| /dports/science/cdk/cdk-cdk-2.3/base/test-valencycheck/src/test/java/org/openscience/cdk/tools/ |
| H A D | DeduceBondOrderTestFromExplicitHydrogens.java | 63 addHydrogens(keto, atom1, 1); in testAcetylene()
65 addHydrogens(keto, atom2, 1); in testAcetylene()
90 addHydrogens(keto, atom1, 3); in testKeto()
92 addHydrogens(keto, atom2, 1); in testKeto()
122 addHydrogens(enol, atom1, 2); in testEnol()
124 addHydrogens(enol, atom2, 1); in testEnol()
126 addHydrogens(enol, atom3, 1); in testEnol()
155 addHydrogens(enol, atom1, 2); in xtestButadiene()
157 addHydrogens(enol, atom2, 1); in xtestButadiene()
159 addHydrogens(enol, atom3, 1); in xtestButadiene()
[all …]
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| /dports/science/cdk/cdk-cdk-2.3/descriptor/signature/src/test/java/org/openscience/cdk/signature/ |
| H A D | AbstractSignatureTest.java | 151 AbstractSignatureTest.addHydrogens(mol, 0, 3); in makeC7H16A()
152 AbstractSignatureTest.addHydrogens(mol, 1, 2); in makeC7H16A()
153 AbstractSignatureTest.addHydrogens(mol, 2, 2); in makeC7H16A()
154 AbstractSignatureTest.addHydrogens(mol, 3, 1); in makeC7H16A()
155 AbstractSignatureTest.addHydrogens(mol, 4, 3); in makeC7H16A()
156 AbstractSignatureTest.addHydrogens(mol, 5, 2); in makeC7H16A()
157 AbstractSignatureTest.addHydrogens(mol, 6, 3); in makeC7H16A()
170 AbstractSignatureTest.addHydrogens(mol, 0, 3); in makeC7H16B()
171 AbstractSignatureTest.addHydrogens(mol, 1, 2); in makeC7H16B()
172 AbstractSignatureTest.addHydrogens(mol, 2, 1); in makeC7H16B()
[all …]
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| H A D | MoleculeSignatureTest.java | 145 public void addHydrogens(IAtomContainer mol, IAtom atom, int n) { in addHydrogens() method in MoleculeSignatureTest
272 addHydrogens(cyclohexane, cyclohexane.getAtom(i), 2); in testCyclohexaneWithHydrogens()
285 AbstractSignatureTest.addHydrogens(benzene, i, 1); in testBenzeneWithDoubleBonds()
346 AbstractSignatureTest.addHydrogens(mol, 1, 2); in methyleneCyclopropeneTest()
347 AbstractSignatureTest.addHydrogens(mol, 2, 1); in methyleneCyclopropeneTest()
348 AbstractSignatureTest.addHydrogens(mol, 3, 1); in methyleneCyclopropeneTest()
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| /dports/science/cdk/cdk-cdk-2.3/base/test-standard/src/test/java/org/openscience/cdk/aromaticity/ |
| H A D | DaylightModelTest.java | 52 test(addHydrogens(TestMoleculeFactory.makeBenzene()), 1, 1, 1, 1, 1, 1); in benzene()
57 test(addHydrogens(TestMoleculeFactory.make123Triazole()), 1, 2, 1, 1, 1); in triazole()
92 test(addHydrogens(TestMoleculeFactory.makePyridineOxide()), 1, 1, 1, 1, 1, 1, -1); in pyridineOxide()
102 test(addHydrogens(TestMoleculeFactory.makeAzulene()), 1, 1, 1, 1, 1, 1, 1, 1, 1, 1); in azulene()
107 test(addHydrogens(TestMoleculeFactory.makeIndole()), 1, 1, 1, 1, 1, 1, 1, 1, 2); in indole()
112 test(addHydrogens(TestMoleculeFactory.makeThiazole()), 1, 1, 1, 2, 1); in thiazole()
215 static IAtomContainer addHydrogens(IAtomContainer container) throws CDKException { in addHydrogens() method in DaylightModelTest
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| /dports/science/avogadrolibs/avogadrolibs-1.94.0/avogadro/qtplugins/hydrogens/ |
| H A D | hydrogens.cpp | 39 connect(action, SIGNAL(triggered()), SLOT(addHydrogens())); in Hydrogens()
86 void Hydrogens::addHydrogens() in addHydrogens() function in Avogadro::QtPlugins::Hydrogens
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| H A D | hydrogens.h | 45 void addHydrogens();
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| /dports/science/py-avogadrolibs/avogadrolibs-1.94.0/avogadro/qtplugins/hydrogens/ |
| H A D | hydrogens.cpp | 39 connect(action, SIGNAL(triggered()), SLOT(addHydrogens())); in Hydrogens()
86 void Hydrogens::addHydrogens() in addHydrogens() function in Avogadro::QtPlugins::Hydrogens
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| H A D | hydrogens.h | 45 void addHydrogens();
|
| /dports/science/openbabel/openbabel-3.1.1/src/ops/ |
| H A D | ophighlight.cpp | 100 bool addHydrogens = (smarts.find("#1]")!=string::npos); in Do() local
112 if(addHydrogens) in Do()
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| H A D | opisomorph.h | 60 bool addHydrogens; //The SMARTS contained one or more #1 to explicitly find hydrogen variable
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| H A D | opisomorph.cpp | 229 addHydrogens = (vec[0].find("#1]")!=string::npos); in Do()
335 if(addHydrogens) in Do()
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| /dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/conf_avg/ |
| H A D | Ensemble_phimap.py | 162 myRoutines.addHydrogens()
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/jvxl/readers/ |
| H A D | Parameters.java | 200 addHydrogens = false; in initialize()
314 boolean addHydrogens; field in Parameters
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| H A D | AtomDataReader.java | 98 …doAddHydrogens = (sg.atomDataServer != null && params.addHydrogens); //Jvxl cannot do this on its … in setup2()
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| H A D | SurfaceGenerator.java | 397 params.addHydrogens = ((Boolean) value).booleanValue(); in setProp()
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| /dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/extensions/ |
| H A D | resinter.py | 264 routines.addHydrogens()
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| H A D | newresinter.py | 251 self.routines.addHydrogens()
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| /dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/pdb2pka/ |
| H A D | pka_old.py | 405 myRoutines.addHydrogens()
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| /dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/ |
| H A D | pka.py | 322 myRoutines.addHydrogens()
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| H A D | main.py | 343 myRoutines.addHydrogens()
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| /dports/science/gabedit/GabeditSrc251_300720/src/Geometry/ |
| H A D | DrawGeomCairo.h | 177 void addHydrogens();
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| H A D | DrawGeomGL.h | 183 void addHydrogens();
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/modelkit/ |
| H A D | ModelKitPopup.java | 1071 vwr.addHydrogens(bsA, Viewer.MIN_SILENT); in assignAtom()
1127 vwr.addHydrogens(bsAtoms, Viewer.MIN_SILENT); in assignBond()
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/modelsetbio/ |
| H A D | BioResolver.java | 404 addHydrogens(); in finalizeHydrogens()
407 private void addHydrogens() { in addHydrogens() method in BioResolver
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| /dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/src/ |
| H A D | routines.py | 774 def addHydrogens(self): member in Routines
|