/usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.MBzKEfC4mJ/cdk_1.2.10-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.MBzKEfC4mJ/cdk_1.2.10-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.MBzKEfC4mJ/cdk_1.2.10-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.MBzKEfC4mJ/b1/cdk_1.2.10-7_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.MBzKEfC4mJ/b2/cdk_1.2.10-7

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1	·~~d08288fda~~216d99~~df7ebcf~~9c1e~~8daf53~~·4786796·java·optional·libcdk-java_1.2.10-7_all.deb	1	·88cc3538b42969943555079ebe04430e·4786964·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
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		1	org/openscience/cdk/tools/DataFeatures.java
1	org/openscience/cdk/annotations/TestMethod.java	2	org/openscience/cdk/annotations/TestMethod.java
2	org/openscience/cdk/annotations/TestClass.java	3	org/openscience/cdk/annotations/TestClass.java
3	org/openscience/cdk/tools/DataFeatures.java


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6	-rw-r--r--···0·root·········(0)·root·········(0)······940·2018-03-30·19:54:21.000000·./usr/share/doc/libcdk-java/README.Debian	6	-rw-r--r--···0·root·········(0)·root·········(0)······940·2018-03-30·19:54:21.000000·./usr/share/doc/libcdk-java/README.Debian
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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/
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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	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
14	-rw-r--r--···0·root·········(0)·root·········(0)·····8695·2018-03-30·20:15:48.000000·./usr/share/java/cdk-builder3dtools-1.2.10.jar	14	-rw-r--r--···0·root·········(0)·root·········(0)·····8695·2018-03-30·20:15:48.000000·./usr/share/java/cdk-builder3dtools-1.2.10.jar
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16	-rw-r--r--···0·root·········(0)·root·········(0)·····4291·2018-03-30·20:15:48.000000·./usr/share/java/cdk-control-1.2.10.jar	16	-rw-r--r--···0·root·········(0)·root·········(0)·····4290·2018-03-30·20:15:48.000000·./usr/share/java/cdk-control-1.2.10.jar
17	-rw-r--r--···0·root·········(0)·root·········(0)···157902·2018-03-30·20:15:48.000000·./usr/share/java/cdk-core-1.2.10.jar	17	-rw-r--r--···0·root·········(0)·root·········(0)···157914·2018-03-30·20:15:48.000000·./usr/share/java/cdk-core-1.2.10.jar
18	-rw-r--r--···0·root·········(0)·root·········(0)···107~~903~~·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)····18019·2018-03-30·20:15:48.000000·./usr/share/java/cdk-dict-1.2.10.jar	19	-rw-r--r--···0·root·········(0)·root·········(0)····18019·2018-03-30·20:15:48.000000·./usr/share/java/cdk-dict-1.2.10.jar
20	-rw-r--r--···0·root·········(0)·root·········(0)····28931·2018-03-30·20:15:48.000000·./usr/share/java/cdk-diff-1.2.10.jar	20	-rw-r--r--···0·root·········(0)·root·········(0)····28940·2018-03-30·20:15:48.000000·./usr/share/java/cdk-diff-1.2.10.jar
21	-rw-r--r--···0·root·········(0)·root·········(0)···266984·2018-03-30·20:15:48.000000·./usr/share/java/cdk-extra-1.2.10.jar	21	-rw-r--r--···0·root·········(0)·root·········(0)···266976·2018-03-30·20:15:48.000000·./usr/share/java/cdk-extra-1.2.10.jar
22	-rw-r--r--···0·root·········(0)·root·········(0)····15314·2018-03-30·20:15:48.000000·./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)···165387·2018-03-30·20:15:48.000000·./usr/share/java/cdk-forcefield-1.2.10.jar	23	-rw-r--r--···0·root·········(0)·root·········(0)···165384·2018-03-30·20:15:48.000000·./usr/share/java/cdk-forcefield-1.2.10.jar
24	-rw-r--r--···0·root·········(0)·root·········(0)····56657·2018-03-30·20:15:48.000000·./usr/share/java/cdk-formula-1.2.10.jar	24	-rw-r--r--···0·root·········(0)·root·········(0)····56654·2018-03-30·20:15:48.000000·./usr/share/java/cdk-formula-1.2.10.jar
25	-rw-r--r--···0·root·········(0)·root·········(0)····26723·2018-03-30·20:15:48.000000·./usr/share/java/cdk-interfaces-1.2.10.jar	25	-rw-r--r--···0·root·········(0)·root·········(0)····26724·2018-03-30·20:15:48.000000·./usr/share/java/cdk-interfaces-1.2.10.jar
26	-rw-r--r--···0·root·········(0)·root·········(0)···515788·2018-03-30·20:15:48.000000·./usr/share/java/cdk-io-1.2.10.jar	26	-rw-r--r--···0·root·········(0)·root·········(0)···515788·2018-03-30·20:15:48.000000·./usr/share/java/cdk-io-1.2.10.jar
27	-rw-r--r--···0·root·········(0)·root·········(0)···105615·2018-03-30·20:15:48.000000·./usr/share/java/cdk-ioformats-1.2.10.jar	27	-rw-r--r--···0·root·········(0)·root·········(0)···105632·2018-03-30·20:15:48.000000·./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)····18457·2018-03-30·20:15:48.000000·./usr/share/java/cdk-isomorphism-1.2.10.jar	29	-rw-r--r--···0·root·········(0)·root·········(0)····18454·2018-03-30·20:15:48.000000·./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)·····1900·2018-03-30·20:15:48.000000·./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)·····6919·2018-03-30·20:15:48.000000·./usr/share/java/cdk-libiomd-1.2.10.jar
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33	-rw-r--r--···0·root·········(0)·root·········(0)····20273·2018-03-30·20:15:48.000000·./usr/share/java/cdk-pcore-1.2.10.jar	33	-rw-r--r--···0·root·········(0)·root·········(0)····20274·2018-03-30·20:15:48.000000·./usr/share/java/cdk-pcore-1.2.10.jar
34	-rw-r--r--···0·root·········(0)·root·········(0)····17752·2018-03-30·20:15:48.000000·./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)····40166·2018-03-30·20:15:48.000000·./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)····54293·2018-03-30·20:15:48.000000·./usr/share/java/cdk-qsar-1.2.10.jar	36	-rw-r--r--···0·root·········(0)·root·········(0)····54279·2018-03-30·20:15:48.000000·./usr/share/java/cdk-qsar-1.2.10.jar
37	-rw-r--r--···0·root·········(0)·root·········(0)···107155·2018-03-30·20:15:48.000000·./usr/share/java/cdk-qsaratomic-1.2.10.jar	37	-rw-r--r--···0·root·········(0)·root·········(0)···107149·2018-03-30·20:15:48.000000·./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)····16472·2018-03-30·20:15:48.000000·./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
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45	-rw-r--r--···0·root·········(0)·root·········(0)···126440·2018-03-30·20:15:48.000000·./usr/share/java/cdk-smarts-1.2.10.jar	45	-rw-r--r--···0·root·········(0)·root·········(0)···126440·2018-03-30·20:15:48.000000·./usr/share/java/cdk-smarts-1.2.10.jar
46	-rw-r--r--···0·root·········(0)·root·········(0)····45463·2018-03-30·20:15:48.000000·./usr/share/java/cdk-smiles-1.2.10.jar	46	-rw-r--r--···0·root·········(0)·root·········(0)····45465·2018-03-30·20:15:48.000000·./usr/share/java/cdk-smiles-1.2.10.jar
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48	-rw-r--r--···0·root·········(0)·root·········(0)····17851·2018-03-30·20:15:48.000000·./usr/share/java/cdk-structgen-1.2.10.jar	48	-rw-r--r--···0·root·········(0)·root·········(0)····17855·2018-03-30·20:15:48.000000·./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
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94	··32-bit·CRC·value·(hex):·························a9f19e29	94	··32-bit·CRC·value·(hex):·························9ef62eb6
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
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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 14, 8 lines modified		Offset 14, 8 lines modified
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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
2	org/openscience/cdk/modeling/builder3d/ModelBuilder3D.java
3	org/openscience/cdk/modeling/builder3d/TemplateHandler3D.java
4	org/openscience/cdk/modeling/builder3d/AtomTetrahedralLigandPlacer3D.java	1	org/openscience/cdk/modeling/builder3d/AtomTetrahedralLigandPlacer3D.java
		2	org/openscience/cdk/modeling/builder3d/TemplateHandler3D.java
		3	org/openscience/cdk/modeling/builder3d/ModelBuilder3D.java
5	org/openscience/cdk/modeling/builder3d/AtomPlacer3D.java	4	org/openscience/cdk/modeling/builder3d/AtomPlacer3D.java
		5	org/openscience/cdk/qsar/descriptors/atomic/PartialTChargeMMFF94Descriptor.java


Offset 1, 8 lines modified		Offset 1, 8 lines modified
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Offset 12, 8 lines modified		Offset 12, 8 lines modified
12	-rw-r--r--··2.0·unx····24460·b-·defN·18-Mar-30·20:15·org/openscience/cdk/charges/GasteigerPEPEPartialCharges.class	12	-rw-r--r--··2.0·unx····24460·b-·defN·18-Mar-30·20:15·org/openscience/cdk/charges/GasteigerPEPEPartialCharges.class
13	-rw-r--r--··2.0·unx······208·b-·defN·18-Mar-30·20:15·org/openscience/cdk/charges/IChargeCalculator.class	13	-rw-r--r--··2.0·unx······208·b-·defN·18-Mar-30·20:15·org/openscience/cdk/charges/IChargeCalculator.class
14	-rw-r--r--··2.0·unx······318·b-·defN·18-Mar-30·20:15·org/openscience/cdk/charges/IElectronicPropertyCalculator.class	14	-rw-r--r--··2.0·unx······318·b-·defN·18-Mar-30·20:15·org/openscience/cdk/charges/IElectronicPropertyCalculator.class
15	-rw-r--r--··2.0·unx····10273·b-·defN·18-Mar-30·20:15·org/openscience/cdk/charges/InductivePartialCharges.class	15	-rw-r--r--··2.0·unx····10273·b-·defN·18-Mar-30·20:15·org/openscience/cdk/charges/InductivePartialCharges.class
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Offset 1, 10 lines modified		Offset 1, 10 lines modified
1	org/openscience/cdk/charges/AtomTypeCharges.java
2	org/openscience/cdk/charges/Polarizability.java	1	org/openscience/cdk/charges/Polarizability.java
3	org/openscience/cdk/charges/IElectronicPropertyCalculator.java
4	org/openscience/cdk/charges/PiElectronegativity.java
5	org/openscience/cdk/charges/GasteigerMarsiliPartialCharges.java	2	org/openscience/cdk/charges/GasteigerMarsiliPartialCharges.java
6	org/openscience/cdk/charges/InductivePartialCharges.java
7	org/openscience/cdk/charges/StabilizationCharges.java
8	org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java	3	org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java
9	org/openscience/cdk/charges/~~ICha~~rgeCal~~cula~~tor.java	4	org/openscience/cdk/charges/PiElectronegativity.java
		5	org/openscience/cdk/charges/IElectronicPropertyCalculator.java
		6	org/openscience/cdk/charges/StabilizationCharges.java
10	org/openscience/cdk/charges/Electronegativity.java	7	org/openscience/cdk/charges/Electronegativity.java
		8	org/openscience/cdk/charges/IChargeCalculator.java
		9	org/openscience/cdk/charges/InductivePartialCharges.java
		10	org/openscience/cdk/charges/AtomTypeCharges.java


Offset 1, 14 lines modified		Offset 1, 14 lines modified
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		1	org/openscience/cdk/controller/UndoAdapter.java
1	org/openscience/cdk/controller/IViewEventRelay.java	2	org/openscience/cdk/controller/IViewEventRelay.java
2	org/openscience/cdk/controller/SwingMouseEventRelay.java
3	org/openscience/cdk/controller/SwingEventRelay.java	3	org/openscience/cdk/controller/SwingEventRelay.java
4	org/openscience/cdk/controller/UndoAdapter.java
5	org/openscience/cdk/controller/IMouseEventRelay.java	4	org/openscience/cdk/controller/IMouseEventRelay.java
		5	org/openscience/cdk/controller/SwingMouseEventRelay.java


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Offset 1, 25 lines modified		Offset 1, 25 lines modified
1	org/openscience/cdk/exception/NoSuchAtomException.java
2	org/openscience/cdk/exception/NoSuchAtomTypeException.java
3	org/openscience/cdk/exception/CDKException.java
4	org/openscience/cdk/CDKConstants.java
5	org/openscience/cdk/tools/manipulator/BondManipulator.java
6	org/openscience/cdk/tools/LoggingTool.java	1	org/openscience/cdk/tools/LoggingTool.java
7	org/openscience/cdk/confi~~g/IA~~to~~mTypeConf~~igurator.java	2	org/openscience/cdk/tools/manipulator/BondManipulator.java
8	org/openscience/cdk/~~config/OWLBasedAtomType~~Con~~fig~~ura~~tor~~.java	3	org/openscience/cdk/CDKConstants.java
9	org/openscience/cdk/config/TXTBasedAtomTypeConfigurator.java
10	org/openscience/cdk/config/AtomTypeFactory.java	4	org/openscience/cdk/config/AtomTypeFactory.java
11	org/openscience/cdk/config/Isotope~~Fac~~tory.java	5	org/openscience/cdk/config/isotopes/IsotopeReader.java
		6	org/openscience/cdk/config/isotopes/IsotopeHandler.java
		7	org/openscience/cdk/config/TXTBasedAtomTypeConfigurator.java
12	org/openscience/cdk/config/atomtypes/OWLAtomTypeHandler.java	8	org/openscience/cdk/config/atomtypes/OWLAtomTypeHandler.java
13	org/openscience/cdk/config/atomtypes/OWLAtomTypeReader.java
14	org/openscience/cdk/config/atomtypes/AtomTypeHandler.java
15	org/openscience/cdk/config/atomtypes/AtomTypeReader.java	9	org/openscience/cdk/config/atomtypes/AtomTypeReader.java
		10	org/openscience/cdk/config/atomtypes/AtomTypeHandler.java
		11	org/openscience/cdk/config/atomtypes/OWLAtomTypeReader.java
		12	org/openscience/cdk/config/OWLBasedAtomTypeConfigurator.java
		13	org/openscience/cdk/config/IAtomTypeConfigurator.java
16	org/openscience/cdk/config/CDKBasedAtomTypeConfigurator.java	14	org/openscience/cdk/config/CDKBasedAtomTypeConfigurator.java
17	org/openscience/cdk/config/~~isotopes/~~IsotopeHa~~ndler~~.java	15	org/openscience/cdk/config/IsotopeFactory.java
18	org/openscience/cdk/c~~onf~~i~~g/is~~ot~~opes/Isoto~~peRe~~ader~~.java	16	org/openscience/cdk/exception/NoSuchAtomTypeException.java
19	org/openscience/cdk/ato~~mtype/I~~Atom~~Typ~~eGu~~esser~~.java	17	org/openscience/cdk/exception/NoSuchAtomException.java
20	org/openscience/cdk/~~atom~~t~~ype~~/CDK~~AtomTyp~~eMatc~~her~~.java	18	org/openscience/cdk/exception/CDKException.java
21	org/openscience/cdk/atomtype/IAtomTypeMatcher.java
22	org/openscience/cdk/graph/SpanningTree.java	19	org/openscience/cdk/graph/SpanningTree.java
23	org/openscience/cdk/graph/matrix/AdjacencyMatrix.java
24	org/openscience/cdk/graph/PathTools.java	20	org/openscience/cdk/graph/PathTools.java
		21	org/openscience/cdk/graph/matrix/AdjacencyMatrix.java
		22	org/openscience/cdk/atomtype/IAtomTypeMatcher.java
		23	org/openscience/cdk/atomtype/IAtomTypeGuesser.java
		24	org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
25	org/openscience/cdk/fingerprint/IFingerprinter.java	25	org/openscience/cdk/fingerprint/IFingerprinter.java


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Offset 1, 41 lines modified		Offset 1, 41 lines modified
1	org/openscience/cdk/R~~eact~~ionSet.java	1	org/openscience/cdk/Ring.java
2	org/openscience/cdk/AtomContainerSet.java
3	org/openscience/cdk/PseudoAtom.java
4	org/openscience/cdk/RingSet.java
5	org/openscience/cdk/MoleculeSet.java
6	org/openscience/cdk/Atom.java
7	org/openscience/cdk/ConformerContainer.java
8	org/openscience/cdk/Isotope.java	2	org/openscience/cdk/Isotope.java
		3	org/openscience/cdk/ConformerContainer.java
		4	org/openscience/cdk/DefaultChemObjectBuilder.java
		5	org/openscience/cdk/FragmentAtom.java
		6	org/openscience/cdk/AminoAcid.java
		7	org/openscience/cdk/ElectronContainer.java
		8	org/openscience/cdk/AtomType.java
9	org/openscience/cdk/Polymer.java	9	org/openscience/cdk/Polymer.java
10	org/openscience/cdk/~~Mapping~~.java	10	org/openscience/cdk/Atom.java
		11	org/openscience/cdk/AtomContainerSet.java
		12	org/openscience/cdk/Reaction.java
		13	org/openscience/cdk/ChemFile.java
		14	org/openscience/cdk/Molecule.java
		15	org/openscience/cdk/Crystal.java
		16	org/openscience/cdk/ChemSequence.java
		17	org/openscience/cdk/MoleculeSet.java
		18	org/openscience/cdk/Bond.java
		19	org/openscience/cdk/Element.java
11	org/openscience/cdk/protein/data/PDBAtom.java	20	org/openscience/cdk/protein/data/PDBAtom.java
		21	org/openscience/cdk/protein/data/PDBMonomer.java
12	org/openscience/cdk/protein/data/PDBStructure.java	22	org/openscience/cdk/protein/data/PDBStructure.java
13	org/openscience/cdk/protein/data/PDBPolymer.java	23	org/openscience/cdk/protein/data/PDBPolymer.java
14	org/openscience/cdk/protein/data/PDBMonomer.java
15	org/openscience/cdk/BioPolymer.java
16	org/openscience/cdk/ChemSequence.java
17	org/openscience/cdk/ElectronContainer.java
18	org/openscience/cdk/AtomParity.java
19	org/openscience/cdk/ReactionScheme.java	24	org/openscience/cdk/ReactionScheme.java
20	org/openscience/cdk/Elem~~ent~~.java	25	org/openscience/cdk/formula/MolecularFormula.java
21	org/openscience/cdk/~~Che~~mModel.java	26	org/openscience/cdk/formula/AdductFormula.java
		27	org/openscience/cdk/formula/MolecularFormulaSet.java


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


Offset 1, 24 lines modified		Offset 1, 24 lines modified
1	org/openscience/cdk/tools/diff/SingleElectronDiff.java
2	org/openscience/cdk/tools/diff/ElectronContainerDiff.java
3	org/openscience/cdk/tools/diff/AtomContainerDiff.java	1	org/openscience/cdk/tools/diff/AtomContainerDiff.java
4	org/openscience/cdk/tools/diff/Ato~~mTyp~~eDiff.java	2	org/openscience/cdk/tools/diff/ElectronContainerDiff.java
5	org/openscience/cdk/tools/diff/BondDiff.java	3	org/openscience/cdk/tools/diff/BondDiff.java
6	org/openscience/cdk/tools/diff/~~tree/D~~o~~ubl~~eDiff~~erence~~.java	4	org/openscience/cdk/tools/diff/AtomDiff.java
7	org/openscience/cdk/tools/diff/~~tree/A~~to~~mTy~~pe~~Hybridization~~Diff~~erence~~.java	5	org/openscience/cdk/tools/diff/IsotopeDiff.java
8	org/openscience/cdk/tools/diff/tree/Bon~~dOrde~~rDiff~~erence~~.java	6	org/openscience/cdk/tools/diff/ElementDiff.java
9	org/openscience/cdk/tools/diff/~~tre~~e/Poi~~nt2~~dDiff~~erence~~.java	7	org/openscience/cdk/tools/diff/LonePairDiff.java
10	org/openscience/cdk/tools/diff/~~tree/~~A~~bstract~~Diff~~erence~~.java	8	org/openscience/cdk/tools/diff/AtomTypeDiff.java
11	org/openscience/cdk/tools/diff/tree/IntegerDifference.java
12	org/openscience/cdk/tools/diff/tree/StringDifference.java
13	org/openscience/cdk/tools/diff/tree/Point3dDifference.java
14	org/openscience/cdk/tools/diff/tree/ChemObjectDifference.java
15	org/openscience/cdk/tools/diff/tree/IDifferenceList.java	9	org/openscience/cdk/tools/diff/tree/IDifferenceList.java
16	org/openscience/cdk/tools/diff/tree/Abst~~ract~~Difference~~List~~.java	10	org/openscience/cdk/tools/diff/tree/IntegerDifference.java
17	org/openscience/cdk/tools/diff/tree/IDifference.java	11	org/openscience/cdk/tools/diff/tree/IDifference.java
		12	org/openscience/cdk/tools/diff/tree/BondOrderDifference.java
		13	org/openscience/cdk/tools/diff/tree/ChemObjectDifference.java
		14	org/openscience/cdk/tools/diff/tree/DoubleDifference.java
18	org/openscience/cdk/tools/diff/tree/BooleanArrayDifference.java	15	org/openscience/cdk/tools/diff/tree/BooleanArrayDifference.java
		16	org/openscience/cdk/tools/diff/tree/AbstractDifferenceList.java
		17	org/openscience/cdk/tools/diff/tree/AtomTypeHybridizationDifference.java
		18	org/openscience/cdk/tools/diff/tree/Point3dDifference.java
		19	org/openscience/cdk/tools/diff/tree/StringDifference.java
19	org/openscience/cdk/tools/diff/tree/BooleanDifference.java	20	org/openscience/cdk/tools/diff/tree/BooleanDifference.java
20	org/openscience/cdk/tools/diff/Iso~~tope~~Diff.java	21	org/openscience/cdk/tools/diff/tree/Point2dDifference.java
		22	org/openscience/cdk/tools/diff/tree/AbstractDifference.java
21	org/openscience/cdk/tools/diff/ChemObjectDiff.java	23	org/openscience/cdk/tools/diff/ChemObjectDiff.java
22	org/openscience/cdk/tools/diff/AtomDiff.java	24	org/openscience/cdk/tools/diff/SingleElectronDiff.java
23	org/openscience/cdk/tools/diff/ElementDiff.java
24	org/openscience/cdk/tools/diff/LonePairDiff.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
125	-rw-r--r--··2.0·unx·····1202·b-·defN·18-Mar-30·20:15·org/openscience/cdk/validate/ValidationTest.class	125	-rw-r--r--··2.0·unx·····1202·b-·defN·18-Mar-30·20:15·org/openscience/cdk/validate/ValidationTest.class
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
127	125·files,·666103·bytes·uncompressed,·246080·bytes·compressed:··63.1%	127	125·files,·666103·bytes·uncompressed,·246072·bytes·compressed:··63.1%


Offset 1, 79 lines modified		Offset 1, 79 lines modified
		1	org/openscience/cdk/tools/DataFeaturesTool.java
		2	org/openscience/cdk/tools/SwissArmyKnife.java
		3	org/openscience/cdk/tools/GridGenerator.java
		4	org/openscience/cdk/tools/HOSECodeAnalyser.java
		5	org/openscience/cdk/tools/BremserOneSphereHOSECodePredictor.java
		6	org/openscience/cdk/tools/CDKUtilities.java
		7	org/openscience/cdk/tools/DeAromatizationTool.java
		8	org/openscience/cdk/tools/GenerateFragments.java
		9	org/openscience/cdk/tools/PeriodicTable.java
		10	org/openscience/cdk/tools/AtomTypeTools.java
		11	org/openscience/cdk/tools/features/MoleculeFeaturesTool.java
		12	org/openscience/cdk/tools/FixedSizeStack.java
		13	org/openscience/cdk/templates/saturatedhydrocarbons/IsoAlkanes.java
		14	org/openscience/cdk/templates/MoleculeFactory.java
		15	org/openscience/cdk/structgen/RandomGenerator.java
		16	org/openscience/cdk/modeling/forcefield/ForceFieldTools.java
1	org/openscience/cdk/ringsearch/FiguerasSSSRFinder.java	17	org/openscience/cdk/ringsearch/FiguerasSSSRFinder.java
2	org/openscience/cdk/exc~~ept~~ion/In~~corr~~ectUs~~eOfCDKCor~~e~~ClassErro~~r.java	18	org/openscience/cdk/config/elements/ElementPTReader.java
3	org/openscience/cdk/val~~ida~~te~~/IValid~~ator.java	19	org/openscience/cdk/config/elements/ElementPTHandler.java
4	org/openscience/cdk/va~~lidate~~/~~Valida~~t~~ionRep~~ort.java	20	org/openscience/cdk/config/ElementPTFactory.java
5	org/openscience/cdk/va~~lidate~~/Val~~idatio~~nTest.java	21	org/openscience/cdk/config/Elements.java
6	org/openscience/cdk/validate/AbstractValidator.java	22	org/openscience/cdk/validate/AbstractValidator.java
7	org/openscience/cdk/validate/CDKValidator.java
8	org/openscience/cdk/validate/Geometry3DValidator.java
9	org/openscience/cdk/validate/DictionaryValidator.java
10	org/openscience/cdk/validate/BasicValidator.java	23	org/openscience/cdk/validate/BasicValidator.java
		24	org/openscience/cdk/validate/ValidationTest.java
		25	org/openscience/cdk/validate/ValidationReport.java
		26	org/openscience/cdk/validate/IValidator.java
11	org/openscience/cdk/validate/ValidatorEngine.java	27	org/openscience/cdk/validate/ValidatorEngine.java
12	org/openscience/cdk/pr~~ote~~i~~n/P~~rotei~~nPocketFinde~~r.java	28	org/openscience/cdk/validate/CDKValidator.java
13	org/openscience/cdk/inde~~x/CASNumbe~~r.java	29	org/openscience/cdk/validate/DictionaryValidator.java
14	org/openscience/cdk/Perio~~dicTableE~~l~~ement~~.java	30	org/openscience/cdk/validate/Geometry3DValidator.java
15	org/openscience/cdk/EnzymeResidueLocator.java	31	org/openscience/cdk/EnzymeResidueLocator.java
		32	org/openscience/cdk/PeriodicTableElement.java
16	org/openscience/cdk/Association.java	33	org/openscience/cdk/Association.java
17	org/openscience/cdk/to~~ols~~/PeriodicTa~~ble~~.java	34	org/openscience/cdk/geometry/Projector.java
18	org/openscience/cdk/tools/AtomTypeTools.java
19	org/openscience/cdk/tools/GenerateFragments.java
20	org/openscience/cdk/tools/CDKUtilities.java
21	org/openscience/cdk/tools/features/MoleculeFeaturesTool.java
22	org/openscience/cdk/tools/HOSECodeAnalyser.java
23	org/openscience/cdk/tools/BremserOneSphereHOSECodePredictor.java
24	org/openscience/cdk/tools/FixedSizeStack.java
25	org/openscience/cdk/tools/DataFeaturesTool.java
26	org/openscience/cdk/tools/DeAromatizationTool.java
27	org/openscience/cdk/tools/SwissArmyKnife.java
28	org/openscience/cdk/tools/GridGenerator.java
29	org/openscience/cdk/config/Elements.java
30	org/openscience/cdk/config/ElementPTFactory.java
31	org/openscience/cdk/config/elements/ElementPTHandler.java
32	org/openscience/cdk/config/elements/ElementPTReader.java
33	org/openscience/cdk/Vibration.java
34	org/openscience/cdk/atomtype/MMFF94AtomTypeMatcher.java
35	org/openscience/cdk/atomtype/MM2AtomTypeMatcher.java
36	org/openscience/cdk/modeling/forcefield/ForceFieldTools.java
37	org/openscience/cdk/iupac/parser/NomParser.java
38	org/openscience/cdk/iupac/parser/MoleculeBuilder.java
39	org/openscience/cdk/iupac/parser/TokenMgrError.java
40	org/openscience/cdk/iupac/parser/SimpleCharStream.java
41	org/openscience/cdk/iupac/parser/Token.java
42	org/openscience/cdk/iupac/parser/ParseException.java
43	org/openscience/cdk/iupac/parser/NomParserConstants.java
44	org/openscience/cdk/iupac/parser/NomParserTokenManager.java
45	org/openscience/cdk/iupac/parser/AttachedGroup.java
46	org/openscience/cdk/geometry/alignment/KabschAlignment.java
47	org/openscience/cdk/geometry/RDFCalculator.java	35	org/openscience/cdk/geometry/RDFCalculator.java
		36	org/openscience/cdk/geometry/IRDFWeightFunction.java
48	org/openscience/cdk/geometry/AtomTools.java	37	org/openscience/cdk/geometry/AtomTools.java
49	org/openscience/cdk/geometry/Projector.java	38	org/openscience/cdk/geometry/surface/NumericalSurface.java
50	org/openscience/cdk/geometry/surface/Tessellate.java	39	org/openscience/cdk/geometry/surface/Tessellate.java
51	org/openscience/cdk/geometry/surface/NeighborList.java	40	org/openscience/cdk/geometry/surface/NeighborList.java
52	org/openscience/cdk/geometry/surface/NumericalSurface.java
53	org/openscience/cdk/geometry/surface/Triangle.java	41	org/openscience/cdk/geometry/surface/Triangle.java
54	org/openscience/cdk/geometry/~~IRDFW~~e~~ightFun~~ction.java	42	org/openscience/cdk/geometry/alignment/KabschAlignment.java
55	org/openscience/cdk/~~gra~~ph/Ato~~mCon~~t~~ainerB~~o~~ndPermut~~or.java	43	org/openscience/cdk/exception/IncorrectUseOfCDKCoreClassError.java
56	org/openscience/cdk/graph/~~AtomCo~~ntain~~erAtom~~Per~~mu~~tor.java	44	org/openscience/cdk/graph/invariant/EquivalentClassPartitioner.java
		45	org/openscience/cdk/graph/invariant/GIMatrix.java
57	org/openscience/cdk/graph/invariant/HuLuIndexTool.java	46	org/openscience/cdk/graph/invariant/HuLuIndexTool.java
58	org/openscience/cdk/graph/invariant/exception/BadMatrixFormatException.java	47	org/openscience/cdk/graph/invariant/exception/BadMatrixFormatException.java
59	org/openscience/cdk/graph/invariant/exception/MatrixNotInvertibleException.java
60	org/openscience/cdk/graph/invariant/exception/IndexOutOfBoundsException.java	48	org/openscience/cdk/graph/invariant/exception/IndexOutOfBoundsException.java
61	org/openscience/cdk/graph/invariant/~~Equ~~iva~~lentClassPa~~rtitioner.java	49	org/openscience/cdk/graph/invariant/exception/MatrixNotInvertibleException.java
62	org/openscience/cdk/graph/invariant/GIMatrix.java
63	org/openscience/cdk/graph/matrix/TopologicalMatrix.java
64	org/openscience/cdk/graph/AtomContainerPermutor.java	50	org/openscience/cdk/graph/AtomContainerPermutor.java
		51	org/openscience/cdk/graph/AtomContainerBondPermutor.java
		52	org/openscience/cdk/graph/matrix/TopologicalMatrix.java
		53	org/openscience/cdk/graph/AtomContainerAtomPermutor.java
		54	org/openscience/cdk/protein/ProteinPocketFinder.java
		55	org/openscience/cdk/atomtype/MM2AtomTypeMatcher.java
		56	org/openscience/cdk/atomtype/MMFF94AtomTypeMatcher.java
		57	org/openscience/cdk/Vibration.java
65	org/openscience/cdk/PhysicalConstants.java	58	org/openscience/cdk/PhysicalConstants.java
		59	org/openscience/cdk/index/CASNumber.java
		60	org/openscience/cdk/iupac/parser/MoleculeBuilder.java
		61	org/openscience/cdk/iupac/parser/NomParserTokenManager.java
		62	org/openscience/cdk/iupac/parser/SimpleCharStream.java
		63	org/openscience/cdk/iupac/parser/Token.java
		64	org/openscience/cdk/iupac/parser/ParseException.java
		65	org/openscience/cdk/iupac/parser/NomParser.java
		66	org/openscience/cdk/iupac/parser/TokenMgrError.java
		67	org/openscience/cdk/iupac/parser/NomParserConstants.java
		68	org/openscience/cdk/iupac/parser/AttachedGroup.java
		69	org/openscience/cdk/io/INChIReader.java
66	org/openscience/cdk/io/CrystClustReader.java	70	org/openscience/cdk/io/CrystClustReader.java
67	org/openscience/cdk/io/ZMatrixReader.java	71	org/openscience/cdk/io/ZMatrixReader.java
68	org/openscience/cdk/io/CrystClustWriter.java
69	org/openscience/cdk/io/ShelXWriter.java	72	org/openscience/cdk/io/ShelXWriter.java
70	org/openscience/cdk/io/INChIReader.java
71	org/openscience/cdk/io/iterator/IteratingMDLConformerReader.java
72	org/openscience/cdk/io/inchi/INChIContentProcessorTool.java
73	org/openscience/cdk/io/inchi/INChIHandler.java
74	org/openscience/cdk/io/GamessReader.java
75	org/openscience/cdk/io/INChIPlainTextReader.java	73	org/openscience/cdk/io/INChIPlainTextReader.java
		74	org/openscience/cdk/io/inchi/INChIHandler.java
		75	org/openscience/cdk/io/inchi/INChIContentProcessorTool.java
		76	org/openscience/cdk/io/iterator/IteratingMDLConformerReader.java
		77	org/openscience/cdk/io/CrystClustWriter.java
76	org/openscience/cdk/io/VASPReader.java	78	org/openscience/cdk/io/VASPReader.java
77	org/openscience/cdk/~~structg~~en/Ra~~ndo~~m~~Gener~~ator.java	79	org/openscience/cdk/io/GamessReader.java
78	org/openscience/cdk/templates/saturatedhydrocarbons/IsoAlkanes.java
79	org/openscience/cdk/templates/MoleculeFactory.java


Offset 1, 7 lines modified		Offset 1, 7 lines modified
1	org/openscience/cdk/similarity/DistanceMoment.java
2	org/openscience/cdk/similarity/Tanimoto.java	1	org/openscience/cdk/similarity/Tanimoto.java
3	org/openscience/cdk/fin~~gerp~~rint~~/Sub~~struc~~tur~~eF~~ing~~e~~rpri~~nter.java	2	org/openscience/cdk/similarity/DistanceMoment.java
4	org/openscience/cdk/fingerprint/EStateFingerprinter.java	3	org/openscience/cdk/fingerprint/EStateFingerprinter.java
5	org/openscience/cdk/fingerprint/MACCSFingerprinter.java
6	org/openscience/cdk/fingerprint/StandardSubstructureSets.java	4	org/openscience/cdk/fingerprint/StandardSubstructureSets.java
7	org/openscience/cdk/fingerprint/ExtendedFingerprinter.java	5	org/openscience/cdk/fingerprint/ExtendedFingerprinter.java
		6	org/openscience/cdk/fingerprint/SubstructureFingerprinter.java
		7	org/openscience/cdk/fingerprint/MACCSFingerprinter.java


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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/
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36	-rw-r--r--··2.0·unx····89941·b-·defN·18-Mar-30·20:15·org/openscience/cdk/modeling/forcefield/data/mm2.prm	36	-rw-r--r--··2.0·unx····89941·b-·defN·18-Mar-30·20:15·org/openscience/cdk/modeling/forcefield/data/mm2.prm
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Offset 1, 23 lines modified		Offset 1, 23 lines modified
1	org/openscience/cdk/~~char~~ges/MM~~FF94Par~~t~~ialCh~~arges.java	1	org/openscience/cdk/modeling/builder3d/MM2BasedAtomTypePattern.java
2	org/openscience/cdk/modeling/for~~cefiel~~d~~/Geo~~metr~~icMinimiz~~er.java	2	org/openscience/cdk/modeling/builder3d/MMFF94BasedParameterSetReader.java
		3	org/openscience/cdk/modeling/builder3d/MMFF94BasedAtomTypePattern.java
		4	org/openscience/cdk/modeling/builder3d/MM2BasedParameterSetReader.java
		5	org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java
		6	org/openscience/cdk/modeling/builder3d/MMFF94ParametersCall.java
		7	org/openscience/cdk/modeling/forcefield/SteepestDescentsMethod.java
		8	org/openscience/cdk/modeling/forcefield/StretchBendInteractions.java
3	org/openscience/cdk/modeling/forcefield/ElectrostaticInteractions.java	9	org/openscience/cdk/modeling/forcefield/ElectrostaticInteractions.java
4	org/openscience/cdk/modeling/forcefield/BondStretching.java
5	org/openscience/cdk/modeling/forcefield/AngleBending.java
6	org/openscience/cdk/modeling/forcefield/SmoothingFunctions.java
7	org/openscience/cdk/modeling/forcefield/Torsions.java
8	org/openscience/cdk/modeling/forcefield/IPotentialFunction.java
9	org/openscience/cdk/modeling/forcefield/ForceField.java
10	org/openscience/cdk/modeling/forcefield/NewtonRaphsonMethod.java
11	org/openscience/cdk/modeling/forcefield/VanDerWaalsInteractions.java	10	org/openscience/cdk/modeling/forcefield/VanDerWaalsInteractions.java
12	org/openscience/cdk/modeling/forcefield/MMFF94EnergyFunction.java	11	org/openscience/cdk/modeling/forcefield/MMFF94EnergyFunction.java
		12	org/openscience/cdk/modeling/forcefield/LineSearch.java
		13	org/openscience/cdk/modeling/forcefield/BondStretching.java
		14	org/openscience/cdk/modeling/forcefield/NewtonRaphsonMethod.java
13	org/openscience/cdk/modeling/forcefield/LineSearchForTheWolfeConditions.java	15	org/openscience/cdk/modeling/forcefield/LineSearchForTheWolfeConditions.java
14	org/openscience/cdk/modeling/forcefield/S~~teep~~est~~Desce~~n~~tsM~~ethod.java	16	org/openscience/cdk/modeling/forcefield/IPotentialFunction.java
15	org/openscience/cdk/modeling/forcefield/ConjugateGradientMethod.java	17	org/openscience/cdk/modeling/forcefield/ConjugateGradientMethod.java
16	org/openscience/cdk/modeling/forcefield/~~StretchBendIn~~teractions.java	18	org/openscience/cdk/modeling/forcefield/Torsions.java
17	org/openscience/cdk/modeling/forcefield/L~~ineS~~earch.java	19	org/openscience/cdk/modeling/forcefield/GeometricMinimizer.java
18	org/openscience/cdk/modeling/~~buil~~der~~3d/MM2BasedA~~t~~omTypePa~~t~~tern~~.java	20	org/openscience/cdk/modeling/forcefield/SmoothingFunctions.java
19	org/openscience/cdk/modeling/~~buil~~der~~3d/MMFF94Ba~~sed~~Paramete~~rSetReader.java	21	org/openscience/cdk/modeling/forcefield/ForceField.java
20	org/openscience/cdk/modeling/~~buil~~der3d~~/MMFF94Param~~eter~~sCall~~.java	22	org/openscience/cdk/modeling/forcefield/AngleBending.java
21	org/openscience/cdk/~~modelin~~g~~/build~~er3d/MM2B~~ased~~Par~~ame~~te~~rSetRead~~er.java	23	org/openscience/cdk/charges/MMFF94PartialCharges.java
22	org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java
23	org/openscience/cdk/modeling/builder3d/MMFF94BasedAtomTypePattern.java


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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/
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28	-rw-r--r--··2.0·unx·····6855·b-·defN·18-Mar-30·20:15·org/openscience/cdk/formula/rules/RDBERule.class	28	-rw-r--r--··2.0·unx·····6855·b-·defN·18-Mar-30·20:15·org/openscience/cdk/formula/rules/RDBERule.class
29	-rw-r--r--··2.0·unx·····1937·b-·defN·18-Mar-30·20:15·org/openscience/cdk/formula/rules/ToleranceRangeRule.class	29	-rw-r--r--··2.0·unx·····1937·b-·defN·18-Mar-30·20:15·org/openscience/cdk/formula/rules/ToleranceRangeRule.class
30	drwxr-xr-x··2.0·unx········0·b-·stor·18-Mar-30·20:15·org/openscience/cdk/tools/	30	drwxr-xr-x··2.0·unx········0·b-·stor·18-Mar-30·20:15·org/openscience/cdk/tools/
31	drwxr-xr-x··2.0·unx········0·b-·stor·18-Mar-30·20:15·org/openscience/cdk/tools/manipulator/	31	drwxr-xr-x··2.0·unx········0·b-·stor·18-Mar-30·20:15·org/openscience/cdk/tools/manipulator/
32	-rw-r--r--··2.0·unx····26089·b-·defN·18-Mar-30·20:15·org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.class	32	-rw-r--r--··2.0·unx····26089·b-·defN·18-Mar-30·20:15·org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.class
33	-rw-r--r--··2.0·unx·····3593·b-·defN·18-Mar-30·20:15·org/openscience/cdk/tools/manipulator/MolecularFormulaRangeManipulator.class	33	-rw-r--r--··2.0·unx·····3593·b-·defN·18-Mar-30·20:15·org/openscience/cdk/tools/manipulator/MolecularFormulaRangeManipulator.class
34	-rw-r--r--··2.0·unx·····6605·b-·defN·18-Mar-30·20:15·org/openscience/cdk/tools/manipulator/MolecularFormulaSetManipulator.class	34	-rw-r--r--··2.0·unx·····6605·b-·defN·18-Mar-30·20:15·org/openscience/cdk/tools/manipulator/MolecularFormulaSetManipulator.class
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Offset 1, 19 lines modified		Offset 1, 19 lines modified
1	org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java
2	org/openscience/cdk/tools/manipulator/MolecularFormulaRangeManipulator.java	1	org/openscience/cdk/tools/manipulator/MolecularFormulaRangeManipulator.java
		2	org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java
3	org/openscience/cdk/tools/manipulator/MolecularFormulaSetManipulator.java	3	org/openscience/cdk/tools/manipulator/MolecularFormulaSetManipulator.java
4	org/openscience/cdk/formula/MassToFormulaTool.java
5	org/openscience/cdk/formula/IsotopeContainer.java
6	org/openscience/cdk/formula/IsotopePatternSimilarity.java	4	org/openscience/cdk/formula/IsotopePatternSimilarity.java
7	org/openscience/cdk/formula/~~Isotop~~e~~Patt~~ernGene~~rator~~.java	5	org/openscience/cdk/formula/rules/ElementRule.java
8	org/openscience/cdk/formula/MolecularFormulaRange.java
9	org/openscience/cdk/formula/rules/IRule.java
10	org/openscience/cdk/formula/rules/NitrogenRule.java	6	org/openscience/cdk/formula/rules/NitrogenRule.java
11	org/openscience/cdk/formula/rules/~~RDB~~ERule.java	7	org/openscience/cdk/formula/rules/IRule.java
12	org/openscience/cdk/formula/rules/ToleranceRangeRule.java	8	org/openscience/cdk/formula/rules/ToleranceRangeRule.java
13	org/openscience/cdk/formula/rules/~~Element~~Rule.java	9	org/openscience/cdk/formula/rules/RDBERule.java
14	org/openscience/cdk/formula/rules/MMElementRule.java
15	org/openscience/cdk/formula/rules/ChargeRule.java	10	org/openscience/cdk/formula/rules/ChargeRule.java
		11	org/openscience/cdk/formula/rules/MMElementRule.java
16	org/openscience/cdk/formula/rules/IsotopePatternRule.java	12	org/openscience/cdk/formula/rules/IsotopePatternRule.java
		13	org/openscience/cdk/formula/IsotopePatternManipulator.java
		14	org/openscience/cdk/formula/IsotopePatternGenerator.java
		15	org/openscience/cdk/formula/MolecularFormulaRange.java
		16	org/openscience/cdk/formula/IsotopeContainer.java
		17	org/openscience/cdk/formula/MassToFormulaTool.java
17	org/openscience/cdk/formula/MolecularFormulaChecker.java	18	org/openscience/cdk/formula/MolecularFormulaChecker.java
18	org/openscience/cdk/formula/IsotopePattern.java	19	org/openscience/cdk/formula/IsotopePattern.java
19	org/openscience/cdk/formula/IsotopePatternManipulator.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
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Offset 1, 45 lines modified		Offset 1, 45 lines modified
1	org/openscience/cdk/~~interf~~a~~ces~~/I~~AtomP~~arity.java	1	org/openscience/cdk/graph/matrix/IGraphMatrix.java
2	org/openscience/cdk/interfaces/I~~ChemFil~~e.java	2	org/openscience/cdk/interfaces/IBioPolymer.java
3	org/openscience/cdk/interfaces/IR~~eact~~ionSet.java	3	org/openscience/cdk/interfaces/IRingSet.java
4	org/openscience/cdk/interfaces/I~~ChemObj~~ec~~tCha~~ngeEvent.java	4	org/openscience/cdk/interfaces/IMoleculeSet.java
5	org/openscience/cdk/interfaces/IStr~~and~~.java	5	org/openscience/cdk/interfaces/IPDBStructure.java
6	org/openscience/cdk/interfaces/IAtomContainerSet.java
7	org/openscience/cdk/interfaces/IMapping.java	6	org/openscience/cdk/interfaces/IMapping.java
8	org/openscience/cdk/interfaces/IMonomer.java	7	org/openscience/cdk/interfaces/IChemObjectChangeEvent.java
9	org/openscience/cdk/interfaces/IMolecularFormulaSet.java
10	org/openscience/cdk/interfaces/IIsotope.java
11	org/openscience/cdk/interfaces/IElement.java	8	org/openscience/cdk/interfaces/IElement.java
12	org/openscience/cdk/interfaces/I~~ChemObject~~.java	9	org/openscience/cdk/interfaces/IPDBAtom.java
13	org/openscience/cdk/interfaces/I~~Ring~~.java	10	org/openscience/cdk/interfaces/IAdductFormula.java
		11	org/openscience/cdk/interfaces/IMolecularFormulaSet.java
		12	org/openscience/cdk/interfaces/IMolecule.java
		13	org/openscience/cdk/interfaces/IMolecularFormula.java
		14	org/openscience/cdk/interfaces/IAtom.java
		15	org/openscience/cdk/interfaces/IAtomContainerSet.java
14	org/openscience/cdk/interfaces/IChemObjectBuilder.java	16	org/openscience/cdk/interfaces/IChemObjectBuilder.java
		17	org/openscience/cdk/interfaces/IPseudoAtom.java
		18	org/openscience/cdk/interfaces/IReactionSet.java
		19	org/openscience/cdk/interfaces/IIsotope.java
15	org/openscience/cdk/interfaces/IPDBMonomer.java	20	org/openscience/cdk/interfaces/IPDBMonomer.java
16	org/openscience/cdk/interfaces/IPDBPolymer.java	21	org/openscience/cdk/interfaces/IPDBPolymer.java
17	org/openscience/cdk/interfaces/IAtomContainer.java
18	org/openscience/cdk/interfaces/IPDBStructure.java
19	org/openscience/cdk/interfaces/IChemObjectListener.java	22	org/openscience/cdk/interfaces/IChemObjectListener.java
20	org/openscience/cdk/interfaces/I~~Cryst~~al.java	23	org/openscience/cdk/interfaces/IAtomParity.java
21	org/openscience/cdk/interfaces/IRe~~action~~.java	24	org/openscience/cdk/interfaces/IChemModel.java
22	org/openscience/cdk/interfaces/I~~Molecu~~le.java	25	org/openscience/cdk/interfaces/IChemFile.java
23	org/openscience/cdk/interfaces/ISingleElectron.java	26	org/openscience/cdk/interfaces/ISingleElectron.java
		27	org/openscience/cdk/interfaces/IBond.java
		28	org/openscience/cdk/interfaces/IChemSequence.java
		29	org/openscience/cdk/interfaces/IReaction.java
24	org/openscience/cdk/interfaces/ILonePair.java	30	org/openscience/cdk/interfaces/ILonePair.java
25	org/openscience/cdk/interfaces/IPolymer.java
26	org/openscience/cdk/interfaces/IChemModel.java
27	org/openscience/cdk/interfaces/IRingSet.java
28	org/openscience/cdk/interfaces/IFragmentAtom.java
29	org/openscience/cdk/interfaces/IAminoAcid.java	31	org/openscience/cdk/interfaces/IAminoAcid.java
30	org/openscience/cdk/interfaces/IP~~seudoAtom~~.java	32	org/openscience/cdk/interfaces/IPolymer.java
31	org/openscience/cdk/interfaces/IAdductFormula.java
32	org/openscience/cdk/interfaces/IMoleculeSet.java
33	org/openscience/cdk/interfaces/IChemSequence.java
34	org/openscience/cdk/interfaces/IMolecularFormula.java
35	org/openscience/cdk/interfaces/IReactionScheme.java
36	org/openscience/cdk/interfaces/IBond.java
37	org/openscience/cdk/interfaces/IBioPolymer.java
38	org/openscience/cdk/interfaces/IElectronContainer.java	33	org/openscience/cdk/interfaces/IElectronContainer.java
39	org/openscience/cdk/interfaces/IPDBAtom.java
40	org/openscience/cdk/interfaces/IAtomType.java	34	org/openscience/cdk/interfaces/IAtomType.java
41	org/openscience/cdk/interfaces/IAtom.java	35	org/openscience/cdk/interfaces/IAtomContainer.java
42	org/openscience/cdk/g~~raph/m~~at~~rix~~/I~~GraphM~~atrix.java	36	org/openscience/cdk/interfaces/IStrand.java
43	org/openscience/cdk/is~~omo~~r~~phism/~~matchers/I~~QueryAtomCont~~ainer.java	37	org/openscience/cdk/interfaces/IRing.java
		38	org/openscience/cdk/interfaces/IChemObject.java
		39	org/openscience/cdk/interfaces/IFragmentAtom.java
		40	org/openscience/cdk/interfaces/ICrystal.java
		41	org/openscience/cdk/interfaces/IReactionScheme.java
		42	org/openscience/cdk/interfaces/IMonomer.java
44	org/openscience/cdk/isomorphism/matchers/IQueryBond.java	43	org/openscience/cdk/isomorphism/matchers/IQueryBond.java
		44	org/openscience/cdk/isomorphism/matchers/IQueryAtomContainer.java
45	org/openscience/cdk/isomorphism/matchers/IQueryAtom.java	45	org/openscience/cdk/isomorphism/matchers/IQueryAtom.java


Offset 1, 79 lines modified		Offset 1, 79 lines modified
1	org/openscience/cdk/geometry/ZMatrixTools.java	1	org/openscience/cdk/geometry/ZMatrixTools.java
2	org/openscience/cdk/io/pubchemxml/PubChemXMLHelper.java
3	org/openscience/cdk/io/Mol2Reader.java	2	org/openscience/cdk/io/Mol2Reader.java
4	org/openscience/cdk/io/~~cml/CMLErrorH~~andler.java	3	org/openscience/cdk/io/HINReader.java
5	org/openscience/cdk/io/cm~~l/I~~C~~MLConv~~ent~~ion~~.java	4	org/openscience/cdk/io/ISimpleChemObjectReader.java
6	org/openscience/cdk/io/~~cml/CMLSt~~ack.java	5	org/openscience/cdk/io/Gaussian98Reader.java
7	org/openscience/cdk/io/cm~~l/~~C~~MLReactionModule~~.java	6	org/openscience/cdk/io/PCCompoundXMLReader.java
		7	org/openscience/cdk/io/XYZWriter.java
		8	org/openscience/cdk/io/MDLRXNV2000Reader.java
		9	org/openscience/cdk/io/PDBWriter.java
		10	org/openscience/cdk/io/DefaultChemObjectWriter.java
		11	org/openscience/cdk/io/Gaussian03Reader.java
		12	org/openscience/cdk/io/DefaultChemObjectReader.java
		13	org/openscience/cdk/io/HINWriter.java
		14	org/openscience/cdk/io/pubchemxml/PubChemXMLHelper.java
		15	org/openscience/cdk/io/IChemObjectIO.java
		16	org/openscience/cdk/io/GhemicalMMReader.java
		17	org/openscience/cdk/io/CIFReader.java
		18	org/openscience/cdk/io/MDLV3000Reader.java
		19	org/openscience/cdk/io/CDKSourceCodeWriter.java
		20	org/openscience/cdk/io/MDLWriter.java
8	org/openscience/cdk/io/cml/JMOLANIMATIONConvention.java	21	org/openscience/cdk/io/cml/JMOLANIMATIONConvention.java
		22	org/openscience/cdk/io/cml/ICMLConvention.java
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		50	org/openscience/cdk/io/iterator/event/DefaultEventChemObjectReader.java
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		62	org/openscience/cdk/io/MDLRXNWriter.java
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Offset 1, 90 lines modified		Offset 1, 90 lines modified
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85	org.openscience.cdk.io.formats.CRK3DFormat	70	org.openscience.cdk.io.formats.MDLRXNV3000Format
86	org.openscience.cdk.io.formats.SDFFormat
87	org.openscience.cdk.io.formats.CDKSourceCodeFormat
88	org.openscience.cdk.io.formats.XYZFormat
89	org.openscience.cdk.io.formats.SpartanFormat	71	org.openscience.cdk.io.formats.SpartanFormat
		72	org.openscience.cdk.io.formats.PCModelFormat
		73	org.openscience.cdk.io.formats.SMILESFIXFormat
		74	org.openscience.cdk.io.formats.MDLV2000Format
		75	org.openscience.cdk.io.formats.PQSChemFormat
		76	org.openscience.cdk.io.formats.GhemicalMMFormat
		77	org.openscience.cdk.io.formats.CACheFormat
		78	org.openscience.cdk.io.formats.MDLFormat
		79	org.openscience.cdk.io.formats.JMEFormat
		80	org.openscience.cdk.io.formats.HINFormat
90	org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat	81	org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
		82	org.openscience.cdk.io.formats.SDFFormat
		83	org.openscience.cdk.io.formats.CMLFormat
		84	org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
		85	org.openscience.cdk.io.formats.MDLV3000Format
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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/FormatFactory.java
2	org/openscience/cdk/io/formats/~~IRe~~s~~ource~~Format.java	2	org/openscience/cdk/io/formats/Gaussian03Format.java
3	org/openscience/cdk/io/formats/~~JME~~Format.java	3	org/openscience/cdk/io/formats/XYZFormat.java
4	org/openscience/cdk/io/formats/ShelXFormat.java	4	org/openscience/cdk/io/formats/QChemFormat.java
5	org/openscience/cdk/io/formats/~~Cry~~s~~tClus~~tFormat.java	5	org/openscience/cdk/io/formats/GaussianInputFormat.java
		6	org/openscience/cdk/io/formats/PubChemSubstancesASNFormat.java
6	org/openscience/cdk/io/formats/MMODFormat.java	7	org/openscience/cdk/io/formats/MMODFormat.java
7	org/openscience/cdk/io/formats/M~~OPAC7~~Format.java	8	org/openscience/cdk/io/formats/PDBMLFormat.java
8	org/openscience/cdk/io/formats/~~Gaussian95~~Format.java	9	org/openscience/cdk/io/formats/PubChemASNFormat.java
9	org/openscience/cdk/io/formats/YasaraFormat.java
10	org/openscience/cdk/io/formats/CIFFormat.java
11	org/openscience/cdk/io/formats/ADFFormat.java
12	org/openscience/cdk/io/formats/MOPAC97Format.java
13	org/openscience/cdk/io/formats/MDLRXNV3000Format.java
14	org/openscience/cdk/io/formats/IChemFormat.java
15	org/openscience/cdk/io/formats/GamessFormat.java
16	org/openscience/cdk/io/formats/INChIPlainTextFormat.java
17	org/openscience/cdk/io/formats/JaguarFormat.java
18	org/openscience/cdk/io/formats/Gaussian90Format.java
19	org/openscience/cdk/io/formats/POVRayFormat.java
20	org/openscience/cdk/io/formats/MDLV2000Format.java
21	org/openscience/cdk/io/formats/SybylDescriptorFormat.java
22	org/openscience/cdk/io/formats/ChemDrawFormat.java
23	org/openscience/cdk/io/formats/RawCopyFormat.java
24	org/openscience/cdk/io/formats/PubChemCompoundsXMLFormat.java
25	org/openscience/cdk/io/formats/MOPAC2002Format.java
26	org/openscience/cdk/io/formats/INChIFormat.java
27	org/openscience/cdk/io/formats/SVGFormat.java
28	org/openscience/cdk/io/formats/PDBFormat.java	10	org/openscience/cdk/io/formats/PDBFormat.java
29	org/openscience/cdk/io/formats/DaltonFormat.java
30	org/openscience/cdk/io/formats/Chem3D_Cartesian_2Format.java
31	org/openscience/cdk/io/formats/Mol2Format.java
32	org/openscience/cdk/io/formats/SMILESFIXFormat.java
33	org/openscience/cdk/io/formats/CMLRSSFormat.java
34	org/openscience/cdk/io/formats/MPQCFormat.java
35	org/openscience/cdk/io/formats/PQSChemFormat.java
36	org/openscience/cdk/io/formats/Gaussian92Format.java
37	org/openscience/cdk/io/formats/TurboMoleFormat.java
38	org/openscience/cdk/io/formats/GaussianInputFormat.java
39	org/openscience/cdk/io/formats/ZMatrixFormat.java	11	org/openscience/cdk/io/formats/ZMatrixFormat.java
40	org/openscience/cdk/io/formats/~~GhemicalMM~~Format.java	12	org/openscience/cdk/io/formats/ABINITFormat.java
41	org/openscience/cdk/io/formats/XEDFormat.java
42	org/openscience/cdk/io/formats/PubChemFormat.java	13	org/openscience/cdk/io/formats/PubChemFormat.java
43	org/openscience/cdk/io/formats/CTXFormat.java	14	org/openscience/cdk/io/formats/INChIFormat.java
44	org/openscience/cdk/io/formats/GRO~~MOS~~96Format.java	15	org/openscience/cdk/io/formats/MOPAC97Format.java
		16	org/openscience/cdk/io/formats/BSFormat.java
45	org/openscience/cdk/io/formats/CacaoCartesianFormat.java	17	org/openscience/cdk/io/formats/CacaoCartesianFormat.java
46	org/openscience/cdk/io/formats/~~MOPAC93~~Format.java	18	org/openscience/cdk/io/formats/ViewmolFormat.java
47	org/openscience/cdk/io/formats/UniCh~~emXYZ~~Format.java	19	org/openscience/cdk/io/formats/INChIPlainTextFormat.java
48	org/openscience/cdk/io/formats/IChemFormatMatcher.java	20	org/openscience/cdk/io/formats/IChemFormatMatcher.java
49	org/openscience/cdk/io/formats/P~~ubChemSubst~~a~~ncesXM~~LFormat.java	21	org/openscience/cdk/io/formats/POVRayFormat.java
50	org/openscience/cdk/io/formats/~~PubChemSubs~~tancesASNFormat.java	22	org/openscience/cdk/io/formats/GamessFormat.java
51	org/openscience/cdk/io/formats/~~HIN~~Format.java	23	org/openscience/cdk/io/formats/DMol3Format.java
52	org/openscience/cdk/io/formats/~~CML~~Format.java	24	org/openscience/cdk/io/formats/SybylDescriptorFormat.java
53	org/openscience/cdk/io/formats/~~Gaussian03~~Format.java	25	org/openscience/cdk/io/formats/CTXFormat.java
		26	org/openscience/cdk/io/formats/CMLRSSFormat.java
		27	org/openscience/cdk/io/formats/CIFFormat.java
		28	org/openscience/cdk/io/formats/YasaraFormat.java
		29	org/openscience/cdk/io/formats/CDKSourceCodeFormat.java
		30	org/openscience/cdk/io/formats/DaltonFormat.java
		31	org/openscience/cdk/io/formats/IChemFormat.java
		32	org/openscience/cdk/io/formats/ShelXFormat.java
		33	org/openscience/cdk/io/formats/FingerprintFormat.java
		34	org/openscience/cdk/io/formats/Gaussian94Format.java
54	org/openscience/cdk/io/formats/Gaussian98Format.java	35	org/openscience/cdk/io/formats/Gaussian98Format.java
		36	org/openscience/cdk/io/formats/Chem3D_Cartesian_1Format.java
		37	org/openscience/cdk/io/formats/DOCK5Format.java
		38	org/openscience/cdk/io/formats/XEDFormat.java
		39	org/openscience/cdk/io/formats/ADFFormat.java
55	org/openscience/cdk/io/formats/NWChemFormat.java	40	org/openscience/cdk/io/formats/NWChemFormat.java
56	org/openscience/cdk/io/formats/~~MacroModel~~Format.java	41	org/openscience/cdk/io/formats/UniChemXYZFormat.java
57	org/openscience/cdk/io/formats/GhemicalSPMFormat.java
58	org/openscience/cdk/io/formats/PCModelFormat.java
59	org/openscience/cdk/io/formats/ABINITFormat.java
60	org/openscience/cdk/io/formats/AlchemyFormat.java	42	org/openscience/cdk/io/formats/AlchemyFormat.java
61	org/openscience/cdk/io/formats/~~CRK~~2DFormat.java	43	org/openscience/cdk/io/formats/Mol2Format.java
62	org/openscience/cdk/io/formats/SMARTSFormat.java
63	org/openscience/cdk/io/formats/Gaussian94Format.java
64	org/openscience/cdk/io/formats/MDLFormat.java
65	org/openscience/cdk/io/formats/Aces2Format.java	44	org/openscience/cdk/io/formats/Aces2Format.java
		45	org/openscience/cdk/io/formats/MOPAC7Format.java
		46	org/openscience/cdk/io/formats/CrystClustFormat.java
		47	org/openscience/cdk/io/formats/PubChemSubstancesXMLFormat.java
		48	org/openscience/cdk/io/formats/TurboMoleFormat.java
		49	org/openscience/cdk/io/formats/IResourceFormat.java
		50	org/openscience/cdk/io/formats/CRK3DFormat.java
		51	org/openscience/cdk/io/formats/RawCopyFormat.java
		52	org/openscience/cdk/io/formats/Gaussian92Format.java
66	org/openscience/cdk/io/formats/PMPFormat.java	53	org/openscience/cdk/io/formats/PMPFormat.java
67	org/openscience/cdk/io/formats/C~~hemtool~~Format.java	54	org/openscience/cdk/io/formats/CRK2DFormat.java
68	org/openscience/cdk/io/formats/~~MDLRXN~~Format.java	55	org/openscience/cdk/io/formats/GROMOS96Format.java
69	org/openscience/cdk/io/formats/~~CAChe~~Format.java	56	org/openscience/cdk/io/formats/ZindoFormat.java
70	org/openscience/cdk/io/formats/~~PDBML~~Format.java	57	org/openscience/cdk/io/formats/Gaussian95Format.java
		58	org/openscience/cdk/io/formats/Chem3D_Cartesian_2Format.java
		59	org/openscience/cdk/io/formats/JaguarFormat.java
		60	org/openscience/cdk/io/formats/MOPAC93Format.java
		61	org/openscience/cdk/io/formats/ChemDrawFormat.java
71	org/openscience/cdk/io/formats/SMILESFormat.java	62	org/openscience/cdk/io/formats/SMILESFormat.java
72	org/openscience/cdk/io/formats/~~Chem3D_~~Car~~tesian_1~~Format.java	63	org/openscience/cdk/io/formats/MacroModelFormat.java
		64	org/openscience/cdk/io/formats/GhemicalSPMFormat.java
		65	org/openscience/cdk/io/formats/BGFFormat.java
		66	org/openscience/cdk/io/formats/MPQCFormat.java
73	org/openscience/cdk/io/formats/PubChemCompoundXMLFormat.java	67	org/openscience/cdk/io/formats/PubChemCompoundXMLFormat.java
74	org/openscience/cdk/io/formats/~~PubChemSubstanceXML~~Format.java	68	org/openscience/cdk/io/formats/MOPAC2002Format.java
75	org/openscience/cdk/io/formats/TinkerMM2Format.java
76	org/openscience/cdk/io/formats/MDLV3000Format.java
77	org/openscience/cdk/io/formats/FingerprintFormat.java
78	org/openscience/cdk/io/formats/PubChemASNFormat.java
79	org/openscience/cdk/io/formats/DOCK5Format.java
80	org/openscience/cdk/io/formats/ZindoFormat.java
81	org/openscience/cdk/io/formats/VASPFormat.java
82	org/openscience/cdk/io/formats/QChemFormat.java
83	org/openscience/cdk/io/formats/TinkerXYZFormat.java	69	org/openscience/cdk/io/formats/TinkerXYZFormat.java
84	org/openscience/cdk/io/formats/BSFormat.java	70	org/openscience/cdk/io/formats/TinkerMM2Format.java
85	org/openscience/cdk/io/formats/~~BGF~~Format.java	71	org/openscience/cdk/io/formats/ChemtoolFormat.java
86	org/openscience/cdk/io/formats/ViewmolFormat.java
87	org/openscience/cdk/io/formats/CacaoInternalFormat.java	72	org/openscience/cdk/io/formats/CacaoInternalFormat.java
88	org/openscience/cdk/io/formats/DM~~ol3~~Format.java	73	org/openscience/cdk/io/formats/SVGFormat.java
89	org/openscience/cdk/io/formats/CRK3DFormat.java	74	org/openscience/cdk/io/formats/MDLRXNV3000Format.java
90	org/openscience/cdk/io/formats/SDFFormat.java
91	org/openscience/cdk/io/formats/CDKSourceCodeFormat.java
92	org/openscience/cdk/io/formats/XYZFormat.java
93	org/openscience/cdk/io/formats/SpartanFormat.java	75	org/openscience/cdk/io/formats/SpartanFormat.java
		76	org/openscience/cdk/io/formats/PCModelFormat.java
		77	org/openscience/cdk/io/formats/SMILESFIXFormat.java
		78	org/openscience/cdk/io/formats/MDLV2000Format.java
		79	org/openscience/cdk/io/formats/PQSChemFormat.java
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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
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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/QueryAtomContainer.java
2	org/openscience/cdk/isomorphism/matchers/OrderQueryBond.java	1	org/openscience/cdk/isomorphism/matchers/OrderQueryBond.java
3	org/openscience/cdk/isomorphism/matchers/Symbol~~AndCharge~~QueryAtom.java	2	org/openscience/cdk/isomorphism/matchers/SymbolQueryAtom.java
4	org/openscience/cdk/isomorphism/matchers/SymbolSetQueryAtom.java	3	org/openscience/cdk/isomorphism/matchers/SymbolSetQueryAtom.java
		4	org/openscience/cdk/isomorphism/matchers/SymbolAndChargeQueryAtom.java
		5	org/openscience/cdk/isomorphism/matchers/QueryAtomContainerCreator.java
		6	org/openscience/cdk/isomorphism/matchers/QueryAtomContainer.java
5	org/openscience/cdk/isomorphism/matchers/SymbolChargeIDQueryAtom.java	7	org/openscience/cdk/isomorphism/matchers/SymbolChargeIDQueryAtom.java
		8	org/openscience/cdk/isomorphism/matchers/OrderQueryBondOrderOnly.java
6	org/openscience/cdk/isomorphism/matchers/InverseSymbolSetQueryAtom.java	9	org/openscience/cdk/isomorphism/matchers/InverseSymbolSetQueryAtom.java
7	org/openscience/cdk/isomorphism/matchers/smarts/~~SMARTS~~Bond.java	10	org/openscience/cdk/isomorphism/matchers/smarts/AnyOrderQueryBond.java
8	org/openscience/cdk/isomorphism/matchers/smarts/AromaticAtom.java	11	org/openscience/cdk/isomorphism/matchers/smarts/AromaticAtom.java
9	org/openscience/cdk/isomorphism/matchers/smarts/AromaticOrSingleQueryBond.java	12	org/openscience/cdk/isomorphism/matchers/smarts/AromaticOrSingleQueryBond.java
10	org/openscience/cdk/isomorphism/matchers/smarts/AnyOrderQueryBond.java
11	org/openscience/cdk/isomorphism/matchers/smarts/AromaticQueryBond.java
12	org/openscience/cdk/isomorphism/matchers/smarts/AnyAtom.java	13	org/openscience/cdk/isomorphism/matchers/smarts/AnyAtom.java
13	org/openscience/cdk/isomorphism/matchers/smarts/SMARTSAtom.java	14	org/openscience/cdk/isomorphism/matchers/smarts/SMARTSAtom.java
14	org/openscience/cdk/isomorphism/matchers/~~Que~~ryAtomContai~~nerC~~r~~eator~~.java	15	org/openscience/cdk/isomorphism/matchers/smarts/AromaticQueryBond.java
15	org/openscience/cdk/isomorphism/matchers/~~OrderQue~~r~~yBondOrderO~~nly.java	16	org/openscience/cdk/isomorphism/matchers/smarts/SMARTSBond.java
16	org/openscience/cdk/isomorphism/matchers/SymbolQueryAtom.java

+org.openscience.cdk.libio.cml.QSARCustomizer
+org.openscience.cdk.libio.cml.PDBAtomCustomizer
+org.openscience.cdk.libio.cml.MDMoleculeCustomizer
+org.openscience.cdk.libio.cml.PDBAtomCustomizer
+org.openscience.cdk.libio.cml.QSARCustomizer


Offset 1, 5 lines modified		Offset 1, 5 lines modified
1	org/openscience/cdk/libio/cml/MDMoleculeCustomizer.java
2	org/openscience/cdk/libio/md/Residue.java
3	org/openscience/cdk/libio/md/ChargeGroup.java
4	org/openscience/cdk/libio/md/MDMolecule.java	1	org/openscience/cdk/libio/md/MDMolecule.java
		2	org/openscience/cdk/libio/md/ChargeGroup.java
		3	org/openscience/cdk/libio/md/Residue.java
		4	org/openscience/cdk/libio/cml/MDMoleculeCustomizer.java
5	org/openscience/cdk/io/cml/MDMoleculeConvention.java	5	org/openscience/cdk/io/cml/MDMoleculeConvention.java


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4	-rw-r--r--··2.0·unx·····1844·b-·defN·18-Mar-30·20:15·nonotify.javafiles	4	-rw-r--r--··2.0·unx·····1844·b-·defN·18-Mar-30·20:15·nonotify.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/nonotify/	8	drwxr-xr-x··2.0·unx········0·b-·stor·18-Mar-30·20:15·org/openscience/cdk/nonotify/
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41	-rw-r--r--··2.0·unx······947·b-·defN·18-Mar-30·20:15·org/openscience/cdk/nonotify/NNReactionScheme.class	41	-rw-r--r--··2.0·unx······947·b-·defN·18-Mar-30·20:15·org/openscience/cdk/nonotify/NNReactionScheme.class
42	-rw-r--r--··2.0·unx······935·b-·defN·18-Mar-30·20:15·org/openscience/cdk/nonotify/NNReactionSet.class	42	-rw-r--r--··2.0·unx······935·b-·defN·18-Mar-30·20:15·org/openscience/cdk/nonotify/NNReactionSet.class
43	-rw-r--r--··2.0·unx·····1406·b-·defN·18-Mar-30·20:15·org/openscience/cdk/nonotify/NNRing.class	43	-rw-r--r--··2.0·unx·····1406·b-·defN·18-Mar-30·20:15·org/openscience/cdk/nonotify/NNRing.class
44	-rw-r--r--··2.0·unx······875·b-·defN·18-Mar-30·20:15·org/openscience/cdk/nonotify/NNRingSet.class	44	-rw-r--r--··2.0·unx······875·b-·defN·18-Mar-30·20:15·org/openscience/cdk/nonotify/NNRingSet.class
45	-rw-r--r--··2.0·unx·····1121·b-·defN·18-Mar-30·20:15·org/openscience/cdk/nonotify/NNSingleElectron.class	45	-rw-r--r--··2.0·unx·····1121·b-·defN·18-Mar-30·20:15·org/openscience/cdk/nonotify/NNSingleElectron.class
46	-rw-r--r--··2.0·unx······915·b-·defN·18-Mar-30·20:15·org/openscience/cdk/nonotify/NNStrand.class	46	-rw-r--r--··2.0·unx······915·b-·defN·18-Mar-30·20:15·org/openscience/cdk/nonotify/NNStrand.class
47	-rw-r--r--··2.0·unx····16986·b-·defN·18-Mar-30·20:15·org/openscience/cdk/nonotify/NoNotificationChemObjectBuilder.class	47	-rw-r--r--··2.0·unx····16986·b-·defN·18-Mar-30·20:15·org/openscience/cdk/nonotify/NoNotificationChemObjectBuilder.class
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Offset 1, 39 lines modified		Offset 1, 39 lines modified
1	org/openscience/cdk/nonotify/NN~~Bio~~Polymer.java	1	org/openscience/cdk/nonotify/NNPolymer.java
2	org/openscience/cdk/nonotify/NNC~~rys~~tal.java	2	org/openscience/cdk/nonotify/NoNotificationChemObjectBuilder.java
3	org/openscience/cdk/nonotify/NNP~~DBStr~~u~~cture~~.java	3	org/openscience/cdk/nonotify/NNMoleculeSet.java
4	org/openscience/cdk/nonotify/NNC~~hemF~~ile.java	4	org/openscience/cdk/nonotify/NNMapping.java
5	org/openscience/cdk/nonotify/NNAtomType.java
6	org/openscience/cdk/nonotify/NNAminoAcid.java
7	org/openscience/cdk/nonotify/NNAtomParity.java	5	org/openscience/cdk/nonotify/NNAtomParity.java
		6	org/openscience/cdk/nonotify/NNReactionScheme.java
		7	org/openscience/cdk/nonotify/NNAtomType.java
8	org/openscience/cdk/nonotify/NNPseudoAtom.java	8	org/openscience/cdk/nonotify/NNPseudoAtom.java
9	org/openscience/cdk/nonotify/NN~~Isotop~~e.java	9	org/openscience/cdk/nonotify/NNChemFile.java
10	org/openscience/cdk/nonotify/NNChemModel.java
11	org/openscience/cdk/nonotify/NNAtomContainerSet.java	10	org/openscience/cdk/nonotify/NNAtomContainerSet.java
12	org/openscience/cdk/nonotify/NN~~Reac~~tion~~Sche~~me.java	11	org/openscience/cdk/nonotify/NNBioPolymer.java
13	org/openscience/cdk/nonotify/NNReaction.java
14	org/openscience/cdk/nonotify/NNAdductFormula.java
15	org/openscience/cdk/nonotify/NNChemObject.java
16	org/openscience/cdk/nonotify/NNRingSet.java
17	org/openscience/cdk/nonotify/NNSingleElectron.java
18	org/openscience/cdk/nonotify/NNMapping.java
19	org/openscience/cdk/nonotify/NNElectronContainer.java	12	org/openscience/cdk/nonotify/NNElectronContainer.java
20	org/openscience/cdk/nonotify/NNLonePair.java
21	org/openscience/cdk/nonotify/NNFragmentAtom.java
22	org/openscience/cdk/nonotify/NNStrand.java	13	org/openscience/cdk/nonotify/NNStrand.java
23	org/openscience/cdk/nonotify/NNBond.java	14	org/openscience/cdk/nonotify/NNPDBPolymer.java
24	org/openscience/cdk/nonotify/NN~~Reacti~~onSet.java	15	org/openscience/cdk/nonotify/NNMonomer.java
25	org/openscience/cdk/nonotify/NN~~ChemSequ~~ence.java	16	org/openscience/cdk/nonotify/NNPDBMonomer.java
26	org/openscience/cdk/nonotify/NoNotificationChemObjectBuilder.java
27	org/openscience/cdk/nonotify/NNMolecule.java	17	org/openscience/cdk/nonotify/NNMolecule.java
		18	org/openscience/cdk/nonotify/NNChemModel.java
		19	org/openscience/cdk/nonotify/NNLonePair.java
		20	org/openscience/cdk/nonotify/NNMolecularFormulaSet.java
		21	org/openscience/cdk/nonotify/NNAminoAcid.java
28	org/openscience/cdk/nonotify/NNMolecularFormula.java	22	org/openscience/cdk/nonotify/NNMolecularFormula.java
29	org/openscience/cdk/nonotify/NNPDBMonomer.java	23	org/openscience/cdk/nonotify/NNIsotope.java
30	org/openscience/cdk/nonotify/NNMon~~ome~~r.java	24	org/openscience/cdk/nonotify/NNBond.java
31	org/openscience/cdk/nonotify/NNRing.java	25	org/openscience/cdk/nonotify/NNFragmentAtom.java
32	org/openscience/cdk/nonotify/NNP~~olymer~~.java	26	org/openscience/cdk/nonotify/NNPDBAtom.java
33	org/openscience/cdk/nonotify/NN~~PDBPolym~~er.java	27	org/openscience/cdk/nonotify/NNChemSequence.java
		28	org/openscience/cdk/nonotify/NNPDBStructure.java
		29	org/openscience/cdk/nonotify/NNCrystal.java
		30	org/openscience/cdk/nonotify/NNRingSet.java
		31	org/openscience/cdk/nonotify/NNChemObject.java
		32	org/openscience/cdk/nonotify/NNElement.java
		33	org/openscience/cdk/nonotify/NNReaction.java
34	org/openscience/cdk/nonotify/NNAtomContainer.java	34	org/openscience/cdk/nonotify/NNAtomContainer.java
35	org/openscience/cdk/nonotify/NNMoleculeSet.java
36	org/openscience/cdk/nonotify/NNAtom.java	35	org/openscience/cdk/nonotify/NNAtom.java
37	org/openscience/cdk/nonotify/NN~~Ele~~ment.java	36	org/openscience/cdk/nonotify/NNRing.java
38	org/openscience/cdk/nonotify/NNMo~~lec~~ularFormula~~Set~~.java	37	org/openscience/cdk/nonotify/NNAdductFormula.java
39	org/openscience/cdk/nonotify/NN~~PDBA~~tom.java	38	org/openscience/cdk/nonotify/NNReactionSet.java
		39	org/openscience/cdk/nonotify/NNSingleElectron.java