/dports/science/cdk/cdk-cdk-2.3/base/data/src/main/java/org/openscience/cdk/ |
H A D | AtomContainer.java | 86 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 …]
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/dports/science/cdk/cdk-cdk-2.3/base/silent/src/main/java/org/openscience/cdk/silent/ |
H A D | AtomContainer.java | 88 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; [all …]
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/dports/science/cdk/cdk-cdk-2.3/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/ |
H A D | QueryAtomContainer.java | 187 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; [all …]
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/modelset/ |
H A D | BondIteratorSelected.java | 35 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()
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H A D | BondCollection.java | 43 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() [all …]
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H A D | Model.java | 128 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()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/smarter/ |
H A D | BondIterator.java | 35 private int bondCount; field in BondIterator 44 bondCount = asc.bondCount; in BondIterator() 50 if (ibond == bondCount) in hasNext() 55 if (ibond == bondCount) in hasNext()
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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 | BondCountDescriptor.java | 139 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()
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/dports/science/cdk/cdk-cdk-2.3/tool/structgen/src/test/java/org/openscience/cdk/structgen/ |
H A D | SingleStructureRandomGeneratorTest.java | 72 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()
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/dports/science/cdk/cdk-cdk-2.3/tool/group/src/main/java/org/openscience/cdk/group/ |
H A D | BondRefinable.java | 109 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()
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/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/tests/core/ |
H A D | moleculetest.cpp | 126 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()
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/dports/science/avogadrolibs/avogadrolibs-1.94.0/tests/core/ |
H A D | moleculetest.cpp | 126 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()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/simple/ |
H A D | JmeReader.java | 73 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()
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H A D | AlchemyReader.java | 53 private int bondCount; field in AlchemyReader 65 bondCount = parseIntStr(tokens[isM3D ? 1 : 2]); in initializeReader() 156 for (int i = bondCount; --i >= 0;) { in readBonds()
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/dports/science/cdk/cdk-cdk-2.3/base/standard/src/main/java/org/openscience/cdk/tools/ |
H A D | IDCreator.java | 67 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()
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/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/tests/io/ |
H A D | xyztest.cpp | 48 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()
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H A D | mdltest.cpp | 79 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()
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/dports/science/avogadrolibs/avogadrolibs-1.94.0/tests/io/ |
H A D | xyztest.cpp | 48 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()
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H A D | mdltest.cpp | 79 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()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/smiles/ |
H A D | SmilesAtom.java | 108 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() [all …]
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/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/tests/qtgui/ |
H A D | rwmoleculetest.cpp | 166 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 …]
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/dports/science/avogadrolibs/avogadrolibs-1.94.0/tests/qtgui/ |
H A D | rwmoleculetest.cpp | 166 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 …]
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/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/avogadro/qtgui/ |
H A D | molecule.cpp | 38 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()
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/dports/science/avogadrolibs/avogadrolibs-1.94.0/avogadro/qtgui/ |
H A D | molecule.cpp | 38 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()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/more/ |
H A D | Mol2Reader.java | 112 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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