| /dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ |
| H A D | HybridizationNumberAtom.java | 50 setHybridization(IAtomType.Hybridization.SP1); in HybridizationNumberAtom()
53 setHybridization(IAtomType.Hybridization.SP2); in HybridizationNumberAtom()
56 setHybridization(IAtomType.Hybridization.SP3); in HybridizationNumberAtom()
59 setHybridization(IAtomType.Hybridization.SP3D1); in HybridizationNumberAtom()
62 setHybridization(IAtomType.Hybridization.SP3D2); in HybridizationNumberAtom()
65 setHybridization(IAtomType.Hybridization.SP3D3); in HybridizationNumberAtom()
68 setHybridization(IAtomType.Hybridization.SP3D4); in HybridizationNumberAtom()
71 setHybridization(IAtomType.Hybridization.SP3D5); in HybridizationNumberAtom()
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| /dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ |
| H A D | ConjugHybrid.cpp | 138 void setHybridization(ROMol &mol) { in setHybridization() function
141 atom->setHybridization(Atom::UNSPECIFIED); in setHybridization()
144 atom->setHybridization(Atom::S); in setHybridization()
150 atom->setHybridization(Atom::S); in setHybridization()
153 atom->setHybridization(Atom::S); in setHybridization()
156 atom->setHybridization(Atom::SP); in setHybridization()
159 atom->setHybridization(Atom::SP2); in setHybridization()
172 atom->setHybridization(Atom::SP3); in setHybridization()
174 atom->setHybridization(Atom::SP2); in setHybridization()
178 atom->setHybridization(Atom::SP3D); in setHybridization()
[all …]
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| /dports/science/cdk/cdk-cdk-2.3/legacy/src/test/java/org/openscience/cdk/smiles/ |
| H A D | DeduceBondSystemToolTest.java | 195 atom1.setHybridization(Hybridization.SP2); in xtestQuinone()
197 atom2.setHybridization(Hybridization.SP2); in xtestQuinone()
199 atom3.setHybridization(Hybridization.SP2); in xtestQuinone()
201 atom4.setHybridization(Hybridization.SP2); in xtestQuinone()
203 atom5.setHybridization(Hybridization.SP2); in xtestQuinone()
205 atom6.setHybridization(Hybridization.SP2); in xtestQuinone()
207 atom7.setHybridization(Hybridization.SP2); in xtestQuinone()
209 atom8.setHybridization(Hybridization.SP2); in xtestQuinone()
266 atom1.setHybridization(Hybridization.SP2); in xtestPyrrole()
268 atom2.setHybridization(Hybridization.SP2); in xtestPyrrole()
[all …]
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| H A D | FixBondOrdersToolTest.java | 168 atom1.setHybridization(Hybridization.SP2); in xtestPyrrole()
170 atom2.setHybridization(Hybridization.SP2); in xtestPyrrole()
172 atom3.setHybridization(Hybridization.SP2); in xtestPyrrole()
174 atom4.setHybridization(Hybridization.SP2); in xtestPyrrole()
176 atom5.setHybridization(Hybridization.SP2); in xtestPyrrole()
219 atom1.setHybridization(Hybridization.SP2); in xtestPyridine()
221 atom2.setHybridization(Hybridization.SP2); in xtestPyridine()
223 atom3.setHybridization(Hybridization.SP2); in xtestPyridine()
225 atom4.setHybridization(Hybridization.SP2); in xtestPyridine()
227 atom5.setHybridization(Hybridization.SP2); in xtestPyridine()
[all …]
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| /dports/science/cdk/cdk-cdk-2.3/base/core/src/main/java/org/openscience/cdk/config/atomtypes/ |
| H A D | OWLAtomTypeHandler.java | 160 currentAtomType.setHybridization(IAtomType.Hybridization.SP3); in startAtomTypeElement()
162 currentAtomType.setHybridization(IAtomType.Hybridization.SP2); in startAtomTypeElement()
164 currentAtomType.setHybridization(IAtomType.Hybridization.SP1); in startAtomTypeElement()
166 currentAtomType.setHybridization(IAtomType.Hybridization.S); in startAtomTypeElement()
168 currentAtomType.setHybridization(IAtomType.Hybridization.PLANAR3); in startAtomTypeElement()
170 currentAtomType.setHybridization(IAtomType.Hybridization.SP3D1); in startAtomTypeElement()
172 currentAtomType.setHybridization(IAtomType.Hybridization.SP3D2); in startAtomTypeElement()
174 currentAtomType.setHybridization(IAtomType.Hybridization.SP3D3); in startAtomTypeElement()
176 currentAtomType.setHybridization(IAtomType.Hybridization.SP3D4); in startAtomTypeElement()
178 currentAtomType.setHybridization(IAtomType.Hybridization.SP3D5); in startAtomTypeElement()
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| H A D | AtomTypeHandler.java | 139 atomType.setHybridization(Hybridization.SP1); in endElement()
141 atomType.setHybridization(Hybridization.SP2); in endElement()
143 atomType.setHybridization(Hybridization.SP3); in endElement()
145 atomType.setHybridization(Hybridization.PLANAR3); in endElement()
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| /dports/science/cdk/cdk-cdk-2.3/descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/ |
| H A D | SimpleAtomComparatorTest.java | 38 a1.setHybridization(IAtomType.Hybridization.SP3); in testCompare_SameHybridization()
39 a2.setHybridization(IAtomType.Hybridization.SP3); in testCompare_SameHybridization()
53 a1.setHybridization(IAtomType.Hybridization.SP2); in testCompare_DifferentHybridization()
54 a2.setHybridization(IAtomType.Hybridization.SP3); in testCompare_DifferentHybridization()
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| /dports/science/cdk/cdk-cdk-2.3/base/test-interfaces/src/test/java/org/openscience/cdk/interfaces/ |
| H A D | AbstractAtomTypeTest.java | 134 atom.setHybridization(hybridization); in testSetHybridization_IAtomType_Hybridization()
148 atom.setHybridization(hybridization); in testSetHybridization_Null()
150 atom.setHybridization(null); in testSetHybridization_Null()
329 at.setHybridization(Hybridization.PLANAR3); in testClone_Hybridization()
332 at.setHybridization(Hybridization.SP1); in testClone_Hybridization()
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| /dports/science/cdk/cdk-cdk-2.3/base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/ |
| H A D | AdductionPBMechanism.java | 100 atom1C.setHybridization(null); in initiate()
105 atom2C.setHybridization(null); in initiate()
112 atom3C.setHybridization(null); in initiate()
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| H A D | RadicalSiteIonizationMechanism.java | 102 atom1C.setHybridization(null); in initiate()
107 atom2C.setHybridization(null); in initiate()
113 atom3C.setHybridization(null); in initiate()
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| H A D | SharingElectronMechanism.java | 99 atom1C.setHybridization(null); in initiate()
105 atom2C.setHybridization(null); in initiate()
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| H A D | RadicalSiteRearrangementMechanism.java | 99 atom2C.setHybridization(null); in initiate()
105 atom3C.setHybridization(null); in initiate()
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| H A D | HomolyticCleavageMechanism.java | 99 atom1C.setHybridization(null); in initiate()
104 atom2C.setHybridization(null); in initiate()
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| H A D | TautomerizationMechanism.java | 103 atom1C.setHybridization(null); in initiate()
108 atom3C.setHybridization(null); in initiate()
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| H A D | AdductionLPMechanism.java | 97 atom1C.setHybridization(null); in initiate()
104 atom2C.setHybridization(null); in initiate()
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| H A D | HeterolyticCleavageMechanism.java | 99 atom1C.setHybridization(null); in initiate()
108 atom2C.setHybridization(null); in initiate()
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| H A D | RemovingSEofBMechanism.java | 102 atom1C.setHybridization(null); in initiate()
106 atom2C.setHybridization(null); in initiate()
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| H A D | RearrangementChargeMechanism.java | 133 atom1C.setHybridization(null); in initiate()
134 atom3C.setHybridization(null); in initiate()
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| /dports/science/cdk/cdk-cdk-2.3/base/test-valencycheck/src/test/java/org/openscience/cdk/tools/ |
| H A D | ATASaturationCheckerTest.java | 73 a0.setHybridization(IAtomType.Hybridization.SP2); in testASimpleCarbonRing()
77 a1.setHybridization(IAtomType.Hybridization.SP2); in testASimpleCarbonRing()
81 a2.setHybridization(IAtomType.Hybridization.SP2); in testASimpleCarbonRing()
85 a3.setHybridization(IAtomType.Hybridization.SP2); in testASimpleCarbonRing()
89 a4.setHybridization(IAtomType.Hybridization.SP2); in testASimpleCarbonRing()
93 a5.setHybridization(IAtomType.Hybridization.SP2); in testASimpleCarbonRing()
601 a0.setHybridization(IAtomType.Hybridization.SP2); in testButadiene()
605 a1.setHybridization(IAtomType.Hybridization.SP2); in testButadiene()
609 a2.setHybridization(IAtomType.Hybridization.SP2); in testButadiene()
613 a3.setHybridization(IAtomType.Hybridization.SP2); in testButadiene()
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| /dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ChemReactions/ |
| H A D | ReactionDepict.cpp | 49 RDKit::MolOps::setHybridization(**templIt); in compute2DCoordsForReaction()
69 RDKit::MolOps::setHybridization(**templIt); in compute2DCoordsForReaction()
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| /dports/science/avogadrolibs/avogadrolibs-1.94.0/avogadro/core/ |
| H A D | atom.h | 146 void setHybridization(AtomHybridization hyb);
299 void AtomTemplate<Molecule_T>::setHybridization(AtomHybridization hyb) in setHybridization() function
301 m_molecule->setHybridization(m_index, hyb); in setHybridization()
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| /dports/science/py-avogadrolibs/avogadrolibs-1.94.0/avogadro/core/ |
| H A D | atom.h | 146 void setHybridization(AtomHybridization hyb);
299 void AtomTemplate<Molecule_T>::setHybridization(AtomHybridization hyb) in setHybridization() function
301 m_molecule->setHybridization(m_index, hyb); in setHybridization()
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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 | XLogPDescriptor.java | 1487 atom5.setHybridization(Hybridization.SP2); in createPaba()
1490 atom6.setHybridization(Hybridization.SP2); in createPaba()
1493 atom7.setHybridization(Hybridization.SP2); in createPaba()
1496 atom8.setHybridization(Hybridization.SP2); in createPaba()
1501 atom10.setHybridization(Hybridization.SP2); in createPaba()
1568 atom4.setHybridization(Hybridization.SP2); in createSalicylicAcid()
1571 atom5.setHybridization(Hybridization.SP2); in createSalicylicAcid()
1574 atom6.setHybridization(Hybridization.SP2); in createSalicylicAcid()
1577 atom7.setHybridization(Hybridization.SP2); in createSalicylicAcid()
1580 atom8.setHybridization(Hybridization.SP2); in createSalicylicAcid()
[all …]
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| /dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/qsar/descriptors/bond/ |
| H A D | IPBondLearningDescriptor.java | 149 bond.getBegin().setHybridization(originalHybridization1); in calculate()
153 bond.getEnd().setHybridization(originalHybridization2); in calculate()
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| /dports/science/cdk/cdk-cdk-2.3/base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ |
| H A D | AtomTypeManipulator.java | 76 atom.setHybridization(atomType.getHybridization()); in configure()
128 atom.setHybridization(atomType.getHybridization()); in configureUnsetProperties()
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