| /dports/science/cdk/cdk-cdk-2.3/storage/ctab/src/test/java/org/openscience/cdk/io/ |
| H A D | MDLValenceTest.java | 50 assertThat(atom.getValency(), is(0)); in sodium_metal()
61 assertThat(atom.getValency(), is(1)); in sodium_hydride()
71 assertThat(atom.getValency(), is(1)); in sodium_implicit()
85 assertThat(bi1.getValency(), is(3)); in bismuth()
86 assertThat(h2.getValency(), is(1)); in bismuth()
98 assertThat(atom.getValency(), is(2)); in tin_ii()
112 assertThat(atom.getValency(), is(4)); in tin_iv()
147 assertThat(c1.getValency(), is(3)); in carbon_cation_doubleBonded()
149 assertThat(c2.getValency(), is(4)); in carbon_cation_doubleBonded()
174 assertThat(bi1.getValency(), is(3)); in bismuth_isImplicit()
[all …]
|
| H A D | MDLV2000AtomBlockTest.java | 175 assertThat(atom.getValency(), is(0)); in valence_0()
182 assertThat(atom.getValency(), is(nullValue())); in valence_unset()
189 assertThat(atom.getValency(), is(1)); in valence_1()
196 assertThat(atom.getValency(), is(14)); in valence_14()
203 assertThat(atom.getValency(), is(nullValue())); in valence_invalid()
|
| /dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/smsd/algorithm/matchers/ |
| H A D | DefaultVFBondMatcher.java | 154 return getValency(atom) - container.countNeighbors(atom); in getUnsaturation()
157 private int getValency(IAtom atom) { in getValency() method in DefaultVFBondMatcher
158 return (atom.getValency() == null) ? 0 : atom.getValency().intValue(); in getValency()
166 return getValency(atom) - (countNeighbors(container, atom) + countImplicitHydrogens(atom)); in getUnsaturation()
|
| H A D | DefaultBondMatcher.java | 146 private int getValency(IAtom atom) { in getValency() method in DefaultBondMatcher
147 return (atom.getValency() == null) ? 0 : atom.getValency().intValue(); in getValency()
155 return getValency(atom) - (countNeighbors(container, atom) + countImplicitHydrogens(atom)); in getUnsaturation()
|
| /dports/science/cdk/cdk-cdk-2.3/base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ |
| H A D | AtomTypeManipulator.java | 74 atom.setValency(atomType.getValency()); in configure()
123 if (atom.getValency() == CDKConstants.UNSET && atomType.getValency() != CDKConstants.UNSET) in configureUnsetProperties()
124 atom.setValency(atomType.getValency()); in configureUnsetProperties()
|
| /dports/science/cdk/cdk-cdk-2.3/base/silent/src/main/java/org/openscience/cdk/silent/ |
| H A D | AtomType.java | 147 this.electronValency = ((IAtomType) element).getValency(); in AtomType()
358 public Integer getValency() { in getValency() method in AtomType
392 if (getValency() != null) { in toString()
393 resultString.append(", EV:").append(getValency()); in toString()
|
| /dports/science/cdk/cdk-cdk-2.3/base/valencycheck/src/main/java/org/openscience/cdk/tools/ |
| H A D | AtomTypeAwareSaturationChecker.java | 294 … double noValenceElectrons = atom.getValency() == CDKConstants.UNSET ? -1 : atom.getValency(); in getMaxNoOfBonds()
318 if (atom.getValency() == CDKConstants.UNSET || atom.getValency() == null) in bondsUsed()
323 implicitHydrogens = (8 - atom.getValency()) - atom.getFormalNeighbourCount(); in bondsUsed()
|
| /dports/science/cdk/cdk-cdk-2.3/base/data/src/main/java/org/openscience/cdk/ |
| H A D | AtomType.java | 150 this.electronValency = ((IAtomType) element).getValency(); in AtomType()
369 public Integer getValency() { in getValency() method in AtomType
403 if (getValency() != null) { in toString()
404 resultString.append(", EV:").append(getValency()); in toString()
|
| /dports/science/cdk/cdk-cdk-2.3/base/core/src/main/java/org/openscience/cdk/config/ |
| H A D | ImmutableAtomType.java | 75 if (type.getValency() != null) { in ImmutableAtomType()
76 this.electronValency = type.getValency(); in ImmutableAtomType()
347 public Integer getValency() { in getValency() method in ImmutableAtomType
376 if (getValency() != null) { in toString()
377 resultString.append(", EV:").append(getValency()); in toString()
|
| /dports/science/opsin/dan2097-opsin-9b25f7546b67/opsin-core/src/main/java/uk/ac/cam/ch/wwmm/opsin/ |
| H A D | StructureBuildingMethods.java | 200 frag.getOutAtom(0).getValency() == 1 && in performLocantedSubstitutiveOperations()
1690 int bondOrder = multiRadicalOutAtom.getValency(); in performMultiplicativeOperations()
1919 if (outAtom.getValency() != firstOutAtomOrder){ in joinFragmentsAdditively()
1928 if (outAtom.getValency() != firstOutAtomOrder){ in joinFragmentsAdditively()
1962 if (outAtom.getValency()==firstOutAtomOrder){ in joinFragmentsAdditively()
1974 int bondOrder = in.getValency(); in joinFragmentsAdditively()
1983 if (fragToBeJoined.getOutAtom(i).getValency() == bondOrder){ in joinFragmentsAdditively()
1998 valency += nextOutAtom.getValency(); in joinFragmentsAdditively()
2045 int bondOrder = out.getValency(); in joinFragmentsSubstitutively()
2117 int bondValency = outAtom2.getValency(); in formEpoxide()
[all …]
|
| H A D | StructureBuilder.java | 212 if (out.getValency()>1){ in buildEster()
304 if (substituent1.getOutAtom(0).getValency() !=1){ in buildDiValentFunctionalGroup()
309 if (substituent1.getOutAtom(1).getValency() !=1){ in buildDiValentFunctionalGroup()
331 if (substituent2.getOutAtom(0).getValency() !=1){ in buildDiValentFunctionalGroup()
374 if (outAtom.getValency()>1){ in buildMonovalentFunctionalGroup()
471 if (substituentBr.getOutAtom(j).getValency() != 1) { in buildFunctionalClassEster()
1221 if (outAtom1.getValency() != 1){ in buildGlycol()
1230 if (outAtom2.getValency() != 1){ in buildGlycol()
1629 state.fragManager.createBond(out.getAtom(), atomToUse, out.getValency()); in connectSubstituentsToAcetal()
1653 state.fragManager.createBond(outAtom, inAtom, peptideBr.getOutAtom(0).getValency()); in buildCyclicPeptide()
[all …]
|
| H A D | OutAtom.java | 42 int getValency() { in getValency() method in OutAtom
|
| /dports/science/cdk/cdk-cdk-2.3/misc/diff/src/main/java/org/openscience/cdk/tools/diff/ |
| H A D | AtomTypeDiff.java | 89 …alDiff.addChild(IntegerDifference.construct("V", firstElem.getValency(), secondElem.getValency())); in difference()
|
| /dports/science/cdk/cdk-cdk-2.3/base/datadebug/src/main/java/org/openscience/cdk/debug/ |
| H A D | DebugAtomType.java | 372 public Integer getValency() { in getValency() method in DebugAtomType
373 logger.debug("Getting valency: ", super.getValency()); in getValency()
374 return super.getValency(); in getValency()
|
| H A D | DebugFragmentAtom.java | 295 public Integer getValency() { in getValency() method in DebugFragmentAtom
296 logger.debug("Getting valency: ", super.getValency()); in getValency()
297 return super.getValency(); in getValency()
|
| H A D | DebugAtom.java | 307 public Integer getValency() { in getValency() method in DebugAtom
308 logger.debug("Getting valency: ", super.getValency()); in getValency()
309 return super.getValency(); in getValency()
|
| H A D | DebugPseudoAtom.java | 281 public Integer getValency() { in getValency() method in DebugPseudoAtom
282 logger.debug("Getting valency: ", super.getValency()); in getValency()
283 return super.getValency(); in getValency()
|
| /dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/qsar/descriptors/bond/ |
| H A D | IPBondLearningDescriptor.java | 121 Integer originalValency1 = bond.getBegin().getValency(); in calculate()
125 Integer originalValency2 = bond.getEnd().getValency(); in calculate()
|
| /dports/science/cdk/cdk-cdk-2.3/base/core/src/main/java/org/openscience/cdk/ |
| H A D | AtomRef.java | 385 public Integer getValency() { in getValency() method in AtomRef
386 return atom.getValency(); in getValency()
|
| /dports/science/cdk/cdk-cdk-2.3/base/interfaces/src/main/java/org/openscience/cdk/interfaces/ |
| H A D | IAtomType.java | 182 public Integer getValency(); in getValency() method
|
| /dports/science/cdk/cdk-cdk-2.3/storage/ctab/src/main/java/org/openscience/cdk/io/ |
| H A D | MDLValence.java | 97 if (atom.getValency() != null) { in apply()
98 atom.setImplicitHydrogenCount(atom.getValency() - explicit); in apply()
|
| /dports/science/cdk/cdk-cdk-2.3/descriptor/qsarbond/src/main/java/org/openscience/cdk/qsar/descriptors/bond/ |
| H A D | BondPartialPiChargeDescriptor.java | 159 Integer originalValency1 = bond.getBegin().getValency(); in calculate()
164 Integer originalValency2 = bond.getEnd().getValency(); in calculate()
|
| H A D | BondPartialTChargeDescriptor.java | 166 Integer originalValency1 = bond.getBegin().getValency(); in calculate()
171 Integer originalValency2 = bond.getEnd().getValency(); in calculate()
|
| /dports/science/cdk/cdk-cdk-2.3/tool/tautomer/src/main/java/org/openscience/cdk/tautomers/ |
| H A D | InChITautomerGenerator.java | 475 other.setValency(other.getValency() - decValence); in constructTautomers()
514 if (atom.getValency() - atom.getFormalCharge() != atom.getImplicitHydrogenCount() in constructTautomers()
608 if (atom.getValency() - atom.getFormalCharge() > (hCnt + conn)) { in combineHydrogenPositions()
664 … if (atom.getValency() != atom.getImplicitHydrogenCount() + getConnectivity(atom, container)) { in tryDoubleBondCombinations()
|
| /dports/science/cdk/cdk-cdk-2.3/descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/ |
| H A D | EffectiveAtomPolarizabilityDescriptor.java | 120 Integer originalValency = atom.getValency(); in calculate()
|