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Searched refs:getAllAtomContainers (Results 1 – 25 of 78) sorted by relevance

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/dports/science/cdk/cdk-cdk-2.3/base/test-core/src/test/java/org/openscience/cdk/atomtype/
H A DCDKAtomTypeMatcherFilesTest.java55 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()
/dports/science/cdk/cdk-cdk-2.3/descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/
H A DLengthOverBreadthDescriptorTest.java39 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()
H A DCPSADescriptorTest.java58 List cList = ChemFileManipulator.getAllAtomContainers(content); in testCPSA()
80 List cList = ChemFileManipulator.getAllAtomContainers(content); in testChargedMolecule()
95 List cList = ChemFileManipulator.getAllAtomContainers(content); in testUnChargedMolecule()
H A DBCUTDescriptorTest.java63 List cList = ChemFileManipulator.getAllAtomContainers(content); in testBCUT()
112 List cList = ChemFileManipulator.getAllAtomContainers(content); in testExtraEigenvalues()
180 List cList = ChemFileManipulator.getAllAtomContainers(content); in testUndefinedValues()
H A DMomentOfInertiaDescriptorTest.java75 List cList = ChemFileManipulator.getAllAtomContainers(content); in testMomentOfInertia1()
95 List cList = ChemFileManipulator.getAllAtomContainers(content); in testMomentOfInertia2()
H A DWeightedPathDescriptorTest.java74 List cList = ChemFileManipulator.getAllAtomContainers(content); in testWeightedPathDescriptor()
90 cList = ChemFileManipulator.getAllAtomContainers(content); in testWeightedPathDescriptor()
H A DEccentricConnectivityIndexDescriptorTest.java58 List cList = ChemFileManipulator.getAllAtomContainers(content); in testEccentricConnectivityIndex()
/dports/science/cdk/cdk-cdk-2.3/storage/io/src/test/java/org/openscience/cdk/io/
H A DCMLReaderTest.java84 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()
H A DHINReaderTest.java144 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()
H A DMol2ReaderTest.java161 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()
H A DReaderFactoryTest.java200 for (IAtomContainer container : ChemFileManipulator.getAllAtomContainers(chemFile)) { in testReadGz()
218 for (IAtomContainer container : ChemFileManipulator.getAllAtomContainers(chemFile)) { in testReadGzWithGzipDetection()
/dports/science/cdk/cdk-cdk-2.3/tool/sdg/src/test/java/org/openscience/cdk/layout/
H A DOverlapResolverTest.java68 …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()
/dports/science/cdk/cdk-cdk-2.3/base/standard/src/main/java/org/openscience/cdk/tools/manipulator/
H A DReactionSchemeManipulator.java49 …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()
H A DMoleculeSetManipulator.java64 public static List<IAtomContainer> getAllAtomContainers(IAtomContainerSet set) { in getAllAtomContainers() method in MoleculeSetManipulator
65 return AtomContainerSetManipulator.getAllAtomContainers(set); in getAllAtomContainers()
H A DChemSequenceManipulator.java75 public static List<IAtomContainer> getAllAtomContainers(IChemSequence sequence) { in getAllAtomContainers() method in ChemSequenceManipulator
78 acList.addAll(ChemModelManipulator.getAllAtomContainers(model)); in getAllAtomContainers()
H A DChemFileManipulator.java102 public static List<IAtomContainer> getAllAtomContainers(IChemFile file) { in getAllAtomContainers() method in ChemFileManipulator
105 acList.addAll(ChemSequenceManipulator.getAllAtomContainers(sequence)); in getAllAtomContainers()
H A DAtomContainerSetManipulator.java99 public static List<IAtomContainer> getAllAtomContainers(IAtomContainerSet set) { in getAllAtomContainers() method in AtomContainerSetManipulator
213 …List<IAtomContainer> atomContainerList = AtomContainerSetManipulator.getAllAtomContainers(atomCont… in sort()
H A DRingSetManipulator.java64 … Iterator<IAtomContainer> containers = RingSetManipulator.getAllAtomContainers(ringSet).iterator(); in getAllInOneContainer()
110 public static List<IAtomContainer> getAllAtomContainers(IRingSet set) { in getAllAtomContainers() method in RingSetManipulator
H A DReactionSetManipulator.java112 public static List<IAtomContainer> getAllAtomContainers(IReactionSet set) { in getAllAtomContainers() method in ReactionSetManipulator
114 return MoleculeSetManipulator.getAllAtomContainers(getAllMolecules(set)); in getAllAtomContainers()
/dports/science/cdk/cdk-cdk-2.3/base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/
H A DReactionSetManipulatorTest.java104 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()
H A DReactionManipulatorTest.java180 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()
H A DReactionSchemeManipulatorTest.java63 …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()
/dports/science/cdk/cdk-cdk-2.3/storage/ctab/src/test/java/org/openscience/cdk/io/
H A DMDLV2000ReaderTest.java122 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 …]
H A DMDLReaderTest.java136 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()
/dports/science/cdk/cdk-cdk-2.3/tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/
H A DModelBuilder3DTest.java220 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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