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/dports/science/p5-Chemistry-Mol/Chemistry-Mol-0.38/t/
H A Dmol.pl1 $mol = bless( {
308 $mol->{'atoms'}[0]{'bonds'}[0]{'bond'}{'atoms'}[0] = $mol->{'atoms'}[0];
313 $mol->{'atoms'}[0]{'bonds'}[0]{'bond'}{'atoms'}[1]{'bonds'}[0]{'bond'}{'parent'} = $mol;
347 $mol->{'atoms'}[0]{'bonds'}[0]{'bond'}{'atoms'}[1]{'parent'} = $mol;
348 $mol->{'atoms'}[0]{'bonds'}[0]{'bond'}{'parent'} = $mol;
350 $mol->{'atoms'}[0]{'parent'} = $mol;
351 $mol->{'atoms'}[1] = $mol->{'atoms'}[0]{'bonds'}[0]{'bond'}{'atoms'}[1];
363 $mol->{'bonds'}[5] = $mol->{'atoms'}[0]{'bonds'}[0]{'bond'};
365 $mol->{'byId'}{'a1'} = $mol->{'atoms'}[0];
366 $mol->{'byId'}{'a2'} = $mol->{'atoms'}[0]{'bonds'}[0]{'bond'}{'atoms'}[1];
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/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-Mol-0.35/t/
H A Dmol.pl1 $mol = bless( {
308 $mol->{'atoms'}[0]{'bonds'}[0]{'bond'}{'atoms'}[0] = $mol->{'atoms'}[0];
313 $mol->{'atoms'}[0]{'bonds'}[0]{'bond'}{'atoms'}[1]{'bonds'}[0]{'bond'}{'parent'} = $mol;
347 $mol->{'atoms'}[0]{'bonds'}[0]{'bond'}{'atoms'}[1]{'parent'} = $mol;
348 $mol->{'atoms'}[0]{'bonds'}[0]{'bond'}{'parent'} = $mol;
350 $mol->{'atoms'}[0]{'parent'} = $mol;
351 $mol->{'atoms'}[1] = $mol->{'atoms'}[0]{'bonds'}[0]{'bond'}{'atoms'}[1];
363 $mol->{'bonds'}[5] = $mol->{'atoms'}[0]{'bonds'}[0]{'bond'};
365 $mol->{'byId'}{'a1'} = $mol->{'atoms'}[0];
366 $mol->{'byId'}{'a2'} = $mol->{'atoms'}[0]{'bonds'}[0]{'bond'}{'atoms'}[1];
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/dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/templates/
H A DMoleculeFactory.java78 return mol; in makeAlphaPinene()
125 return mol; in makeEthylCyclohexane()
148 return mol; in makeCyclohexene()
171 return mol; in makeCyclohexane()
192 return mol; in makeCyclopentane()
211 return mol; in makeCyclobutane()
230 return mol; in makeCyclobutadiene()
248 return mol; in makePropylCycloPropane()
285 return mol; in makeBiphenyl()
321 return mol; in makePhenylEthylBenzene()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/PgSQL/rdkit/sql/
H A Drdkit-91.sql136 select 'Cc1ccccc1'::mol@='c1ccccc1C'::mol;
137 select 'Cc1ccccc1'::mol@='c1ccccc1CC'::mol;
138 select 'Cc1ccccc1'::mol@='c1cccnc1C'::mol;
231 select 'C[C@H](F)Cl'::mol@='CC(F)Cl'::mol;
233 select 'CC(F)Cl'::mol@='C[C@H](F)Cl'::mol;
234 select 'CC(F)Cl'::mol@='CC(F)Cl'::mol;
238 select 'C[C@H](F)Cl'::mol@='CC(F)Cl'::mol;
240 select 'CC(F)Cl'::mol@='C[C@H](F)Cl'::mol;
241 select 'CC(F)Cl'::mol@='CC(F)Cl'::mol;
323 select 'C1CC1OC'::mol @> 'C1CC1O*'::mol;
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H A Dprops.sql2 SELECT mol_amw('c1ccccc1'::mol) mol_amw;
3 SELECT mol_logp('c1ccccc1'::mol) mol_logp;
4 SELECT mol_hba('c1ccccc1'::mol) mol_hba;
5 SELECT mol_hbd('c1ccccc1'::mol) mol_hbd;
6 SELECT mol_hba('c1ccncc1'::mol) mol_hba;
11 SELECT mol_chi0n('c1ccccc1O'::mol) v;
12 SELECT mol_chi1n('c1ccccc1O'::mol) v;
13 SELECT mol_chi2n('c1ccccc1O'::mol) v;
14 SELECT mol_chi3n('c1ccccc1O'::mol) v;
48 SELECT mol_tpsa('CCC'::mol) val;
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H A Dfps.sql2 SELECT dice_sml(rdkit_fp('c1ccccc1'::mol),rdkit_fp('c1ccncc1'::mol));
3 SELECT tversky_sml(rdkit_fp('c1ccccc1'::mol),rdkit_fp('c1ccncc1'::mol),0.5,0.5);
4 SELECT tanimoto_sml(rdkit_fp('c1ccccc1'::mol),rdkit_fp('c1ccncc1'::mol));
5 SELECT tversky_sml(rdkit_fp('c1ccccc1'::mol),rdkit_fp('c1ccncc1'::mol),1.0,1.0);
6 SELECT dice_sml(atompair_fp('c1ccccc1'::mol),atompair_fp('c1ccncc1'::mol));
7 SELECT dice_sml(torsion_fp('c1ccccc1'::mol),torsion_fp('c1ccncc1'::mol));
8 SELECT dice_sml(morgan_fp('c1ccccc1'::mol,2),morgan_fp('c1ccncc1'::mol,2));
9 SELECT dice_sml(morgan_fp('c1ccccc1'::mol),morgan_fp('c1ccncc1'::mol));
11 SELECT dice_sml(morganbv_fp('c1ccccc1'::mol),morganbv_fp('c1ccncc1'::mol));
16 SELECT tanimoto_sml(maccs_fp('c1ccccc1'::mol),maccs_fp('c1ccncc1'::mol));
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/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/tests/qtgui/
H A Drwmoleculetest.cpp314 mol.addAtom(1); in TEST()
315 mol.addAtom(2); in TEST()
316 mol.addAtom(3); in TEST()
317 mol.addAtom(4); in TEST()
318 mol.addAtom(5); in TEST()
341 mol.addAtom(1); in TEST()
342 mol.addAtom(2); in TEST()
343 mol.addAtom(3); in TEST()
538 mol.removeBond(mol.atom(1), mol.atom(2)); in TEST()
549 mol.removeBond(mol.bond(0)); in TEST()
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H A Dhydrogentoolstest.cpp138 mol.addBond(C1, mol.addAtom(1)); in TEST()
139 mol.addBond(C1, mol.addAtom(1)); in TEST()
140 mol.addBond(C1, mol.addAtom(1)); in TEST()
141 mol.addBond(C1, mol.addAtom(1)); in TEST()
142 mol.addBond(C1, mol.addAtom(1)); in TEST()
143 mol.addBond(C1, mol.addAtom(1)); in TEST()
144 mol.addBond(C1, mol.addAtom(1)); in TEST()
145 mol.addBond(C1, mol.addAtom(1)); in TEST()
146 mol.addBond(C1, mol.addAtom(1)); in TEST()
147 mol.addBond(C1, mol.addAtom(1)); in TEST()
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/dports/science/avogadrolibs/avogadrolibs-1.94.0/tests/qtgui/
H A Drwmoleculetest.cpp314 mol.addAtom(1); in TEST()
315 mol.addAtom(2); in TEST()
316 mol.addAtom(3); in TEST()
317 mol.addAtom(4); in TEST()
318 mol.addAtom(5); in TEST()
341 mol.addAtom(1); in TEST()
342 mol.addAtom(2); in TEST()
343 mol.addAtom(3); in TEST()
538 mol.removeBond(mol.atom(1), mol.atom(2)); in TEST()
549 mol.removeBond(mol.bond(0)); in TEST()
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H A Dhydrogentoolstest.cpp138 mol.addBond(C1, mol.addAtom(1)); in TEST()
139 mol.addBond(C1, mol.addAtom(1)); in TEST()
140 mol.addBond(C1, mol.addAtom(1)); in TEST()
141 mol.addBond(C1, mol.addAtom(1)); in TEST()
142 mol.addBond(C1, mol.addAtom(1)); in TEST()
143 mol.addBond(C1, mol.addAtom(1)); in TEST()
144 mol.addBond(C1, mol.addAtom(1)); in TEST()
145 mol.addBond(C1, mol.addAtom(1)); in TEST()
146 mol.addBond(C1, mol.addAtom(1)); in TEST()
147 mol.addBond(C1, mol.addAtom(1)); in TEST()
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/dports/science/cdk/cdk-cdk-2.3/tool/forcefield/src/test/java/org/openscience/cdk/forcefield/mmff/
H A DMmffTest.java91 mmff.clearProps(mol); in clearProps()
118 assertPartialCharges(mol, in methanol()
128 assertPartialCharges(mol, in methylamine()
138 assertPartialCharges(mol, in acetonitrile()
148 assertPartialCharges(mol, in dimethylether()
158 assertPartialCharges(mol, in methanethiol()
168 assertPartialCharges(mol, in chloromethane()
178 assertPartialCharges(mol, in ethane()
188 assertPartialCharges(mol, in acetamide()
325 return mol; in loadSmi()
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/dports/science/cdk/cdk-cdk-2.3/base/data/src/test/java/org/openscience/cdk/templates/
H A DTestMoleculeFactory.java78 return mol; in makeAlphaPinene()
124 return mol; in makeEthylCyclohexane()
147 return mol; in makeCyclohexene()
170 return mol; in makeCyclohexane()
191 return mol; in makeCyclopentane()
210 return mol; in makeCyclobutane()
229 return mol; in makeCyclobutadiene()
247 return mol; in makePropylCycloPropane()
284 return mol; in makeBiphenyl()
320 return mol; in makePhenylEthylBenzene()
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/dports/science/openbabel/openbabel-3.1.1/test/
H A Dphmodel.cpp53 OBMol mol; in phmodel() local
71 conv.Write(&mol, &cout); in phmodel()
73 if (mol.NumAtoms() == 17) in phmodel()
82 conv.Write(&mol, &cout); in phmodel()
84 if (mol.NumAtoms() == 16) in phmodel()
93 conv.Write(&mol, &cout); in phmodel()
104 conv.Write(&mol, &cout); in phmodel()
119 conv.Write(&mol, &cout); in phmodel()
130 conv.Write(&mol, &cout); in phmodel()
142 conv.Write(&mol, &cout); in phmodel()
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H A Duniqueidtest.cpp19 OBMol mol; in testIdsNewAtom1() local
38 OBMol mol; in testIdsNewAtom2() local
58 OBMol mol; in testIdsDeleteAtom() local
66 mol.DeleteAtom(mol.GetAtomById(4)); in testIdsDeleteAtom()
77 OBMol mol; in testIdsAddAtom() local
85 mol.AddAtom(a); in testIdsAddAtom()
101 OBMol mol; in testIdsNewBond1() local
120 OBMol mol; in testIdsNewBond2() local
140 OBMol mol; in testIdsDeleteBond() local
154 mol.DeleteBond(mol.GetBondById(4)); in testIdsDeleteBond()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/SLNParse/
H A Dtest.cpp58 delete mol; in test1()
65 delete mol; in test1()
72 delete mol; in test1()
79 delete mol; in test1()
86 delete mol; in test1()
93 delete mol; in test1()
100 delete mol; in test1()
111 delete mol; in test1()
124 delete mol; in test1()
133 delete mol; in test1()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/JavaWrappers/gmwrapper/src-test/org/RDKit/
H A DSmilesDetailsTests.java42 ROMol mol; in testDetails() local
71 ROMol mol; in testProblems() local
111 ROMol mol; in testBasicCanon() local
188 ROMol mol; in testStereochem() local
622 ROMol mol; in testIssue143() local
833 ROMol mol; in testIssue159() local
856 ROMol mol; in testIssue175() local
872 ROMol mol; in testIssue176() local
898 ROMol mol; in testIssue184() local
926 ROMol mol; in testIssue185() local
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Descriptors/
H A Dtest.cpp66 ROMol *mol; in test2() local
89 delete mol; in test2()
96 delete mol; in test2()
103 delete mol; in test2()
110 delete mol; in test2()
117 delete mol; in test2()
124 delete mol; in test2()
131 delete mol; in test2()
138 delete mol; in test2()
174 delete mol; in testIssue262()
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/dports/science/cdk/cdk-cdk-2.3/storage/ctab/src/test/java/org/openscience/cdk/io/
H A DMDLV3000WriterTest.java115 mol.addBond(new Bond(mol.getAtom(0), mol.getAtom(1), null)); in nullBondOrder()
119 writeToStr(mol); in nullBondOrder()
131 writeToStr(mol); in unsetBondOrder()
187 mol.addAtom(atom); in writeLeadingZero()
211 mol.addStereoElement(new TetrahedralChirality(mol.getAtom(1), in writeParity()
241 mol.addStereoElement(new TetrahedralChirality(mol.getAtom(1), in writeParityHNotLast()
270 mol.addStereoElement(new TetrahedralChirality(mol.getAtom(1), in writeParityImplH()
297 mol.addStereoElement(new TetrahedralChirality(mol.getAtom(1), in writeParityImplHInverted()
350 mol.getAtom(mol.getAtomCount() - 1).setImplicitHydrogenCount(1); in writeMultipleGroup()
357 sgroup.addBond(mol.getBond(mol.getBondCount() - 1)); in writeMultipleGroup()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/FileParsers/
H A DSequenceParsers.cpp59 bond->setOwningMol(mol); in CreateAABond()
655 delete mol; in AASequenceToMol()
789 return mol; in AASequenceToMol()
1043 delete mol; in NASequenceToMol()
1076 return mol; in NASequenceToMol()
1084 RWMol *mol; in SequenceToMol() local
1109 return mol; in SequenceToMol()
1141 return mol; in FASTAToMol()
1875 return mol; in HELMToMol()
1882 return mol; in HELMToMol()
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/dports/science/cdk/cdk-cdk-2.3/base/test-standard/src/test/java/org/openscience/cdk/atomtype/
H A DEStateAtomTypeMatcherTest.java89 IAtomType type = matcher.findMatchingAtomType(mol, mol.getAtom(i)); in testFindMatchingAtomType_IAtomContainer()
99 mol.addAtom(a1); in testSP3Atoms()
101 mol.addAtom(a2); in testSP3Atoms()
103 mol.addAtom(a3); in testSP3Atoms()
105 mol.addAtom(a4); in testSP3Atoms()
107 mol.addAtom(a5); in testSP3Atoms()
109 mol.addAtom(a6); in testSP3Atoms()
111 mol.addAtom(a7); in testSP3Atoms()
113 mol.addAtom(a8); in testSP3Atoms()
115 mol.addAtom(a9); in testSP3Atoms()
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/dports/biology/babel/babel-1.6/
H A Dbabel.h9 extern void add_hydrogens(ums_type *mol);
39 extern void fast_radii(ums_type *mol);
55 extern int phase1(ums_type *mol);
56 extern int phase2(ums_type *mol);
57 extern int phase3(ums_type *mol);
58 extern int phase4(ums_type *mol);
59 extern int phase5(ums_type *mol);
60 extern int phase6(ums_type *mol);
64 extern int valence_two(ums_type *mol);
85 extern void set_bo(ums_type *mol);
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Subgraphs/
H A Dtest1.cpp23 RWMol mol; in testSubgraphs() local
110 delete mol; in testSubgraphs2a()
132 delete mol; in testSubgraphs2()
149 delete mol; in testSubgraphs2()
170 RWMol mol; in testPaths() local
258 RWMol mol; in testPaths2() local
285 RWMol mol; in testUniqueSubgraphs() local
383 delete mol; in testUniqueSubgraphs2()
409 delete mol; in testLeak()
441 delete mol; in testRootedSubgraphs()
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/dports/science/cdk/cdk-cdk-2.3/base/test-core/src/test/java/org/openscience/cdk/atomtype/
H A DCDKAtomTypeMatcherTest.java106 IAtomType type = matcher.findMatchingAtomType(mol, mol.getAtom(i)); in testFindMatchingAtomType_IAtomContainer()
3061 mol.addBond(new Bond(mol.getAtom(i + 1), mol.getAtom(0), IBond.Order.SINGLE)); in testAssumeExplicitHydrogens()
3498 mol.addAtom(mol.getBuilder().newInstance(IAtom.class, "C")); in testDimethylThiirane()
3499 mol.addAtom(mol.getBuilder().newInstance(IAtom.class, "C")); in testDimethylThiirane()
3500 mol.addAtom(mol.getBuilder().newInstance(IAtom.class, "C")); in testDimethylThiirane()
3501 mol.addAtom(mol.getBuilder().newInstance(IAtom.class, "C")); in testDimethylThiirane()
3502 mol.addAtom(mol.getBuilder().newInstance(IAtom.class, "S")); in testDimethylThiirane()
3519 mol.addAtom(mol.getBuilder().newInstance(IAtom.class, "C")); in testSulphonylLookalike()
3520 mol.addAtom(mol.getBuilder().newInstance(IAtom.class, "C")); in testSulphonylLookalike()
3521 mol.addAtom(mol.getBuilder().newInstance(IAtom.class, "C")); in testSulphonylLookalike()
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/dports/science/cdk/cdk-cdk-2.3/descriptor/signature/src/test/java/org/openscience/cdk/signature/
H A DAbstractSignatureTest.java110 return mol; in makeCycleWheel()
136 mol.addBond(0, mol.getAtomCount() - 1, IBond.Order.SINGLE); in makeSandwich()
139 return mol; in makeSandwich()
158 return mol; in makeC7H16A()
177 return mol; in makeC7H16B()
196 return mol; in makeC7H16C()
295 return mol; in makeCubane()
313 return mol; in makeCuneane()
323 return mol; in makeCyclobutane()
329 return mol; in makeBridgedCyclobutane()
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/dports/science/shelxle/shelxle-1.0.1352/
H A DeacDlg.cpp237 if (!mol->useShaders) mol->atoms(xd,proba); in draw()
314 mol->g_program=mol->installShader(); in initializeGL()
473 mol->einstellung->setValue("Element",mol->pse(mol->theseAreDonors.at(i))); in colorDLGenvidef()
523 mol->einstellung->setValue("Element",mol->pse(mol->theseAreDonors.at(i))); in colorDLGenvibon()
574 mol->einstellung->setValue("Element",mol->pse(mol->theseAreDonors.at(i))); in colorDLGenvihbo()
707 eacGLW->mol->bondColor = mol->bondColor; in unicolor()
720 mol->einstellung->setValue("Element",mol->pse(mol->theseAreDonors.at(i))); in unicolor()
749 mol->einstellung->setValue("Element",mol->pse(mol->theseAreDonors.at(i))); in strengthChanged()
764 eacGLW->mol->qPeakRad=mol->qPeakRad=d; in QPeakRadChanged()
879 mol->einstellung->setValue("Element",mol->pse(mol->theseAreDonors.at(i))); in importSettings()
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