/dports/science/cdk/cdk-cdk-2.3/base/test-core/src/test/java/org/openscience/cdk/atomtype/ |
H A D | CDKAtomTypeMatcherFilesTest.java | 55 IAtomContainer mol = ChemFileManipulator.getAllAtomContainers(chemFile).get(0); in testFile3() 74 IAtomContainer mol = ChemFileManipulator.getAllAtomContainers(chemFile).get(0); in testBug3141611() 90 IAtomContainer mol = ChemFileManipulator.getAllAtomContainers(chemFile).get(0); in testOla28() 108 IAtomContainer mol1 = ChemFileManipulator.getAllAtomContainers(chemFile).get(0); in testSmilesFiles() 116 IAtomContainer mol2 = ChemFileManipulator.getAllAtomContainers(chemFile).get(0); in testSmilesFiles()
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/dports/science/cdk/cdk-cdk-2.3/descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/ |
H A D | LengthOverBreadthDescriptorTest.java | 39 List cList = ChemFileManipulator.getAllAtomContainers(content); in testLOBDescriptorCholesterol() 55 List cList = ChemFileManipulator.getAllAtomContainers(content); in testLOBDescriptorCyclohexane() 71 List cList = ChemFileManipulator.getAllAtomContainers(content); in testLOBDescriptorNaphthalene() 88 List cList = ChemFileManipulator.getAllAtomContainers(content); in testLOBDescriptorNButane() 107 List cList = ChemFileManipulator.getAllAtomContainers(content); in testLOBDescriptor2()
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H A D | CPSADescriptorTest.java | 58 List cList = ChemFileManipulator.getAllAtomContainers(content); in testCPSA() 80 List cList = ChemFileManipulator.getAllAtomContainers(content); in testChargedMolecule() 95 List cList = ChemFileManipulator.getAllAtomContainers(content); in testUnChargedMolecule()
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H A D | BCUTDescriptorTest.java | 63 List cList = ChemFileManipulator.getAllAtomContainers(content); in testBCUT() 112 List cList = ChemFileManipulator.getAllAtomContainers(content); in testExtraEigenvalues() 180 List cList = ChemFileManipulator.getAllAtomContainers(content); in testUndefinedValues()
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H A D | MomentOfInertiaDescriptorTest.java | 75 List cList = ChemFileManipulator.getAllAtomContainers(content); in testMomentOfInertia1() 95 List cList = ChemFileManipulator.getAllAtomContainers(content); in testMomentOfInertia2()
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H A D | WeightedPathDescriptorTest.java | 74 List cList = ChemFileManipulator.getAllAtomContainers(content); in testWeightedPathDescriptor() 90 cList = ChemFileManipulator.getAllAtomContainers(content); in testWeightedPathDescriptor()
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H A D | EccentricConnectivityIndexDescriptorTest.java | 58 List cList = ChemFileManipulator.getAllAtomContainers(content); in testEccentricConnectivityIndex()
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/dports/science/cdk/cdk-cdk-2.3/storage/io/src/test/java/org/openscience/cdk/io/ |
H A D | CMLReaderTest.java | 84 List<IAtomContainer> containers = ChemFileManipulator.getAllAtomContainers(cfile); in testBug1248() 119 List<IAtomContainer> containers = ChemFileManipulator.getAllAtomContainers(cfile); in testBug1245() 173 List<IAtomContainer> containers = ChemFileManipulator.getAllAtomContainers(cfile); in testBug1274() 207 List<IAtomContainer> containers = ChemFileManipulator.getAllAtomContainers(cfile); in testBug1275() 233 List<IAtomContainer> containers = ChemFileManipulator.getAllAtomContainers(cfile); in testWedgeBondParsing() 301 List<IAtomContainer> containers = ChemFileManipulator.getAllAtomContainers(cfile); in testSFBug1085912_1()
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H A D | HINReaderTest.java | 144 List<IAtomContainer> cList = ChemFileManipulator.getAllAtomContainers(content); in testIsConnectedFromHINFile() 161 List<IAtomContainer> cList = ChemFileManipulator.getAllAtomContainers(content); in testAromaticRingsLine() 176 List<IAtomContainer> cList = ChemFileManipulator.getAllAtomContainers(content); in testReadAromaticRingsKeyword()
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H A D | Mol2ReaderTest.java | 161 List<IAtomContainer> mols = ChemFileManipulator.getAllAtomContainers(chemFile); in testMultiMol() 176 List<IAtomContainer> mols = ChemFileManipulator.getAllAtomContainers(chemFile); in testMultiMolButSingle() 376 List<IAtomContainer> containers = ChemModelManipulator.getAllAtomContainers(model); in testBug1714794()
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H A D | ReaderFactoryTest.java | 200 for (IAtomContainer container : ChemFileManipulator.getAllAtomContainers(chemFile)) { in testReadGz() 218 for (IAtomContainer container : ChemFileManipulator.getAllAtomContainers(chemFile)) { in testReadGzWithGzipDetection()
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/dports/science/cdk/cdk-cdk-2.3/tool/sdg/src/test/java/org/openscience/cdk/layout/ |
H A D | OverlapResolverTest.java | 68 …IAtomContainer atomContainer = (IAtomContainer) ChemFileManipulator.getAllAtomContainers(chemFile)… in testResolveOverlap1() 95 …IAtomContainer atomContainer = (IAtomContainer) ChemFileManipulator.getAllAtomContainers(chemFile)… in testResolveOverlap2() 115 …IAtomContainer atomContainer = (IAtomContainer) ChemFileManipulator.getAllAtomContainers(chemFile)… in testResolveOverlap3() 136 …IAtomContainer atomContainer = (IAtomContainer) ChemFileManipulator.getAllAtomContainers(chemFile)… in testResolveOverlap4()
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/dports/science/cdk/cdk-cdk-2.3/base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ |
H A D | ReactionSchemeManipulator.java | 49 …public static IAtomContainerSet getAllAtomContainers(IReactionScheme scheme, IAtomContainerSet mol… in getAllAtomContainers() method in ReactionSchemeManipulator 52 for (IAtomContainer ac : getAllAtomContainers(rm, molSet).atomContainers()) { in getAllAtomContainers() 64 … List<IAtomContainer> newAtomContainerSet = ReactionManipulator.getAllAtomContainers(reaction); in getAllAtomContainers() 87 public static IAtomContainerSet getAllAtomContainers(IReactionScheme scheme) { in getAllAtomContainers() method in ReactionSchemeManipulator 88 … return getAllAtomContainers(scheme, scheme.getBuilder().newInstance(IAtomContainerSet.class)); in getAllAtomContainers()
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H A D | MoleculeSetManipulator.java | 64 public static List<IAtomContainer> getAllAtomContainers(IAtomContainerSet set) { in getAllAtomContainers() method in MoleculeSetManipulator 65 return AtomContainerSetManipulator.getAllAtomContainers(set); in getAllAtomContainers()
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H A D | ChemSequenceManipulator.java | 75 public static List<IAtomContainer> getAllAtomContainers(IChemSequence sequence) { in getAllAtomContainers() method in ChemSequenceManipulator 78 acList.addAll(ChemModelManipulator.getAllAtomContainers(model)); in getAllAtomContainers()
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H A D | ChemFileManipulator.java | 102 public static List<IAtomContainer> getAllAtomContainers(IChemFile file) { in getAllAtomContainers() method in ChemFileManipulator 105 acList.addAll(ChemSequenceManipulator.getAllAtomContainers(sequence)); in getAllAtomContainers()
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H A D | AtomContainerSetManipulator.java | 99 public static List<IAtomContainer> getAllAtomContainers(IAtomContainerSet set) { in getAllAtomContainers() method in AtomContainerSetManipulator 213 …List<IAtomContainer> atomContainerList = AtomContainerSetManipulator.getAllAtomContainers(atomCont… in sort()
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H A D | RingSetManipulator.java | 64 … Iterator<IAtomContainer> containers = RingSetManipulator.getAllAtomContainers(ringSet).iterator(); in getAllInOneContainer() 110 public static List<IAtomContainer> getAllAtomContainers(IRingSet set) { in getAllAtomContainers() method in RingSetManipulator
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H A D | ReactionSetManipulator.java | 112 public static List<IAtomContainer> getAllAtomContainers(IReactionSet set) { in getAllAtomContainers() method in ReactionSetManipulator 114 return MoleculeSetManipulator.getAllAtomContainers(getAllMolecules(set)); in getAllAtomContainers()
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/dports/science/cdk/cdk-cdk-2.3/base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/ |
H A D | ReactionSetManipulatorTest.java | 104 Assert.assertEquals(3, ReactionSetManipulator.getAllAtomContainers(set).size()); in testGetAllAtomContainers_IReactionSet() 109 …Iterator<IAtomContainer> atomContainers = ReactionSetManipulator.getAllAtomContainers(set).iterato… in testGetRelevantReaction_IReactionSet_IAtom() 119 …Iterator<IAtomContainer> atomContainers = ReactionSetManipulator.getAllAtomContainers(set).iterato… in testGetRelevantReaction_IReactionSet_IBond() 129 …Iterator<IAtomContainer> atomContainers = ReactionSetManipulator.getAllAtomContainers(set).iterato… in testGetRelevantAtomContainer_IReactionSet_IAtom() 139 …Iterator<IAtomContainer> atomContainers = ReactionSetManipulator.getAllAtomContainers(set).iterato… in testGetRelevantAtomContainer_IReactionSet_IBond() 150 …Iterator<IAtomContainer> atomContainers = ReactionSetManipulator.getAllAtomContainers(set).iterato… in testSetAtomProperties_IReactionSet_Object_Object()
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H A D | ReactionManipulatorTest.java | 180 Assert.assertEquals(3, ReactionManipulator.getAllAtomContainers(reaction).size()); in testGetAllAtomContainers_IReaction() 186 …Iterator<IAtomContainer> atomContainers = ReactionManipulator.getAllAtomContainers(reaction).itera… in testSetAtomProperties_IReactionSet_Object_Object() 208 …Iterator<IAtomContainer> atomContainers = ReactionManipulator.getAllAtomContainers(reaction).itera… in testGetRelevantAtomContainer_IReaction_IAtom() 218 …Iterator<IAtomContainer> atomContainers = ReactionManipulator.getAllAtomContainers(reaction).itera… in testGetRelevantAtomContainer_IReaction_IBond()
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H A D | ReactionSchemeManipulatorTest.java | 63 …Assert.assertEquals(2, ReactionSchemeManipulator.getAllAtomContainers(reactionScheme).getAtomConta… in testGetAllMolecules_IReactionScheme() 79 ReactionSchemeManipulator.getAllAtomContainers(reactionScheme, in testGetAllMolecules_IReactionScheme_IAtomContainerSet() 97 …Assert.assertEquals(3, ReactionSchemeManipulator.getAllAtomContainers(reactionScheme).getAtomConta… in testGetAllMolecules_IReactionScheme2() 128 …Assert.assertEquals(5, ReactionSchemeManipulator.getAllAtomContainers(scheme1).getAtomContainerCou… in testGetAllMolecules_IReactionScheme3()
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/dports/science/cdk/cdk-cdk-2.3/storage/ctab/src/test/java/org/openscience/cdk/io/ |
H A D | MDLV2000ReaderTest.java | 122 List<IAtomContainer> mols = ChemFileManipulator.getAllAtomContainers(chemFile); in testBug3084064() 191 List<IAtomContainer> containersList = ChemFileManipulator.getAllAtomContainers(chemFile); in testAPinene() 206 List<IAtomContainer> containersList = ChemFileManipulator.getAllAtomContainers(chemFile); in testReadingMISOLines() 224 List<IAtomContainer> containersList = ChemFileManipulator.getAllAtomContainers(chemFile); in testMassNumber() 240 List<IAtomContainer> containersList = ChemFileManipulator.getAllAtomContainers(chemFile); in testAlkane() 275 List<IAtomContainer> containersList = ChemFileManipulator.getAllAtomContainers(chemFile); in testFourRing() 290 List<IAtomContainer> containersList = ChemFileManipulator.getAllAtomContainers(chemFile); in testHydrozyamino() 305 List<IAtomContainer> containersList = ChemFileManipulator.getAllAtomContainers(chemFile); in testMethylBenzol() 320 List<IAtomContainer> containersList = ChemFileManipulator.getAllAtomContainers(chemFile); in testPolycarpol() 335 List<IAtomContainer> containersList = ChemFileManipulator.getAllAtomContainers(chemFile); in testReserpine() [all …]
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H A D | MDLReaderTest.java | 136 List<IAtomContainer> containersList = ChemFileManipulator.getAllAtomContainers(chemFile); in testBug1542467() 168 List<IAtomContainer> containersList = ChemFileManipulator.getAllAtomContainers(chemFile); in testSDF() 189 List<IAtomContainer> containersList = ChemFileManipulator.getAllAtomContainers(chemFile); in testStereoReadZeroDefault() 266 … IAtomContainer container = ChemFileManipulator.getAllAtomContainers(chemfile).iterator().next(); in properties()
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/dports/science/cdk/cdk-cdk-2.3/tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/ |
H A D | ModelBuilder3DTest.java | 220 List<IAtomContainer> containersList = ChemFileManipulator.getAllAtomContainers(chemFile); in testModelBuilder3D_232() 247 List<IAtomContainer> containersList = ChemFileManipulator.getAllAtomContainers(chemFile); in testModelBuilder3D_231() 375 List<IAtomContainer> containersList = ChemFileManipulator.getAllAtomContainers(chemFile); in testModelBuilder3D_bug_1241421() 390 List<IAtomContainer> containersList = ChemFileManipulator.getAllAtomContainers(chemFile); in testModelBuilder3D_reserpine()
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