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Searched refs:bondCount (Results 1 – 25 of 160) sorted by relevance

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/dports/science/cdk/cdk-cdk-2.3/base/data/src/main/java/org/openscience/cdk/
H A DAtomContainer.java86 protected int bondCount; field in AtomContainer
190 this.bondCount = 0; in AtomContainer()
194 bonds = new IBond[bondCount]; in AtomContainer()
534 number -= this.bondCount;
567 return this.bondCount;
870 bonds[bondCount++] = bond;
961 bonds[bondCount - 1] = null;
962 bondCount--;
1046 number -= this.bondCount;
1162 bondCount = 0;
[all …]
/dports/science/cdk/cdk-cdk-2.3/base/silent/src/main/java/org/openscience/cdk/silent/
H A DAtomContainer.java88 protected int bondCount; field in AtomContainer
188 this.bondCount = 0; in AtomContainer()
192 bonds = new IBond[bondCount]; in AtomContainer()
514 number -= this.bondCount;
547 return this.bondCount;
849 bonds[bondCount++] = bond;
934 bonds[bondCount - 1] = null;
935 bondCount--;
1014 number -= this.bondCount;
1115 bondCount = 0;
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/dports/science/cdk/cdk-cdk-2.3/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/
H A DQueryAtomContainer.java187 this.bondCount = 0; in QueryAtomContainer()
191 bonds = new IBond[bondCount]; in QueryAtomContainer()
244 this.bondCount = bonds.length;
537 if (pointer < bondCount)
682 number -= this.bondCount;
723 return this.bondCount;
1033 bonds[bondCount] = bond;
1034 ++bondCount;
1144 bondCount--;
1245 number -= this.bondCount;
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/modelset/
H A DBondIteratorSelected.java35 private int bondCount; field in BondIteratorSelected
41 BondIteratorSelected(Bond[] bonds, int bondCount, int bondType, in BondIteratorSelected() argument
44 this.bondCount = bondCount; in BondIteratorSelected()
55 return (iBond >= 0 && iBond < bondCount); in hasNext()
57 for (; iBond < bondCount; ++iBond) { in hasNext()
H A DBondCollection.java43 public int bondCount; field in BondCollection
108 for (int i = bondCount; --i >= 0;) in getBondCountInModel()
154 if (bondCount == bo.length) in getOrAddBond()
157 i = setBond(bondCount++, in getOrAddBond()
219 if (bondCount == bo.length) in addHBond()
228 for (int i = bondCount; --i >= 0;) { in deleteAllBonds2()
232 bondCount = 0; in deleteAllBonds2()
342 for (int i = bondCount; --i >= iDst;) in dBb()
344 bondCount = iDst; in dBb()
423 for (int i = bondCount; --i >= 0;) { in resetAromatic()
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H A DModel.java128 private int bondCount = -1; field in Model
226 bondCount = -1; in resetBoundCount()
230 if (bondCount >= 0) in getBondCount()
231 return bondCount; in getBondCount()
233 bondCount = 0; in getBondCount()
234 for (int i = ms.bondCount; --i >= 0;) in getBondCount()
236 bondCount++; in getBondCount()
237 return bondCount; in getBondCount()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/smarter/
H A DBondIterator.java35 private int bondCount; field in BondIterator
44 bondCount = asc.bondCount; in BondIterator()
50 if (ibond == bondCount) in hasNext()
55 if (ibond == bondCount) in hasNext()
/dports/science/cdk/cdk-cdk-2.3/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/
H A DBondCountDescriptor.java139 int bondCount = 0; in calculate() local
148 if (!hasHydrogen) bondCount++; in calculate()
152 bondCount), getDescriptorNames(), null); in calculate()
155 int bondCount = 0; in calculate() local
158 bondCount += 1; in calculate()
163 bondCount), getDescriptorNames()); in calculate()
/dports/science/cdk/cdk-cdk-2.3/tool/structgen/src/test/java/org/openscience/cdk/structgen/
H A DSingleStructureRandomGeneratorTest.java72 double bondCount = 0; in fixCarbonHCount() local
76 bondCount = mol.getBondOrderSum(atom); in fixCarbonHCount()
77 if (bondCount > 4) System.out.println("bondCount: " + bondCount); in fixCarbonHCount()
78 atom.setImplicitHydrogenCount(4 - (int) bondCount in fixCarbonHCount()
/dports/science/cdk/cdk-cdk-2.3/tool/group/src/main/java/org/openscience/cdk/group/
H A DBondRefinable.java109 int bondCount = atomContainer.getBondCount(); in getInitialPartition() local
113 for (int bondIndex = 0; bondIndex < bondCount; bondIndex++) { in getInitialPartition()
157 int bondCount = atomContainer.getBondCount(); in setupConnectionTable() local
161 for (int bondIndexI = 0; bondIndexI < bondCount; bondIndexI++) { in setupConnectionTable()
190 connectionTable = new int[bondCount][]; in setupConnectionTable()
191 for (int bondIndexI = 0; bondIndexI < bondCount; bondIndexI++) { in setupConnectionTable()
194 for (int bondIndexJ = 0; bondIndexJ < bondCount; bondIndexJ++) { in setupConnectionTable()
/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/tests/core/
H A Dmoleculetest.cpp126 EXPECT_EQ(4, molecule.bondCount()); in TEST_F()
131 EXPECT_EQ(0, molecule.bondCount()); in TEST_F()
141 EXPECT_EQ(molecule.bondCount(), static_cast<Index>(0)); in TEST_F()
148 EXPECT_EQ(molecule.bondCount(), static_cast<Index>(1)); in TEST_F()
157 EXPECT_EQ(molecule.bondCount(), static_cast<Index>(2)); in TEST_F()
190 EXPECT_EQ(2, molecule.bondCount()); in TEST_F()
197 EXPECT_EQ(1, molecule.bondCount()); in TEST_F()
203 EXPECT_EQ(0, molecule.bondCount()); in TEST_F()
262 EXPECT_EQ(molecule.bondCount(), 0); in TEST_F()
265 EXPECT_EQ(molecule.bondCount(), 2); in TEST_F()
/dports/science/avogadrolibs/avogadrolibs-1.94.0/tests/core/
H A Dmoleculetest.cpp126 EXPECT_EQ(4, molecule.bondCount()); in TEST_F()
131 EXPECT_EQ(0, molecule.bondCount()); in TEST_F()
141 EXPECT_EQ(molecule.bondCount(), static_cast<Index>(0)); in TEST_F()
148 EXPECT_EQ(molecule.bondCount(), static_cast<Index>(1)); in TEST_F()
157 EXPECT_EQ(molecule.bondCount(), static_cast<Index>(2)); in TEST_F()
190 EXPECT_EQ(2, molecule.bondCount()); in TEST_F()
197 EXPECT_EQ(1, molecule.bondCount()); in TEST_F()
203 EXPECT_EQ(0, molecule.bondCount()); in TEST_F()
262 EXPECT_EQ(molecule.bondCount(), 0); in TEST_F()
265 EXPECT_EQ(molecule.bondCount(), 2); in TEST_F()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/simple/
H A DJmeReader.java73 int bondCount = parseInt(); in initializeReader() local
75 readBonds(bondCount); in initializeReader()
108 private void readBonds(int bondCount) throws Exception { in readBonds() argument
109 for (int i = 0; i < bondCount; ++i) { in readBonds()
H A DAlchemyReader.java53 private int bondCount; field in AlchemyReader
65 bondCount = parseIntStr(tokens[isM3D ? 1 : 2]); in initializeReader()
156 for (int i = bondCount; --i >= 0;) { in readBonds()
/dports/science/cdk/cdk-cdk-2.3/base/standard/src/main/java/org/openscience/cdk/tools/
H A DIDCreator.java67 private static int bondCount = 0; field in IDCreator
158 bondCount = 0; in resetCounters()
204 bondCount = 0; in createIDsForAtomContainer()
221 bondCount = setID(BOND_PREFIX, bondCount, bond, internalTabuList); in createIDsForAtomContainer()
242 bondCount = 0; in createIDsForAtomContainerSet()
266 bondCount = 0; in createIDsForReaction()
339 bondCount = 0; in createIDsForChemModel()
/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/tests/io/
H A Dxyztest.cpp48 EXPECT_EQ(molecule.bondCount(), 4); in TEST()
73 EXPECT_EQ(molecule.bondCount(), 0); in TEST()
96 EXPECT_EQ(molecule.bondCount(), 4); in TEST()
170 EXPECT_EQ(molecule.bondCount(), 4); in TEST()
188 EXPECT_EQ(molecule2.bondCount(), 0); in TEST()
223 EXPECT_EQ(mol[i].bondCount(), ref[i].bondCount()); in TEST()
H A Dmdltest.cpp79 EXPECT_EQ(molecule.bondCount(), static_cast<size_t>(7)); in TEST()
110 EXPECT_EQ(molecule.bondCount(), static_cast<size_t>(7)); in TEST()
135 EXPECT_EQ(molecule.bondCount(), 4); in TEST()
153 EXPECT_EQ(molecule2.bondCount(), 25); in TEST()
188 EXPECT_EQ(mol[i].bondCount(), ref[i].bondCount()); in TEST()
/dports/science/avogadrolibs/avogadrolibs-1.94.0/tests/io/
H A Dxyztest.cpp48 EXPECT_EQ(molecule.bondCount(), 4); in TEST()
73 EXPECT_EQ(molecule.bondCount(), 0); in TEST()
96 EXPECT_EQ(molecule.bondCount(), 4); in TEST()
170 EXPECT_EQ(molecule.bondCount(), 4); in TEST()
188 EXPECT_EQ(molecule2.bondCount(), 0); in TEST()
223 EXPECT_EQ(mol[i].bondCount(), ref[i].bondCount()); in TEST()
H A Dmdltest.cpp79 EXPECT_EQ(molecule.bondCount(), static_cast<size_t>(7)); in TEST()
110 EXPECT_EQ(molecule.bondCount(), static_cast<size_t>(7)); in TEST()
135 EXPECT_EQ(molecule.bondCount(), 4); in TEST()
153 EXPECT_EQ(molecule2.bondCount(), 25); in TEST()
188 EXPECT_EQ(mol[i].bondCount(), ref[i].bondCount()); in TEST()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/smiles/
H A DSmilesAtom.java108 int bondCount; field in SmilesAtom
229 if (elementNumber == 7 && isAromatic && bondCount == 2) { in setHydrogenCount()
235 for (int i = 0; i < bondCount; i++) { in setHydrogenCount()
528 if (bondCount >= bonds.length) in addBond()
532 bonds[bondCount] = bond; in addBond()
533 bondCount++; in addBond()
537 if (bonds.length > bondCount) in setBondArray()
571 && number < bondCount ? bonds[number] : null); in getBond()
586 return (parent != null ? parent.getBondCount() : bondCount); in getBondCount()
612 if (i >= bondCount) in getMatchingBondedAtom()
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/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/tests/qtgui/
H A Drwmoleculetest.cpp166 ASSERT_EQ(10, mol.bondCount()); in TEST()
170 EXPECT_EQ(6, mol.bondCount()); in TEST()
180 EXPECT_EQ(3, mol.bondCount()); in TEST()
197 EXPECT_EQ(6, mol.bondCount()); in TEST()
217 ASSERT_EQ(10, mol.bondCount()); in TEST()
279 EXPECT_EQ(0, mol.bondCount()); in TEST()
494 ASSERT_EQ(0, mol.bondCount()); in TEST()
500 EXPECT_EQ(2, mol.bondCount()); in TEST()
502 EXPECT_EQ(1, mol.bondCount()); in TEST()
508 EXPECT_EQ(2, mol.bondCount()); in TEST()
[all …]
/dports/science/avogadrolibs/avogadrolibs-1.94.0/tests/qtgui/
H A Drwmoleculetest.cpp166 ASSERT_EQ(10, mol.bondCount()); in TEST()
170 EXPECT_EQ(6, mol.bondCount()); in TEST()
180 EXPECT_EQ(3, mol.bondCount()); in TEST()
197 EXPECT_EQ(6, mol.bondCount()); in TEST()
217 ASSERT_EQ(10, mol.bondCount()); in TEST()
279 EXPECT_EQ(0, mol.bondCount()); in TEST()
494 ASSERT_EQ(0, mol.bondCount()); in TEST()
500 EXPECT_EQ(2, mol.bondCount()); in TEST()
502 EXPECT_EQ(1, mol.bondCount()); in TEST()
508 EXPECT_EQ(2, mol.bondCount()); in TEST()
[all …]
/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/avogadro/qtgui/
H A Dmolecule.cpp38 for (Index i = 0; i < bondCount(); i++) in Molecule()
49 for (Index i = 0; i < bondCount(); i++) in Molecule()
76 for (Index i = 0; i < bondCount(); ++i) in operator =()
187 m_bondUniqueIds.push_back(bondCount()); in addBond()
199 m_bondUniqueIds.push_back(bondCount()); in addBond()
211 m_bondUniqueIds[uniqueId] = bondCount(); in addBond()
217 if (index >= bondCount()) in removeBond()
/dports/science/avogadrolibs/avogadrolibs-1.94.0/avogadro/qtgui/
H A Dmolecule.cpp38 for (Index i = 0; i < bondCount(); i++) in Molecule()
49 for (Index i = 0; i < bondCount(); i++) in Molecule()
76 for (Index i = 0; i < bondCount(); ++i) in operator =()
187 m_bondUniqueIds.push_back(bondCount()); in addBond()
199 m_bondUniqueIds.push_back(bondCount()); in addBond()
211 m_bondUniqueIds[uniqueId] = bondCount(); in addBond()
217 if (index >= bondCount()) in removeBond()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/more/
H A DMol2Reader.java112 int bondCount = parseInt(); in processMolecule() local
113 if (bondCount == 0) in processMolecule()
146 readBonds(bondCount); in processMolecule()
270 private void readBonds(int bondCount) throws Exception { in readBonds() argument
273 for (int i = 0; i < bondCount; ++i) { in readBonds()

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