrixNotInvertibleException.java	62	org/openscience/cdk/graph/invariant/exception/MatrixNotInvertibleException.java
64	org/openscience/cdk/graph/invariant/EquivalentClassPartitioner.java	63	org/openscience/cdk/graph/invariant/EquivalentClassPartitioner.java
		64	org/openscience/cdk/graph/AtomContainerAtomPermutor.java
65	org/openscience/cdk/graph/AtomContainerBondPermutor.java	65	org/openscience/cdk/graph/AtomContainerBondPermutor.java
66	org/openscience/cdk/iupac~~/parser/At~~tachedGroup.java	66	org/openscience/cdk/graph/AtomContainerPermutor.java
67	org/openscience/cdk/~~iupac~~/pa~~rser~~/No~~mParserToken~~Man~~ager~~.java	67	org/openscience/cdk/graph/matrix/TopologicalMatrix.java
68	org/openscience/cdk/iupac/parse~~r/N~~omParser.java	68	org/openscience/cdk/exception/IncorrectUseOfCDKCoreClassError.java
69	org/openscience/cdk/i~~upa~~c/~~parser/S~~impleC~~harStr~~eam.java	69	org/openscience/cdk/io/INChIPlainTextReader.java
70	org/openscience/cdk/i~~upac/parse~~r/Mo~~lecul~~e~~Bui~~lder.java	70	org/openscience/cdk/io/VASPReader.java
71	org/openscience/cdk/i~~upac/p~~arser/~~NomP~~a~~rser~~Consta~~nts~~.java	71	org/openscience/cdk/io/iterator/IteratingMDLConformerReader.java
72	org/openscience/cdk/i~~upac/parse~~r/Toke~~nMg~~rE~~rro~~r.java	72	org/openscience/cdk/io/ShelXWriter.java
73	org/openscience/cdk/i~~upa~~c/parse~~r/Par~~seExcep~~tion~~.java	73	org/openscience/cdk/io/GamessReader.java
74	org/openscience/cdk/i~~upac/parser/Tok~~en.java	74	org/openscience/cdk/io/CrystClustReader.java
75	org/openscience/cdk/ri~~ngse~~a~~rch/F~~iguera~~sSSSRFin~~der.java	75	org/openscience/cdk/io/ZMatrixReader.java
76	org/openscience/cdk/~~Physical~~Constants.java	76	org/openscience/cdk/io/CrystClustWriter.java
77	org/openscience/cdk/t~~emplates~~/~~MoleculeF~~a~~ctory~~.java	77	org/openscience/cdk/io/inchi/INChIHandler.java
78	org/openscience/cdk/~~templates/satura~~ted~~hyd~~roc~~arbo~~ns~~/I~~soAl~~kanes~~.java	78	org/openscience/cdk/io/inchi/INChIContentProcessorTool.java
79	org/openscience/cdk/~~model~~i~~ng/f~~o~~rcefield~~/F~~orceFi~~eld~~Too~~ls.java	79	org/openscience/cdk/io/INChIReader.java


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		1	org/openscience/cdk/similarity/DistanceMoment.java
		2	org/openscience/cdk/similarity/Tanimoto.java
		3	org/openscience/cdk/fingerprint/ExtendedFingerprinter.java
		4	org/openscience/cdk/fingerprint/MACCSFingerprinter.java
1	org/openscience/cdk/fingerprint/EStateFingerprinter.java	5	org/openscience/cdk/fingerprint/EStateFingerprinter.java
2	org/openscience/cdk/fingerprint/SubstructureFingerprinter.java
3	org/openscience/cdk/fingerprint/StandardSubstructureSets.java	6	org/openscience/cdk/fingerprint/StandardSubstructureSets.java
4	org/openscience/cdk/fingerprint/~~MACCS~~Fingerprinter.java	7	org/openscience/cdk/fingerprint/SubstructureFingerprinter.java
5	org/openscience/cdk/fingerprint/ExtendedFingerprinter.java
6	org/openscience/cdk/similarity/Tanimoto.java
7	org/openscience/cdk/similarity/DistanceMoment.java


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1	org/openscience/cdk/~~char~~g~~es/MMFF94Part~~i~~alCh~~arges.java	1	org/openscience/cdk/modeling/forcefield/LineSearch.java
		2	org/openscience/cdk/modeling/forcefield/ElectrostaticInteractions.java
		3	org/openscience/cdk/modeling/forcefield/ForceField.java
2	org/openscience/cdk/modeling/forcefield/BondStretching.java	4	org/openscience/cdk/modeling/forcefield/BondStretching.java
		5	org/openscience/cdk/modeling/forcefield/NewtonRaphsonMethod.java
3	org/openscience/cdk/modeling/forcefield/Torsions.java	6	org/openscience/cdk/modeling/forcefield/Torsions.java
4	org/openscience/cdk/modeling/forcefield/Geometri~~cMi~~nimi~~zer~~.java	7	org/openscience/cdk/modeling/forcefield/SmoothingFunctions.java
5	org/openscience/cdk/modeling/forcefield/ForceField.java
6	org/openscience/cdk/modeling/forcefield/StretchBendInteractions.java
7	org/openscience/cdk/modeling/forcefield/AngleBending.java
8	org/openscience/cdk/modeling/forcefield/SteepestDescentsMethod.java
9	org/openscience/cdk/modeling/forcefield/ElectrostaticInteractions.java
10	org/openscience/cdk/modeling/forcefield/MMFF94EnergyFunction.java
11	org/openscience/cdk/modeling/forcefield/LineSearch.java
12	org/openscience/cdk/modeling/forcefield/VanDerWaalsInteractions.java	8	org/openscience/cdk/modeling/forcefield/VanDerWaalsInteractions.java
13	org/openscience/cdk/modeling/forcefield/IPotentialFunction.java
14	org/openscience/cdk/modeling/forcefield/NewtonRaphsonMethod.java
15	org/openscience/cdk/modeling/forcefield/LineSearchForTheWolfeConditions.java	9	org/openscience/cdk/modeling/forcefield/LineSearchForTheWolfeConditions.java
16	org/openscience/cdk/modeling/forcefield/SmoothingFunctions.java
17	org/openscience/cdk/modeling/forcefield/ConjugateGradientMethod.java	10	org/openscience/cdk/modeling/forcefield/ConjugateGradientMethod.java
18	org/openscience/cdk/modeling/~~buil~~der~~3d/MM2Base~~d~~Para~~met~~erSetRead~~er.java	11	org/openscience/cdk/modeling/forcefield/GeometricMinimizer.java
19	org/openscience/cdk/modeling/~~builder3~~d/MMFF94~~ParametersCall~~.java	12	org/openscience/cdk/modeling/forcefield/MMFF94EnergyFunction.java
		13	org/openscience/cdk/modeling/forcefield/AngleBending.java
		14	org/openscience/cdk/modeling/forcefield/StretchBendInteractions.java
		15	org/openscience/cdk/modeling/forcefield/IPotentialFunction.java
		16	org/openscience/cdk/modeling/forcefield/SteepestDescentsMethod.java
20	org/openscience/cdk/modeling/builder3d/MMFF94BasedAtomTypePattern.java	17	org/openscience/cdk/modeling/builder3d/MMFF94BasedAtomTypePattern.java
		18	org/openscience/cdk/modeling/builder3d/MM2BasedParameterSetReader.java
		19	org/openscience/cdk/modeling/builder3d/MM2BasedAtomTypePattern.java
21	org/openscience/cdk/modeling/builder3d/MMFF94BasedParameterSetReader.java	20	org/openscience/cdk/modeling/builder3d/MMFF94BasedParameterSetReader.java
22	org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java	21	org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java
23	org/openscience/cdk/modeling/builder3d/MM2~~BasedAto~~mTypeP~~attern~~.java	22	org/openscience/cdk/modeling/builder3d/MMFF94ParametersCall.java
		23	org/openscience/cdk/charges/MMFF94PartialCharges.java


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1	org/openscience/cdk/formula/MolecularFormulaRange.java
2	org/openscience/cdk/formula/IsotopeContainer.java	1	org/openscience/cdk/formula/IsotopeContainer.java
3	org/openscience/cdk/formula/MassToFormulaTool.java
4	org/openscience/cdk/formula/IsotopePatternSimilarity.java
5	org/openscience/cdk/formula/IsotopePatternGenerator.java
6	org/openscience/cdk/formula/IsotopePatternManipulator.java
7	org/openscience/cdk/formula/IsotopePattern.java	2	org/openscience/cdk/formula/IsotopePattern.java
8	org/openscience/cdk/formula/~~rul~~e~~s/Cha~~r~~geR~~ule.java	3	org/openscience/cdk/formula/IsotopePatternManipulator.java
9	org/openscience/cdk/formula/rules/Toleran~~ceR~~ang~~eRu~~le.java	4	org/openscience/cdk/formula/MassToFormulaTool.java
10	org/openscience/cdk/formula/rules/ElementRule.java
11	org/openscience/cdk/formula/rules/IRule.java	5	org/openscience/cdk/formula/rules/IRule.java
12	org/openscience/cdk/formula/rules/Isot~~opePatt~~ernRule.java	6	org/openscience/cdk/formula/rules/NitrogenRule.java
13	org/openscience/cdk/formula/rules/MMElementRule.java	7	org/openscience/cdk/formula/rules/MMElementRule.java
		8	org/openscience/cdk/formula/rules/IsotopePatternRule.java
14	org/openscience/cdk/formula/rules/RDBERule.java	9	org/openscience/cdk/formula/rules/RDBERule.java
15	org/openscience/cdk/formula/rules/~~Nit~~rogenRule.java	10	org/openscience/cdk/formula/rules/ToleranceRangeRule.java
		11	org/openscience/cdk/formula/rules/ChargeRule.java
		12	org/openscience/cdk/formula/rules/ElementRule.java
		13	org/openscience/cdk/formula/MolecularFormulaRange.java
		14	org/openscience/cdk/formula/IsotopePatternGenerator.java
		15	org/openscience/cdk/formula/IsotopePatternSimilarity.java
16	org/openscience/cdk/formula/MolecularFormulaChecker.java	16	org/openscience/cdk/formula/MolecularFormulaChecker.java
17	org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java	17	org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java
18	org/openscience/cdk/tools/manipulator/MolecularFormulaSetManipulator.java
19	org/openscience/cdk/tools/manipulator/MolecularFormulaRangeManipulator.java	18	org/openscience/cdk/tools/manipulator/MolecularFormulaRangeManipulator.java
		19	org/openscience/cdk/tools/manipulator/MolecularFormulaSetManipulator.java


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54	-rw-r--r--··2.0·unx······385·b-·defN·18-Mar-30·20:15·org/openscience/cdk/interfaces/ISingleElectron.class	54	-rw-r--r--··2.0·unx······385·b-·defN·18-Mar-30·20:15·org/openscience/cdk/interfaces/ISingleElectron.class
55	-rw-r--r--··2.0·unx······869·b-·defN·18-Mar-30·20:15·org/openscience/cdk/interfaces/IStrand.class	55	-rw-r--r--··2.0·unx······869·b-·defN·18-Mar-30·20:15·org/openscience/cdk/interfaces/IStrand.class
56	drwxr-xr-x··2.0·unx········0·b-·stor·18-Mar-30·20:15·org/openscience/cdk/isomorphism/	56	drwxr-xr-x··2.0·unx········0·b-·stor·18-Mar-30·20:15·org/openscience/cdk/isomorphism/
57	drwxr-xr-x··2.0·unx········0·b-·stor·18-Mar-30·20:15·org/openscience/cdk/isomorphism/matchers/	57	drwxr-xr-x··2.0·unx········0·b-·stor·18-Mar-30·20:15·org/openscience/cdk/isomorphism/matchers/
58	-rw-r--r--··2.0·unx······248·b-·defN·18-Mar-30·20:15·org/openscience/cdk/isomorphism/matchers/IQueryAtom.class	58	-rw-r--r--··2.0·unx······248·b-·defN·18-Mar-30·20:15·org/openscience/cdk/isomorphism/matchers/IQueryAtom.class
59	-rw-r--r--··2.0·unx······213·b-·defN·18-Mar-30·20:15·org/openscience/cdk/isomorphism/matchers/IQueryAtomContainer.class	59	-rw-r--r--··2.0·unx······213·b-·defN·18-Mar-30·20:15·org/openscience/cdk/isomorphism/matchers/IQueryAtomContainer.class
60	-rw-r--r--··2.0·unx······204·b-·defN·18-Mar-30·20:15·org/openscience/cdk/isomorphism/matchers/IQueryBond.class	60	-rw-r--r--··2.0·unx······204·b-·defN·18-Mar-30·20:15·org/openscience/cdk/isomorphism/matchers/IQueryBond.class
61	59·files,·44438·bytes·uncompressed,·16945·bytes·compressed:··61.9%	61	59·files,·44438·bytes·uncompressed,·16943·bytes·compressed:··61.9%


Offset 1, 45 lines modified		Offset 1, 45 lines modified
1	org/openscience/cdk/isomorphism/matchers/IQueryAtomContainer.java
2	org/openscience/cdk/isomorphism/matchers/IQueryAtom.java
3	org/openscience/cdk/isomorphism/matchers/IQueryBond.java
4	org/openscience/cdk/graph/matrix/IGraphMatrix.java
5	org/openscience/cdk/interfaces/IRingSet.java
6	org/openscience/cdk/interfaces/IReactionSet.java
7	org/openscience/cdk/interfaces/IMolecularFormulaSet.java
8	org/openscience/cdk/interfaces/IFragmentAtom.java
9	org/openscience/cdk/interfaces/IChemModel.java	1	org/openscience/cdk/interfaces/IChemModel.java
		2	org/openscience/cdk/interfaces/IMolecularFormula.java
		3	org/openscience/cdk/interfaces/IChemObject.java
		4	org/openscience/cdk/interfaces/IAminoAcid.java
10	org/openscience/cdk/interfaces/IRing.java	5	org/openscience/cdk/interfaces/IRing.java
11	org/openscience/cdk/interfaces/I~~React~~ionScheme.java	6	org/openscience/cdk/interfaces/IMonomer.java
		7	org/openscience/cdk/interfaces/IRingSet.java
		8	org/openscience/cdk/interfaces/IAtom.java
		9	org/openscience/cdk/interfaces/IAdductFormula.java
		10	org/openscience/cdk/interfaces/IMoleculeSet.java
		11	org/openscience/cdk/interfaces/IAtomContainerSet.java
		12	org/openscience/cdk/interfaces/IMolecularFormulaSet.java
		13	org/openscience/cdk/interfaces/ISingleElectron.java
		14	org/openscience/cdk/interfaces/IPDBAtom.java
		15	org/openscience/cdk/interfaces/IChemObjectBuilder.java
		16	org/openscience/cdk/interfaces/IReaction.java
		17	org/openscience/cdk/interfaces/IChemSequence.java
		18	org/openscience/cdk/interfaces/ICrystal.java
12	org/openscience/cdk/interfaces/IChemObjectListener.java	19	org/openscience/cdk/interfaces/IChemObjectListener.java
13	org/openscience/cdk/interfaces/I~~PseudoAtom~~.java	20	org/openscience/cdk/interfaces/IBioPolymer.java
14	org/openscience/cdk/interfaces/I~~ChemObj~~ect.java	21	org/openscience/cdk/interfaces/IMolecule.java
15	org/openscience/cdk/interfaces/IMo~~lecul~~a~~rFo~~r~~mula~~.java	22	org/openscience/cdk/interfaces/IAtomContainer.java
16	org/openscience/cdk/interfaces/I~~Iso~~tope.java	23	org/openscience/cdk/interfaces/IPDBStructure.java
17	org/openscience/cdk/interfaces/IChemObjectChangeEvent.java	24	org/openscience/cdk/interfaces/IChemObjectChangeEvent.java
18	org/openscience/cdk/interfaces/I~~Strand~~.java	25	org/openscience/cdk/interfaces/IPolymer.java
19	org/openscience/cdk/interfaces/I~~Rea~~ction.java	26	org/openscience/cdk/interfaces/IElectronContainer.java
		27	org/openscience/cdk/interfaces/IIsotope.java
20	org/openscience/cdk/interfaces/IAtomType.java	28	org/openscience/cdk/interfaces/IAtomType.java
21	org/openscience/cdk/interfaces/I~~Eleme~~nt.java	29	org/openscience/cdk/interfaces/IMapping.java
22	org/openscience/cdk/interfaces/IPDBStructure.java
23	org/openscience/cdk/interfaces/IChemObjectBuilder.java
24	org/openscience/cdk/interfaces/IAtomContainer.java
25	org/openscience/cdk/interfaces/IPDBAtom.java
26	org/openscience/cdk/interfaces/IBond.java	30	org/openscience/cdk/interfaces/IBond.java
27	org/openscience/cdk/interfaces/I~~Sing~~leElectron.java	31	org/openscience/cdk/interfaces/IReactionSet.java
28	org/openscience/cdk/interfaces/IChe~~mSequen~~ce.java	32	org/openscience/cdk/interfaces/IReactionScheme.java
		33	org/openscience/cdk/interfaces/IPseudoAtom.java
		34	org/openscience/cdk/interfaces/IPDBMonomer.java
		35	org/openscience/cdk/interfaces/ILonePair.java
29	org/openscience/cdk/interfaces/IAtomParity.java	36	org/openscience/cdk/interfaces/IAtomParity.java
30	org/openscience/cdk/interfaces/IAtom.java
31	org/openscience/cdk/interfaces/IPDBPolymer.java	37	org/openscience/cdk/interfaces/IPDBPolymer.java
		38	org/openscience/cdk/interfaces/IFragmentAtom.java
32	org/openscience/cdk/interfaces/IChemFile.java	39	org/openscience/cdk/interfaces/IChemFile.java
33	org/openscience/cdk/interfaces/I~~Mappi~~ng.java	40	org/openscience/cdk/interfaces/IElement.java
34	org/openscience/cdk/interfaces/ILo~~neP~~air.java	41	org/openscience/cdk/interfaces/IStrand.java
35	org/openscience/cdk/i~~nte~~rfaces/IMolec~~uleSet~~.java	42	org/openscience/cdk/isomorphism/matchers/IQueryAtom.java
36	org/openscience/cdk/i~~nte~~rfaces/I~~PDBM~~onomer.java	43	org/openscience/cdk/isomorphism/matchers/IQueryAtomContainer.java
37	org/openscience/cdk/i~~nte~~r~~faces~~/~~IElect~~r~~onContainer~~.java	44	org/openscience/cdk/isomorphism/matchers/IQueryBond.java
38	org/openscience/cdk/~~interf~~a~~ces~~/I~~Molecule~~.java	45	org/openscience/cdk/graph/matrix/IGraphMatrix.java
39	org/openscience/cdk/interfaces/IMonomer.java
40	org/openscience/cdk/interfaces/IPolymer.java
41	org/openscience/cdk/interfaces/IAtomContainerSet.java
42	org/openscience/cdk/interfaces/ICrystal.java
43	org/openscience/cdk/interfaces/IAdductFormula.java
44	org/openscience/cdk/interfaces/IBioPolymer.java
45	org/openscience/cdk/interfaces/IAminoAcid.java


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1	Zip·file·size:·515787·bytes,·number·of·entries:·105	1	Zip·file·size:·515774·bytes,·number·of·entries:·105
2	drwxr-xr-x··2.0·unx········0·bx·stor·18-Mar-30·20:15·META-INF/	2	drwxr-xr-x··2.0·unx········0·bx·stor·18-Mar-30·20:15·META-INF/
3	-rw-r--r--··2.0·unx······132·b-·defN·18-Mar-30·20:15·META-INF/MANIFEST.MF	3	-rw-r--r--··2.0·unx······132·b-·defN·18-Mar-30·20:15·META-INF/MANIFEST.MF
4	-rw-r--r--··2.0·unx·····3863·b-·defN·18-Mar-30·20:15·io.javafiles	4	-rw-r--r--··2.0·unx·····3863·b-·defN·18-Mar-30·20:15·io.javafiles
5	drwxr-xr-x··2.0·unx········0·b-·stor·18-Mar-30·20:15·org/	5	drwxr-xr-x··2.0·unx········0·b-·stor·18-Mar-30·20:15·org/
6	drwxr-xr-x··2.0·unx········0·b-·stor·18-Mar-30·20:15·org/openscience/	6	drwxr-xr-x··2.0·unx········0·b-·stor·18-Mar-30·20:15·org/openscience/
7	drwxr-xr-x··2.0·unx········0·b-·stor·18-Mar-30·20:15·org/openscience/cdk/	7	drwxr-xr-x··2.0·unx········0·b-·stor·18-Mar-30·20:15·org/openscience/cdk/
8	drwxr-xr-x··2.0·unx········0·b-·stor·18-Mar-30·20:15·org/openscience/cdk/geometry/	8	drwxr-xr-x··2.0·unx········0·b-·stor·18-Mar-30·20:15·org/openscience/cdk/geometry/
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100	-rw-r--r--··2.0·unx·····4047·b-·defN·18-Mar-30·20:15·org/openscience/cdk/io/random/RandomAccessSDFReader.class	100	-rw-r--r--··2.0·unx·····4047·b-·defN·18-Mar-30·20:15·org/openscience/cdk/io/random/RandomAccessSDFReader.class
101	drwxr-xr-x··2.0·unx········0·b-·stor·18-Mar-30·20:15·org/openscience/cdk/io/setting/	101	drwxr-xr-x··2.0·unx········0·b-·stor·18-Mar-30·20:15·org/openscience/cdk/io/setting/
102	-rw-r--r--··2.0·unx·····1321·b-·defN·18-Mar-30·20:15·org/openscience/cdk/io/setting/BooleanIOSetting.class	102	-rw-r--r--··2.0·unx·····1321·b-·defN·18-Mar-30·20:15·org/openscience/cdk/io/setting/BooleanIOSetting.class
103	-rw-r--r--··2.0·unx·····1293·b-·defN·18-Mar-30·20:15·org/openscience/cdk/io/setting/IOSetting.class	103	-rw-r--r--··2.0·unx·····1293·b-·defN·18-Mar-30·20:15·org/openscience/cdk/io/setting/IOSetting.class
104	-rw-r--r--··2.0·unx·····1331·b-·defN·18-Mar-30·20:15·org/openscience/cdk/io/setting/IntegerIOSetting.class	104	-rw-r--r--··2.0·unx·····1331·b-·defN·18-Mar-30·20:15·org/openscience/cdk/io/setting/IntegerIOSetting.class
105	-rw-r--r--··2.0·unx·····1985·b-·defN·18-Mar-30·20:15·org/openscience/cdk/io/setting/OptionIOSetting.class	105	-rw-r--r--··2.0·unx·····1985·b-·defN·18-Mar-30·20:15·org/openscience/cdk/io/setting/OptionIOSetting.class
106	-rw-r--r--··2.0·unx······732·b-·defN·18-Mar-30·20:15·org/openscience/cdk/io/setting/StringIOSetting.class	106	-rw-r--r--··2.0·unx······732·b-·defN·18-Mar-30·20:15·org/openscience/cdk/io/setting/StringIOSetting.class
107	105·files,·2254978·bytes·uncompressed,·498~~407~~·bytes·compressed:··77.9%	107	105·files,·2254978·bytes·uncompressed,·498394·bytes·compressed:··77.9%


Offset 1, 79 lines modified		Offset 1, 79 lines modified
1	org/openscience/cdk/io/~~PDBW~~ri~~ter~~.java	1	org/openscience/cdk/geometry/ZMatrixTools.java
2	org/openscience/cdk/io/Wri~~terFac~~t~~ory~~.java	2	org/openscience/cdk/io/setting/IOSetting.java
3	org/openscience/cdk/io/HINWriter.java	3	org/openscience/cdk/io/setting/IntegerIOSetting.java
		4	org/openscience/cdk/io/setting/StringIOSetting.java
		5	org/openscience/cdk/io/setting/OptionIOSetting.java
		6	org/openscience/cdk/io/setting/BooleanIOSetting.java
		7	org/openscience/cdk/io/CIFReader.java
		8	org/openscience/cdk/io/Gaussian03Reader.java
		9	org/openscience/cdk/io/MDLRXNV2000Reader.java
		10	org/openscience/cdk/io/IChemObjectWriter.java
		11	org/openscience/cdk/io/ReaderEvent.java
		12	org/openscience/cdk/io/MDLRXNReader.java
4	org/openscience/cdk/io/IChemObjectIO.java	13	org/openscience/cdk/io/IChemObjectIO.java
5	org/openscience/cdk/io/Defa~~ultC~~hemO~~bje~~ct~~Reader~~.java	14	org/openscience/cdk/io/ReaderFactory.java
6	org/openscience/cdk/io/~~MDLV2000~~Reader.java	15	org/openscience/cdk/io/PMPReader.java
7	org/openscience/cdk/io/MDL~~Writ~~er.java	16	org/openscience/cdk/io/MDLV3000Reader.java
8	org/openscience/cdk/io/~~SDFWr~~iter.java	17	org/openscience/cdk/io/Gaussian98Reader.java
9	org/openscience/cdk/io/XYZReader.java
10	org/openscience/cdk/io/MDLRXNWriter.java
11	org/openscience/cdk/io/MDLRXNV3000Reader.java
12	org/openscience/cdk/io/CDKSourceCodeWriter.java	18	org/openscience/cdk/io/CDKSourceCodeWriter.java
13	org/openscience/cdk/io/p~~rogram/Gaussi~~a~~nInputWri~~ter.java	19	org/openscience/cdk/io/MDLRXNV3000Reader.java
14	org/openscience/cdk/io/~~PCSubstance~~X~~MLRead~~er.java	20	org/openscience/cdk/io/XYZWriter.java
15	org/openscience/cdk/io/IChemObjectReader.java	21	org/openscience/cdk/io/DefaultChemObjectReader.java
16	org/openscience/cdk/io/ISimpleChemObjectReader.java
17	org/openscience/cdk/io/ReaderEvent.java
18	org/openscience/cdk/io/PCCompoundXMLReader.java
19	org/openscience/cdk/io/PCCompoundASNReader.java
20	org/openscience/cdk/io/random/IRandomAccessChemObjectReader.java	22	org/openscience/cdk/io/random/IRandomAccessChemObjectReader.java
21	org/openscience/cdk/io/random/RandomAccessReader.java
22	org/openscience/cdk/io/random/RandomAccessSDFReader.java
23	org/openscience/cdk/io/random/DefaultRandomAccessChemObjectReader.java	23	org/openscience/cdk/io/random/DefaultRandomAccessChemObjectReader.java
24	org/openscience/cdk/io/~~CTX~~Reader.java	24	org/openscience/cdk/io/random/RandomAccessSDFReader.java
25	org/openscience/cdk/io/Mol2Reader.java	25	org/openscience/cdk/io/random/RandomAccessReader.java
26	org/openscience/cdk/io/De~~fau~~ltChem~~ObjectWrit~~er.java	26	org/openscience/cdk/io/pubchemxml/PubChemXMLHelper.java
27	org/openscience/cdk/io/~~HIN~~Reader.java	27	org/openscience/cdk/io/IChemObjectReader.java
28	org/openscience/cdk/io/~~IChe~~m~~Objec~~tWriter.java	28	org/openscience/cdk/io/program/GaussianInputWriter.java
29	org/openscience/cdk/io/Sh~~elX~~Reader.java	29	org/openscience/cdk/io/XYZReader.java
30	org/openscience/cdk/io/CI~~FRead~~er.java	30	org/openscience/cdk/io/listener/TextGUIListener.java
31	org/openscience/cdk/io/~~MDLRXN~~Reader.java	31	org/openscience/cdk/io/listener/IReaderListener.java
32	org/openscience/cdk/io/CML~~Read~~er.java	32	org/openscience/cdk/io/listener/SwingGUIListener.java
33	org/openscience/cdk/io/setting/OptionIOSetting.java
34	org/openscience/cdk/io/setting/BooleanIOSetting.java
35	org/openscience/cdk/io/setting/StringIOSetting.java
36	org/openscience/cdk/io/setting/IntegerIOSetting.java
37	org/openscience/cdk/io/setting/IOSetting.java
38	org/openscience/cdk/io/ReaderFactory.java
39	org/openscience/cdk/io/listener/IWriterListener.java	33	org/openscience/cdk/io/listener/IWriterListener.java
40	org/openscience/cdk/io/listener/PropertiesListener.java	34	org/openscience/cdk/io/listener/PropertiesListener.java
41	org/openscience/cdk/io/listener/IChemObjectIOListener.java	35	org/openscience/cdk/io/listener/IChemObjectIOListener.java
42	org/openscience/cdk/io/listener/SwingGUILi~~sten~~er.java	36	org/openscience/cdk/io/iterator/IteratingMDLReader.java
43	org/openscience/cdk/io/listener/IReade~~rLis~~tener.java	37	org/openscience/cdk/io/iterator/IIteratingChemObjectReader.java
44	org/openscience/cdk/io/~~lis~~tener/Text~~GUILis~~tener.java	38	org/openscience/cdk/io/iterator/event/IEventChemObjectReader.java
45	org/openscience/cdk/io/~~pubch~~e~~mxml~~/PubChem~~XMLH~~elper.java	39	org/openscience/cdk/io/iterator/event/DefaultEventChemObjectReader.java
46	org/openscience/cdk/io/~~cml/CMLR~~eactionM~~odul~~e.java	40	org/openscience/cdk/io/iterator/event/EventCMLReader.java
47	org/openscience/cdk/io/~~cml~~/ICML~~Modu~~le.java	41	org/openscience/cdk/io/iterator/event/EventCMLHandler.java
48	org/openscience/cdk/io/~~cml~~/P~~DBCo~~nve~~ntion~~.java	42	org/openscience/cdk/io/iterator/IteratingPCSubstancesXMLReader.java
49	org/openscience/cdk/io/~~cml~~/IC~~MLC~~on~~vention~~.java	43	org/openscience/cdk/io/iterator/IteratingPCCompoundXMLReader.java
50	org/openscience/cdk/io/~~cml~~/C~~MLResolv~~er.java	44	org/openscience/cdk/io/iterator/IteratingPCCompoundASNReader.java
51	org/openscience/cdk/io/cml~~/QSAR~~C~~onv~~ent~~ion~~.java	45	org/openscience/cdk/io/iterator/DefaultIteratingChemObjectReader.java
52	org/openscience/cdk/io/cm~~l/C~~MLStack.java	46	org/openscience/cdk/io/PCCompoundXMLReader.java
		47	org/openscience/cdk/io/MDLReader.java
		48	org/openscience/cdk/io/PCSubstanceXMLReader.java
53	org/openscience/cdk/io/cml/CDKConvention.java	49	org/openscience/cdk/io/cml/CDKConvention.java
54	org/openscience/cdk/io/cml/MDLMolConvention.java	50	org/openscience/cdk/io/cml/MDLMolConvention.java
		51	org/openscience/cdk/io/cml/ICMLModule.java
		52	org/openscience/cdk/io/cml/PMPConvention.java
		53	org/openscience/cdk/io/cml/CMLStack.java
		54	org/openscience/cdk/io/cml/CMLHandler.java
55	org/openscience/cdk/io/cml/CMLCoreModule.java	55	org/openscience/cdk/io/cml/CMLCoreModule.java
		56	org/openscience/cdk/io/cml/PDBConvention.java
56	org/openscience/cdk/io/cml/CMLErrorHandler.java	57	org/openscience/cdk/io/cml/CMLErrorHandler.java
57	org/openscience/cdk/io/cml/CMLHandler.java
58	org/openscience/cdk/io/cml/PMPConvention.java
59	org/openscience/cdk/io/cml/JMOLANIMATIONConvention.java	58	org/openscience/cdk/io/cml/JMOLANIMATIONConvention.java
60	org/openscience/cdk/io/~~XYZWr~~i~~ter~~.java	59	org/openscience/cdk/io/cml/CMLReactionModule.java
61	org/openscience/cdk/io/~~Gaussian03R~~e~~ader~~.java	60	org/openscience/cdk/io/cml/ICMLConvention.java
62	org/openscience/cdk/io/MD~~LRXNV2000Read~~er.java	61	org/openscience/cdk/io/cml/CMLResolver.java
63	org/openscience/cdk/io/~~PMP~~Re~~ader~~.java	62	org/openscience/cdk/io/cml/QSARConvention.java
		63	org/openscience/cdk/io/MDLRXNWriter.java
		64	org/openscience/cdk/io/MDLV2000Reader.java
		65	org/openscience/cdk/io/CMLReader.java
		66	org/openscience/cdk/io/DefaultChemObjectWriter.java
		67	org/openscience/cdk/io/Mol2Reader.java
		68	org/openscience/cdk/io/CTXReader.java
		69	org/openscience/cdk/io/SDFWriter.java
		70	org/openscience/cdk/io/PCCompoundASNReader.java
		71	org/openscience/cdk/io/ShelXReader.java
		72	org/openscience/cdk/io/HINReader.java
64	org/openscience/cdk/io/GhemicalMMReader.java	73	org/openscience/cdk/io/GhemicalMMReader.java
65	org/openscience/cdk/io/M~~DLV3000Reader~~.java	74	org/openscience/cdk/io/WriterFactory.java
66	org/openscience/cdk/io/~~Gaussian98~~Reader.java	75	org/openscience/cdk/io/ISimpleChemObjectReader.java
67	org/openscience/cdk/io/~~iterator~~/Iterati~~ngPCCompoundXMLRea~~der.java	76	org/openscience/cdk/io/HINWriter.java
68	org/openscience/cdk/io/~~iterator/Ite~~rati~~ngPCCompoundASNRea~~der.java	77	org/openscience/cdk/io/PDBWriter.java
69	org/openscience/cdk/io/iterator/event/EventCMLHandler.java
70	org/openscience/cdk/io/iterator/event/DefaultEventChemObjectReader.java
71	org/openscience/cdk/io/iterator/event/IEventChemObjectReader.java
72	org/openscience/cdk/io/iterator/event/EventCMLReader.java
73	org/openscience/cdk/io/iterator/IIteratingChemObjectReader.java
74	org/openscience/cdk/io/iterator/DefaultIteratingChemObjectReader.java
75	org/openscience/cdk/io/iterator/IteratingPCSubstancesXMLReader.java
76	org/openscience/cdk/io/iterator/IteratingMDLReader.java
77	org/openscience/cdk/io/MDLReader.java
78	org/openscience/cdk/io/Mol2Writer.java	78	org/openscience/cdk/io/Mol2Writer.java
79	org/openscience/cdk/geo~~metry~~/~~ZMat~~ri~~xTools~~.java	79	org/openscience/cdk/io/MDLWriter.java


Offset 1, 8 lines modified		Offset 1, 8 lines modified
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Offset 98, 8 lines modified		Offset 98, 8 lines modified
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103	-rw-r--r--··2.0·unx·····2430·b-·defN·18-Mar-30·20:15·org/openscience/cdk/io/formats/ZMatrixFormat.class	103	-rw-r--r--··2.0·unx·····2430·b-·defN·18-Mar-30·20:15·org/openscience/cdk/io/formats/ZMatrixFormat.class
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Offset 1, 90 lines modified		Offset 1, 90 lines modified
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		8	org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
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Offset 1, 94 lines modified		Offset 1, 94 lines modified
1	org/openscience/cdk/io/FormatFactory.java	1	org/openscience/cdk/io/formats/DaltonFormat.java
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		7	org/openscience/cdk/io/formats/PubChemSubstancesXMLFormat.java
		8	org/openscience/cdk/io/formats/PubChemSubstanceXMLFormat.java
		9	org/openscience/cdk/io/formats/POVRayFormat.java
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		11	org/openscience/cdk/io/formats/ShelXFormat.java
		12	org/openscience/cdk/io/formats/Gaussian90Format.java
		13	org/openscience/cdk/io/formats/CIFFormat.java
		14	org/openscience/cdk/io/formats/XEDFormat.java
		15	org/openscience/cdk/io/formats/JMEFormat.java
		16	org/openscience/cdk/io/formats/INChIPlainTextFormat.java
		17	org/openscience/cdk/io/formats/XYZFormat.java
		18	org/openscience/cdk/io/formats/FingerprintFormat.java
		19	org/openscience/cdk/io/formats/ADFFormat.java
		20	org/openscience/cdk/io/formats/CMLFormat.java
		21	org/openscience/cdk/io/formats/ChemDrawFormat.java
		22	org/openscience/cdk/io/formats/GROMOS96Format.java
		23	org/openscience/cdk/io/formats/ViewmolFormat.java
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		25	org/openscience/cdk/io/formats/SMARTSFormat.java
		26	org/openscience/cdk/io/formats/SDFFormat.java
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5	org/openscience/cdk/io/formats/CRK3DFormat.java
6	org/openscience/cdk/io/formats/IChemFormatMatcher.java
7	org/openscience/cdk/io/formats/Chem3D_Cartesian_2Format.java
8	org/openscience/cdk/io/formats/MPQCFormat.java
9	org/openscience/cdk/io/formats/ABINITFormat.java
10	org/openscience/cdk/io/formats/XYZFormat.java
11	org/openscience/cdk/io/formats/PubChemFormat.java	28	org/openscience/cdk/io/formats/PubChemFormat.java
12	org/openscience/cdk/io/formats/SVGFormat.java
13	org/openscience/cdk/io/formats/CMLFormat.java
14	org/openscience/cdk/io/formats/CMLRSSFormat.java
15	org/openscience/cdk/io/formats/PubChemCompoundXMLFormat.java
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17	org/openscience/cdk/io/formats/CIFFormat.java
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19	org/openscience/cdk/io/formats/GhemicalSPMFormat.java
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21	org/openscience/cdk/io/formats/PCModelFormat.java
22	org/openscience/cdk/io/formats/MDLV3000Format.java
23	org/openscience/cdk/io/formats/IChemFormat.java
24	org/openscience/cdk/io/formats/TinkerXYZFormat.java
25	org/openscience/cdk/io/formats/PubChemCompoundsXMLFormat.java
26	org/openscience/cdk/io/formats/MOPAC2002Format.java
27	org/openscience/cdk/io/formats/ZMatrixFormat.java
28	org/openscience/cdk/io/formats/IResourceFormat.java
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31	org/openscience/cdk/io/formats/~~SDF~~Format.java	33	org/openscience/cdk/io/formats/IResourceFormat.java
32	org/openscience/cdk/io/formats/INChIFormat.java
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35	org/openscience/cdk/io/formats/YasaraFormat.java
36	org/openscience/cdk/io/formats/ShelXFormat.java
37	org/openscience/cdk/io/formats/HINFormat.java	34	org/openscience/cdk/io/formats/HINFormat.java
38	org/openscience/cdk/io/formats/~~MDL~~Format.java	35	org/openscience/cdk/io/formats/CACheFormat.java
39	org/openscience/cdk/io/formats/PDBMLFormat.java
40	org/openscience/cdk/io/formats/Gaussian92Format.java
41	org/openscience/cdk/io/formats/MDLRXNV3000Format.java
42	org/openscience/cdk/io/formats/PMPFormat.java
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44	org/openscience/cdk/io/formats/QChemFormat.java	37	org/openscience/cdk/io/formats/CTXFormat.java
45	org/openscience/cdk/io/formats/MOPAC93Format.java	38	org/openscience/cdk/io/formats/MOPAC97Format.java
46	org/openscience/cdk/io/formats/CD~~KSou~~r~~ceCo~~deFormat.java	39	org/openscience/cdk/io/formats/ZMatrixFormat.java
47	org/openscience/cdk/io/formats/~~Gamess~~Format.java	40	org/openscience/cdk/io/formats/MDLV2000Format.java
		41	org/openscience/cdk/io/formats/FenskeHall_ZMatrixFormat.java
		42	org/openscience/cdk/io/formats/MMODFormat.java
		43	org/openscience/cdk/io/formats/ABINITFormat.java
48	org/openscience/cdk/io/formats/ZindoFormat.java	44	org/openscience/cdk/io/formats/ZindoFormat.java
		45	org/openscience/cdk/io/formats/Gaussian98Format.java
		46	org/openscience/cdk/io/formats/PubChemCompoundXMLFormat.java
		47	org/openscience/cdk/io/formats/PCModelFormat.java
		48	org/openscience/cdk/io/formats/TinkerXYZFormat.java
49	org/openscience/cdk/io/formats/GaussianInputFormat.java	49	org/openscience/cdk/io/formats/GaussianInputFormat.java
		50	org/openscience/cdk/io/formats/IChemFormat.java
		51	org/openscience/cdk/io/formats/MDLFormat.java
		52	org/openscience/cdk/io/formats/IChemFormatMatcher.java
50	org/openscience/cdk/io/formats/GhemicalMMFormat.java	53	org/openscience/cdk/io/formats/GhemicalMMFormat.java
51	org/openscience/cdk/io/formats/NWChemFormat.java
52	org/openscience/cdk/io/formats/SybylDescriptorFormat.java
53	org/openscience/cdk/io/formats/Gaussian98Format.java
54	org/openscience/cdk/io/formats/CacaoCartesianFormat.java
55	org/openscience/cdk/io/formats/ADFFormat.java
56	org/openscience/cdk/io/formats/Gaussian95Format.java
57	org/openscience/cdk/io/formats/SMARTSFormat.java
58	org/openscience/cdk/io/formats/DMol3Format.java
59	org/openscience/cdk/io/formats/MacroModelFormat.java
60	org/openscience/cdk/io/formats/MMODFormat.java
61	org/openscience/cdk/io/formats/PDBFormat.java
62	org/openscience/cdk/io/formats/ChemtoolFormat.java
63	org/openscience/cdk/io/formats/PubChemSubstancesXMLFormat.java
64	org/openscience/cdk/io/formats/PubChemASNFormat.java
65	org/openscience/cdk/io/formats/PubChemSubstanceXMLFormat.java
66	org/openscience/cdk/io/formats/ChemDrawFormat.java
67	org/openscience/cdk/io/formats/CTXFormat.java
68	org/openscience/cdk/io/formats/SpartanFormat.java	54	org/openscience/cdk/io/formats/SpartanFormat.java
69	org/openscience/cdk/io/formats/V~~iewmol~~Format.java	55	org/openscience/cdk/io/formats/GamessFormat.java
70	org/openscience/cdk/io/formats/Ra~~wCopy~~Format.java	56	org/openscience/cdk/io/formats/Chem3D_Cartesian_2Format.java
71	org/openscience/cdk/io/formats/Tur~~boMo~~leFormat.java	57	org/openscience/cdk/io/formats/CrystClustFormat.java
72	org/openscience/cdk/io/formats/~~Pub~~C~~hemSubstancesASN~~Format.java	58	org/openscience/cdk/io/formats/CRK3DFormat.java
73	org/openscience/cdk/io/formats/~~MOPAC~~97Format.java	59	org/openscience/cdk/io/formats/Gaussian92Format.java
74	org/openscience/cdk/io/formats/~~FenskeHall_~~ZMat~~rix~~Format.java	60	org/openscience/cdk/io/formats/DMol3Format.java
75	org/openscience/cdk/io/formats/MD~~LV2000~~Format.java	61	org/openscience/cdk/io/formats/PDBMLFormat.java
76	org/openscience/cdk/io/formats/INChIPlainTextFormat.java
77	org/openscience/cdk/io/formats/PQSChemFormat.java	62	org/openscience/cdk/io/formats/PQSChemFormat.java
78	org/openscience/cdk/io/formats/~~GROMOS96~~Format.java	63	org/openscience/cdk/io/formats/PDBFormat.java
79	org/openscience/cdk/io/formats/~~POVRay~~Format.java	64	org/openscience/cdk/io/formats/YasaraFormat.java
		65	org/openscience/cdk/io/formats/CDKSourceCodeFormat.java
		66	org/openscience/cdk/io/formats/QChemFormat.java
80	org/openscience/cdk/io/formats/Gaussian94Format.java	67	org/openscience/cdk/io/formats/Gaussian94Format.java
81	org/openscience/cdk/io/formats/C~~AChe~~Format.java	68	org/openscience/cdk/io/formats/MPQCFormat.java
82	org/openscience/cdk/io/formats/SMILESFormat.java	69	org/openscience/cdk/io/formats/MDLRXNV3000Format.java
83	org/openscience/cdk/io/formats/UniChemXYZFormat.java
84	org/openscience/cdk/io/formats/Gaussian03Format.java
85	org/openscience/cdk/io/formats/VASPFormat.java
86	org/openscience/cdk/io/formats/CRK2DFormat.java	70	org/openscience/cdk/io/formats/CRK2DFormat.java
		71	org/openscience/cdk/io/formats/INChIFormat.java
		72	org/openscience/cdk/io/formats/MOPAC93Format.java
		73	org/openscience/cdk/io/formats/CacaoCartesianFormat.java
		74	org/openscience/cdk/io/formats/SybylDescriptorFormat.java
		75	org/openscience/cdk/io/formats/TurboMoleFormat.java
		76	org/openscience/cdk/io/formats/GhemicalSPMFormat.java
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7	drwxr-xr-x··2.0·unx········0·b-·stor·18-Mar-30·20:15·org/openscience/cdk/	7	drwxr-xr-x··2.0·unx········0·b-·stor·18-Mar-30·20:15·org/openscience/cdk/
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20	-rw-r--r--··2.0·unx·····1062·b-·defN·18-Mar-30·20:15·org/openscience/cdk/isomorphism/matchers/smarts/AnyAtom.class	20	-rw-r--r--··2.0·unx·····1062·b-·defN·18-Mar-30·20:15·org/openscience/cdk/isomorphism/matchers/smarts/AnyAtom.class
21	-rw-r--r--··2.0·unx·····1290·b-·defN·18-Mar-30·20:15·org/openscience/cdk/isomorphism/matchers/smarts/AnyOrderQueryBond.class	21	-rw-r--r--··2.0·unx·····1290·b-·defN·18-Mar-30·20:15·org/openscience/cdk/isomorphism/matchers/smarts/AnyOrderQueryBond.class
22	-rw-r--r--··2.0·unx······901·b-·defN·18-Mar-30·20:15·org/openscience/cdk/isomorphism/matchers/smarts/AromaticAtom.class	22	-rw-r--r--··2.0·unx······901·b-·defN·18-Mar-30·20:15·org/openscience/cdk/isomorphism/matchers/smarts/AromaticAtom.class
23	-rw-r--r--··2.0·unx·····1578·b-·defN·18-Mar-30·20:15·org/openscience/cdk/isomorphism/matchers/smarts/AromaticOrSingleQueryBond.class	23	-rw-r--r--··2.0·unx·····1578·b-·defN·18-Mar-30·20:15·org/openscience/cdk/isomorphism/matchers/smarts/AromaticOrSingleQueryBond.class
24	-rw-r--r--··2.0·unx·····1409·b-·defN·18-Mar-30·20:15·org/openscience/cdk/isomorphism/matchers/smarts/AromaticQueryBond.class	24	-rw-r--r--··2.0·unx·····1409·b-·defN·18-Mar-30·20:15·org/openscience/cdk/isomorphism/matchers/smarts/AromaticQueryBond.class
25	-rw-r--r--··2.0·unx······598·b-·defN·18-Mar-30·20:15·org/openscience/cdk/isomorphism/matchers/smarts/SMARTSAtom.class	25	-rw-r--r--··2.0·unx······598·b-·defN·18-Mar-30·20:15·org/openscience/cdk/isomorphism/matchers/smarts/SMARTSAtom.class
26	-rw-r--r--··2.0·unx·····1298·b-·defN·18-Mar-30·20:15·org/openscience/cdk/isomorphism/matchers/smarts/SMARTSBond.class	26	-rw-r--r--··2.0·unx·····1298·b-·defN·18-Mar-30·20:15·org/openscience/cdk/isomorphism/matchers/smarts/SMARTSBond.class
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1	org/openscience/cdk/isomorphism/matchers/Quer~~yAtomContain~~erCr~~eator~~.java	1	org/openscience/cdk/isomorphism/matchers/OrderQueryBond.java
2	org/openscience/cdk/isomorphism/matchers/SymbolSetQueryAtom.java	2	org/openscience/cdk/isomorphism/matchers/SymbolChargeIDQueryAtom.java
		3	org/openscience/cdk/isomorphism/matchers/SymbolAndChargeQueryAtom.java
3	org/openscience/cdk/isomorphism/matchers/smarts/AnyOrderQueryBond.java	4	org/openscience/cdk/isomorphism/matchers/smarts/AnyOrderQueryBond.java
		5	org/openscience/cdk/isomorphism/matchers/smarts/AromaticAtom.java
		6	org/openscience/cdk/isomorphism/matchers/smarts/AnyAtom.java
4	org/openscience/cdk/isomorphism/matchers/smarts/AromaticOrSingleQueryBond.java	7	org/openscience/cdk/isomorphism/matchers/smarts/AromaticOrSingleQueryBond.java
5	org/openscience/cdk/isomorphism/matchers/smarts/SMARTSAtom.java	8	org/openscience/cdk/isomorphism/matchers/smarts/SMARTSAtom.java
6	org/openscience/cdk/isomorphism/matchers/smarts/AromaticAtom.java
7	org/openscience/cdk/isomorphism/matchers/smarts/AromaticQueryBond.java	9	org/openscience/cdk/isomorphism/matchers/smarts/AromaticQueryBond.java
8	org/openscience/cdk/isomorphism/matchers/smarts/SMARTSBond.java	10	org/openscience/cdk/isomorphism/matchers/smarts/SMARTSBond.java
9	org/openscience/cdk/isomorphism/matchers/smarts/AnyAtom.java
10	org/openscience/cdk/isomorphism/matchers/SymbolChargeIDQueryAtom.java
11	org/openscience/cdk/isomorphism/matchers/QueryAtomContainer.java
12	org/openscience/cdk/isomorphism/matchers/OrderQueryBondOrderOnly.java
13	org/openscience/cdk/isomorphism/matchers/InverseSymbolSetQueryAtom.java	11	org/openscience/cdk/isomorphism/matchers/InverseSymbolSetQueryAtom.java
14	org/openscience/cdk/isomorphism/matchers/~~Ord~~erQuery~~Bond~~.java	12	org/openscience/cdk/isomorphism/matchers/SymbolSetQueryAtom.java
		13	org/openscience/cdk/isomorphism/matchers/QueryAtomContainerCreator.java
15	org/openscience/cdk/isomorphism/matchers/SymbolQueryAtom.java	14	org/openscience/cdk/isomorphism/matchers/SymbolQueryAtom.java
16	org/openscience/cdk/isomorphism/matchers/S~~ymbol~~A~~ndChargeQu~~er~~yAtom~~.java	15	org/openscience/cdk/isomorphism/matchers/QueryAtomContainer.java
		16	org/openscience/cdk/isomorphism/matchers/OrderQueryBondOrderOnly.java