| /dports/science/cdk/cdk-cdk-2.3/storage/ctab/src/test/java/org/openscience/cdk/io/ |
| H A D | MDLRXNReaderTest.java | 158 .getReactants().getAtomContainer(0).getAtomCount()); in testRDFChemFile()
160 .getReactants().getAtomContainer(1).getAtomCount()); in testRDFChemFile()
164 .getProducts().getAtomContainer(0).getAtomCount()); in testRDFChemFile()
166 .getProducts().getAtomContainer(1).getAtomCount()); in testRDFChemFile()
175 .getProducts().getAtomContainer(0).getAtomCount()); in testRDFChemFile()
195 .getAtomCount()); in testRDFModel()
197 .getAtomCount()); in testRDFModel()
200 .getAtomCount()); in testRDFModel()
202 .getAtomCount()); in testRDFModel()
206 .getAtomCount()); in testRDFModel()
[all …]
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| /dports/science/cdk/cdk-cdk-2.3/storage/io/src/test/java/org/openscience/cdk/io/cml/ |
| H A D | CMLFragmentsTest.java | 59 Assert.assertEquals(1, mol.getAtomCount()); in testAtomId()
71 Assert.assertEquals(1, mol.getAtomCount()); in testAtomId2()
83 Assert.assertEquals(3, mol.getAtomCount()); in testAtomId3()
95 Assert.assertEquals(1, mol.getAtomCount()); in testAtomElementType()
107 Assert.assertEquals(1, mol.getAtomCount()); in testAtomElementType2()
119 Assert.assertEquals(1, mol.getAtomCount()); in testAtomElementType3()
131 Assert.assertEquals(1, mol.getAtomCount()); in test2dCoord()
146 Assert.assertEquals(1, mol.getAtomCount()); in test2dCoord2()
161 Assert.assertEquals(2, mol.getAtomCount()); in testBond()
178 Assert.assertEquals(2, mol.getAtomCount()); in testBond2()
[all …]
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| H A D | CML23FragmentsTest.java | 67 Assert.assertEquals(1, mol.getAtomCount()); in testAtomId()
79 Assert.assertEquals(3, mol.getAtomCount()); in testAtomId3()
91 Assert.assertEquals(1, mol.getAtomCount()); in testAtomElementType3()
103 Assert.assertEquals(1, mol.getAtomCount()); in testMassNumber()
116 Assert.assertEquals(1, mol.getAtomCount()); in testAtomicNumber()
129 Assert.assertEquals(1, mol.getAtomCount()); in testIsotopicMass()
144 Assert.assertEquals(5, mol.getAtomCount()); in testAtomParity()
166 Assert.assertEquals(2, mol.getAtomCount()); in testBond()
183 Assert.assertEquals(3, mol.getAtomCount()); in testBond4()
201 Assert.assertEquals(3, mol.getAtomCount()); in testBond5()
[all …]
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| H A D | Jumbo46CMLFragmentsTest.java | 59 Assert.assertEquals(1, mol.getAtomCount()); in testAtomId()
71 Assert.assertEquals(3, mol.getAtomCount()); in testAtomId3()
83 Assert.assertEquals(1, mol.getAtomCount()); in testAtomElementType3()
95 Assert.assertEquals(2, mol.getAtomCount()); in testBond()
98 Assert.assertEquals(2, bond.getAtomCount()); in testBond()
112 Assert.assertEquals(3, mol.getAtomCount()); in testBond4()
115 Assert.assertEquals(2, bond.getAtomCount()); in testBond4()
130 Assert.assertEquals(3, mol.getAtomCount()); in testBond5()
146 Assert.assertEquals(2, mol.getAtomCount()); in testBondAromatic()
160 Assert.assertEquals(2, mol.getAtomCount()); in testBondId()
[all …]
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| /dports/science/cdk/cdk-cdk-2.3/base/test-standard/src/test/java/org/openscience/cdk/ringsearch/ |
| H A D | RingSearchTest_Bicyclo.java | 48 int n = bicyclo.getAtomCount(); in testCyclic()
55 int n = bicyclo.getAtomCount(); in testCyclic_Int()
77 int n = bicyclo.getAtomCount(); in testRingFragments()
80 assertThat(fragment.getAtomCount(), is(bicyclo.getAtomCount())); in testRingFragments()
87 int n = bicyclo.getAtomCount(); in testIsolatedRingFragments()
100 assertThat(fragment.getAtomCount(), is(bicyclo.getAtomCount())); in testFusedRingFragments()
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| H A D | RingSearchTest_SpiroRings.java | 48 assertThat(new RingSearch(spiro).cyclic().length, is(spiro.getAtomCount())); in testCyclic()
53 int n = spiro.getAtomCount(); in testCyclic_Int()
77 assertThat(fragment.getAtomCount(), is(spiro.getAtomCount())); in testRingFragments()
86 … assertThat(4, anyOf(is(isolated.get(0).getAtomCount()), is(isolated.get(1).getAtomCount()))); in testIsolatedRingFragments()
87 … assertThat(7, anyOf(is(isolated.get(0).getAtomCount()), is(isolated.get(1).getAtomCount()))); in testIsolatedRingFragments()
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| H A D | RingSearchTest_Biphenyl.java | 47 assertThat(new RingSearch(biphenyl).cyclic().length, is(biphenyl.getAtomCount())); in testCyclic()
52 int n = biphenyl.getAtomCount(); in testCyclic_Int()
76 assertThat(fragment.getAtomCount(), is(biphenyl.getAtomCount())); in testRingFragments()
85 assertThat(isolated.get(0).getAtomCount(), is(6)); in testIsolatedRingFragments()
87 assertThat(isolated.get(1).getAtomCount(), is(6)); in testIsolatedRingFragments()
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| H A D | RingSearchTest_Benzene.java | 47 assertThat(new RingSearch(benzene).cyclic().length, is(benzene.getAtomCount())); in testCyclic()
52 int n = benzene.getAtomCount(); in testCyclic_Int()
75 assertThat(fragment.getAtomCount(), is(benzene.getAtomCount())); in testRingFragments()
84 assertThat(isolated.get(0).getAtomCount(), is(6)); in testIsolatedRingFragments()
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| /dports/science/cdk/cdk-cdk-2.3/base/reaction/src/test/java/org/openscience/cdk/graph/invariant/ |
| H A D | ConjugatedPiSystemsDetectorTest.java | 83 Assert.assertEquals(4, ac.getAtomCount()); in testDetectButadiene()
86 for (int i = 0; i < ac.getAtomCount(); i++) { in testDetectButadiene()
114 Assert.assertEquals(10, ac.getAtomCount()); in testDetectNaphtalene()
145 Assert.assertEquals(6, ac.getAtomCount()); in testDetectToluene()
178 Assert.assertEquals(4, ac1.getAtomCount()); in testNonConnectedPiSystems()
190 Assert.assertEquals(4, ac2.getAtomCount()); in testNonConnectedPiSystems()
224 Assert.assertEquals(4, ac1.getAtomCount()); in testPiSystemWithCarbokation()
234 Assert.assertEquals(4, ac2.getAtomCount()); in testPiSystemWithCarbokation()
267 Assert.assertEquals(4, ac1.getAtomCount()); in testPiSystemWithCumulativeDB()
279 Assert.assertEquals(4, ac2.getAtomCount()); in testPiSystemWithCumulativeDB()
[all …]
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| /dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/tools/ |
| H A D | DeAromatizationTool.java | 187 int maxAtomsRingA = ringA.getAtomCount(); in Dearomatize666Rings()
188 int maxAtomsRingB = ringB.getAtomCount(); in Dearomatize666Rings()
189 int maxAtomsRingC = ringC.getAtomCount(); in Dearomatize666Rings()
229 if (ringA.getAtomCount() > ringB.getAtomCount()) in Dearomatize566Rings()
235 else if (ringA.getAtomCount() > ringC.getAtomCount()) in Dearomatize566Rings()
250 int maxAtomsRingA = ringA.getAtomCount(); in Dearomatize566Rings()
251 int maxAtomsRingB = ringB.getAtomCount(); in Dearomatize566Rings()
252 int maxAtomsRingC = ringC.getAtomCount(); in Dearomatize566Rings()
305 int maxAtomsRingA = ringA.getAtomCount(); in Dearomatize66Rings()
306 int maxAtomsRingB = ringB.getAtomCount(); in Dearomatize66Rings()
[all …]
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| /dports/science/cdk/cdk-cdk-2.3/base/test-core/src/test/java/org/openscience/cdk/atomtype/ |
| H A D | CDKAtomTypeMatcherSMILESTest.java | 59 Assert.assertEquals(mol1.getAtomCount(), mol2.getAtomCount()); in testIdenticalTypes()
64 for (int i = 0; i < mol1.getAtomCount(); i++) { in testIdenticalTypes()
76 Assert.assertEquals(9, mol1.getAtomCount()); in testNitrogen()
90 Assert.assertEquals(9, mol1.getAtomCount()); in testNitrogen_SP2()
106 Assert.assertEquals(8, mol1.getAtomCount()); in testAnotherNitrogen_SP2()
124 Assert.assertEquals(mol1.getAtomCount(), mol2.getAtomCount()); in testBug1294()
129 for (int i = 0; i < mol1.getAtomCount(); i++) { in testBug1294()
157 Assert.assertEquals(13, mol1.getAtomCount()); in testPlatinum4()
167 Assert.assertEquals(5, mol1.getAtomCount()); in testPlatinum6()
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| /dports/science/cdk/cdk-cdk-2.3/base/data/src/main/java/org/openscience/cdk/ |
| H A D | ConformerContainer.java | 68 Point3d[] tmp = new Point3d[atomContainer.getAtomCount()]; in getCoordinateList()
69 for (int i = 0; i < atomContainer.getAtomCount(); i++) { in getCoordinateList()
247 if (atomContainer.getAtomCount() != this.atomContainer.getAtomCount()) in add()
317 for (int j = 0; j < atomContainer.getAtomCount(); j++) { in get()
346 if (atomContainer.getAtomCount() != this.atomContainer.getAtomCount()) in add()
381 if (atomContainer.getAtomCount() != this.atomContainer.getAtomCount()) return -1; in indexOf()
387 for (int i = 0; i < atomContainer.getAtomCount(); i++) { in indexOf()
415 if (atomContainer.getAtomCount() != coordinates.get(0).length) return -1; in lastIndexOf()
421 for (int i = 0; i < atomContainer.getAtomCount(); i++) { in lastIndexOf()
461 for (int j = 0; j < atomContainer.getAtomCount(); j++) { in next()
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| /dports/science/cdk/cdk-cdk-2.3/storage/smiles/src/test/java/org/openscience/cdk/smiles/ |
| H A D | SmilesParserTest.java | 153 Assert.assertEquals(18, mol.getAtomCount()); in testBug1363882()
164 Assert.assertEquals(18, mol.getAtomCount()); in testBug1535587()
177 Assert.assertEquals(9, mol.getAtomCount()); in testBug1579235()
228 Assert.assertEquals(7, mol.getAtomCount()); in testPyridine_N_oxideUncharged()
236 Assert.assertEquals(7, mol.getAtomCount()); in testPyridine_N_oxideCharged()
503 assertTrue(mol.getAtomCount() > 0); in testSFBug630475()
513 assertTrue(mol.getAtomCount() > 0); in testSFBug585811()
780 assertThat(mol.getAtomCount(), is(1)); in testSingleH()
789 assertThat(mol.getAtomCount(), is(1)); in testSingleD()
800 assertThat(mol.getAtomCount(), is(1)); in testSingleT()
[all …]
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| /dports/science/cdk/cdk-cdk-2.3/tool/sdg/src/main/java/org/openscience/cdk/layout/ |
| H A D | AtomPlacer.java | 144 if (placedNeighbours.getAtomCount() == 1) { in distributePartners()
150 … addAngle = Math.PI * 2 / (unplacedNeighbours.getAtomCount() + placedNeighbours.getAtomCount()); in distributePartners()
307 if (placedNeighbours.getAtomCount() != 2) in doAngleSnap()
721 for (int f = 0; f < ac.getAtomCount(); f++) { in listPlaced()
747 for (int f = 0; f < ac.getAtomCount(); f++) { in listNumbers()
779 for (int f = 0; f < ac.getAtomCount(); f++) { in allPlaced()
793 for (int f = 0; f < ac.getAtomCount(); f++) { in markNotPlaced()
806 for (int f = 0; f < ac.getAtomCount(); f++) { in markPlaced()
819 for (int f = 0; f < ac.getAtomCount(); f++) { in getPlacedAtoms()
860 for (int f = 0; f < ac.getAtomCount(); f++) { in getDegreeSum()
[all …]
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| /dports/science/cdk/cdk-cdk-2.3/tool/fragment/src/main/java/org/openscience/cdk/fragment/ |
| H A D | FragmentUtils.java | 84 …if (partContainer.getAtomCount() > 2 && partContainer.getAtomCount() != atomContainer.getAtomCount… in splitMolecule()
89 …if (partContainer.getAtomCount() > 2 && partContainer.getAtomCount() != atomContainer.getAtomCount… in splitMolecule()
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| /dports/science/cdk/cdk-cdk-2.3/storage/libiocml/src/test/java/org/openscience/cdk/io/cml/ |
| H A D | CMLRoundTripTest.java | 87 Assert.assertEquals(1, roundTrippedMol.getAtomCount()); in testAtom()
101 Assert.assertEquals(1, roundTrippedMol.getAtomCount()); in testAtomId()
116 Assert.assertEquals(1, roundTrippedMol.getAtomCount()); in testAtom2D()
131 Assert.assertEquals(1, roundTrippedMol.getAtomCount()); in testAtom3D()
148 Assert.assertEquals(1, roundTrippedMol.getAtomCount()); in testAtom2DAnd3D()
164 Assert.assertEquals(1, roundTrippedMol.getAtomCount()); in testAtomFract3D()
178 Assert.assertEquals(1, roundTrippedMol.getAtomCount()); in testPseudoAtom()
218 Assert.assertEquals(1, roundTrippedMol.getAtomCount()); in testAtomFormalCharge()
235 Assert.assertEquals(1, roundTrippedMol.getAtomCount()); in testHydrogenCount()
252 Assert.assertEquals(1, roundTrippedMol.getAtomCount()); in testHydrogenCount_UNSET()
[all …]
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| /dports/science/cdk/cdk-cdk-2.3/misc/test-extra/src/test/java/org/openscience/cdk/ |
| H A D | CloneAtomContainerTest.java | 44 Assert.assertTrue(molecule.getAtomCount() == clonedMol.getAtomCount()); in testClone()
45 for (int f = 0; f < molecule.getAtomCount(); f++) { in testClone()
46 for (int g = 0; g < clonedMol.getAtomCount(); g++) { in testClone()
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| /dports/science/cdk/cdk-cdk-2.3/misc/diff/src/main/java/org/openscience/cdk/tools/diff/ |
| H A D | BondDiff.java | 75 ….addChild(IntegerDifference.construct("atomCount", firstB.getAtomCount(), secondB.getAtomCount())); in difference()
76 if (firstB.getAtomCount() == secondB.getAtomCount()) { in difference()
79 for (int i = 2; i < firstB.getAtomCount(); i++) { in difference()
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| H A D | AtomContainerDiff.java | 75 …addChild(IntegerDifference.construct("atomCount", firstAC.getAtomCount(), secondAC.getAtomCount())… in difference()
76 if (firstAC.getAtomCount() == secondAC.getAtomCount()) { in difference()
77 for (int i = 0; i < firstAC.getAtomCount(); i++) { in difference()
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| /dports/science/cdk/cdk-cdk-2.3/tool/builder3d/src/main/java/org/openscience/cdk/modeling/builder3d/ |
| H A D | ModelBuilder3D.java | 160 for (int i = 0; i < molecule.getAtomCount(); i++) { in generate3DCoordinates()
165 logger.debug("#atoms>" + molecule.getAtomCount()); in generate3DCoordinates()
348 for (int i = 0; i < ac.getAtomCount(); i++) { in layoutRingSystem()
380 for (int i = 0; i < ac.getAtomCount(); i++) { in layoutRingSystem()
441 if (atomNeighbours.getAtomCount() > 1) { in setBranchAtom()
465 for (int i = 0; i < chain.getAtomCount(); i++) { in searchAndPlaceBranches()
504 if (startAtoms.getAtomCount() == 0) { in placeLinearChains3D()
547 for (int i = 0; i < ac.getAtomCount(); i++) { in translateStructure()
562 for (int i = 0; i < ac.getAtomCount(); i++) { in checkAllRingAtomsHasCoordinates()
578 for (int i = 0; i < ac.getAtomCount(); i++) { in setAtomsToPlace()
[all …]
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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 | AminoAcidManipulatorTest.java | 44 Assert.assertEquals(5, glycine.getAtomCount()); in testRemoveAcidicOxygen_IAminoAcid()
47 Assert.assertEquals(4, glycine.getAtomCount()); in testRemoveAcidicOxygen_IAminoAcid()
58 Assert.assertEquals(4, glycine.getAtomCount()); in testAddAcidicOxygen_IAminoAcid()
61 Assert.assertEquals(5, glycine.getAtomCount()); in testAddAcidicOxygen_IAminoAcid()
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| /dports/science/cdk/cdk-cdk-2.3/descriptor/signature/src/test/java/org/openscience/cdk/signature/ |
| H A D | MoleculeFromSignatureBuilderTest.java | 67 Assert.assertEquals(2, reconstructed.getAtomCount()); in ccBondTest()
88 Assert.assertEquals(ringSize, reconstructedRing.getAtomCount()); in ringTest()
139 Assert.assertEquals(1, product.getAtomCount()); in makeVertexTest()
151 Assert.assertEquals(2, product.getAtomCount()); in makeEdgeTest_singleBond()
165 Assert.assertEquals(2, product.getAtomCount()); in makeEdgeTest_doubleBond()
179 Assert.assertEquals(2, product.getAtomCount()); in makeEdgeTest_tripleBond()
193 Assert.assertEquals(2, product.getAtomCount()); in makeEdgeTest_aromaticBond()
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| /dports/science/cdk/cdk-cdk-2.3/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ |
| H A D | AtomCountDescriptor.java | 153 if (container.getAtomCount() == 0) { in calculate()
160 for (int i = 0; i < container.getAtomCount(); i++) { in calculate()
165 atomCount += container.getAtomCount(); in calculate()
167 for (int i = 0; i < container.getAtomCount(); i++) { in calculate()
177 for (int i = 0; i < container.getAtomCount(); i++) { in calculate()
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| /dports/science/cdk/cdk-cdk-2.3/misc/extra/src/main/java/org/openscience/cdk/geometry/alignment/ |
| H A D | KabschAlignment.java | 114 Point3d[] p = new Point3d[ac.getAtomCount()]; in getPoint3dArray()
115 for (int i = 0; i < ac.getAtomCount(); i++) { in getPoint3dArray()
139 double[] am = new double[ac.getAtomCount()]; in getAtomicMasses()
149 for (int i = 0; i < ac.getAtomCount(); i++) { in getAtomicMasses()
235 if (ac1.getAtomCount() != ac2.getAtomCount()) { in KabschAlignment()
238 this.npoint = ac1.getAtomCount(); in KabschAlignment()
260 if (ac1.getAtomCount() != ac2.getAtomCount()) { in KabschAlignment()
263 if (ac1.getAtomCount() != wts.length) { in KabschAlignment()
266 this.npoint = ac1.getAtomCount(); in KabschAlignment()
471 for (int i = 0; i < ac.getAtomCount(); i++) { in rotateAtomContainer()
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| /dports/science/cdk/cdk-cdk-2.3/base/data/src/test/java/org/openscience/cdk/ |
| H A D | RingTest.java | 55 Assert.assertEquals(5, r.getAtomCount()); in testRing_int_String()
62 Assert.assertEquals(0, r.getAtomCount()); in testRing_int()
70 Assert.assertEquals(0, ring.getAtomCount()); in testRing()
82 Assert.assertEquals(2, ring.getAtomCount()); in testRing_IAtomContainer()
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