/dports/science/openbabel/openbabel-3.1.1/src/ |
H A D | tautomer.cpp | 278 switch (atomTypes[i]) { in PrintAtomTypes() 426 if (atomTypes[atom->GetIndex()] == Acceptor || atomTypes[atom->GetIndex()] == Hybridized) { in IsPropagationValid() 529 if (atomTypes[atom->GetIndex()] != Acceptor && atomTypes[atom->GetIndex()] != Hybridized) in AssignmentPropagation() 554 if (atomTypes[atom->GetIndex()] != Acceptor && atomTypes[atom->GetIndex()] != Hybridized) in AssignmentPropagation() 586 if (IsLeafNode(atomTypes)) { in AssignmentPropagation() 655 return std::count(atomTypes.begin(), atomTypes.end(), Unassigned) < numHydrogens; in HasTooManyHydrogensLeft() 775 PrintAtomTypes(atomTypes); in Enumerate() 791 if (atomTypes[i] == Donor) { in Enumerate() 796 if (atomTypes[i] == Donor || atomTypes[i] == Acceptor) in Enumerate() 797 atomTypes[i] = Unassigned; in Enumerate() [all …]
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/dports/science/cdk/cdk-cdk-2.3/base/core/src/main/java/org/openscience/cdk/config/ |
H A D | AtomTypeFactory.java | 98 private Map<String,IAtomType> atomTypes = null; field in AtomTypeFactory 106 atomTypes = new HashMap<String,IAtomType>(100); in AtomTypeFactory() 115 atomTypes = new HashMap<String,IAtomType>(100); in AtomTypeFactory() 238 atomTypes.put(type.getAtomTypeName(), new ImmutableAtomType(type)); in readConfiguration() 246 atomTypes = new HashMap<String,IAtomType>(); in readConfiguration() 256 return atomTypes.size(); in getSize() 267 IAtomType type = atomTypes.get(identifier); in getAtomType() 283 for (IAtomType atomType : atomTypes.values()) { in getAtomTypes() 289 if (atomTypes.length > 0) in getAtomTypes() 293 return atomTypes; in getAtomTypes() [all …]
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H A D | OWLBasedAtomTypeConfigurator.java | 60 List<IAtomType> atomTypes; in readAtomTypes() local 63 atomTypes = reader.readAtomTypes(builder); in readAtomTypes() 64 for (IAtomType atomType : atomTypes) { in readAtomTypes() 69 return atomTypes; in readAtomTypes()
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H A D | CDKBasedAtomTypeConfigurator.java | 64 List<IAtomType> atomTypes; in readAtomTypes() local 87 atomTypes = reader.readAtomTypes(builder); in readAtomTypes() 88 for (IAtomType atomType : atomTypes) { in readAtomTypes() 93 return atomTypes; in readAtomTypes()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ReducedGraphs/ |
H A D | ReducedGraphs.cpp | 117 ROMol *rg = generateMolExtendedReducedGraph(mol, atomTypes); in getErGFingerprint() 124 *rg, atomTypes, fuzzIncrement, minPath, maxPath); in getErGFingerprint() 135 if (atomTypes) { in generateErGFingerprintForReducedGraph() 136 nTypes = atomTypes->size(); in generateErGFingerprintForReducedGraph() 205 if (!atomTypes) { in generateMolExtendedReducedGraph() 207 atomTypes = latomTypes; in generateMolExtendedReducedGraph() 208 getErGAtomTypes(mol, *atomTypes); in generateMolExtendedReducedGraph() 212 const int aliphaticFlag = atomTypes->size() - 1; // the last type in generateMolExtendedReducedGraph() 213 const int aromaticFlag = atomTypes->size(); in generateMolExtendedReducedGraph() 219 for (unsigned int i = 0; i < atomTypes->size(); ++i) { in generateMolExtendedReducedGraph() [all …]
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H A D | ReducedGraphs.h | 36 std::vector<boost::dynamic_bitset<>> *atomTypes = nullptr); 57 const ROMol &mol, std::vector<boost::dynamic_bitset<>> *atomTypes = nullptr, 79 const ROMol &mol, std::vector<boost::dynamic_bitset<>> *atomTypes = nullptr,
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/dports/biology/protomol/protomol/applications/iSGProtomol-app/integrators/ |
H A D | ModifierISG.cpp | 310 topo->atomTypes[i].name, in indexBonds() 311 topo->atomTypes[i].symbolName)); in indexBonds() 321 string myName = atomTypes[i].name; in indexBonds() 328 if (myName == trans.atomTypes[j].type_name) { in indexBonds() 329 atomTypes[i].mass = trans.atomTypes[j].mass; in indexBonds() 330 atomTypes[i].charge = trans.atomTypes[j].charge; in indexBonds() 331 atomTypes[i].stageNumber = trans.atomTypes[j].stage; in indexBonds() 470 string myName(topo->atomTypes[I].name); in setForcesAfterTransformation() 570 string myName(topo->atomTypes[I].name); in pickNewMolecule() 827 string myName(topo->atomTypes[I].name); in readXSCs() [all …]
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/dports/science/cdk/cdk-cdk-2.3/base/valencycheck/src/main/java/org/openscience/cdk/tools/ |
H A D | SaturationChecker.java | 89 if (atomTypes.length == 0) return true; in hasPerfectConfiguration() 97 for (int f = 0; f < atomTypes.length; f++) { in hasPerfectConfiguration() 98 …if (bondOrderSum == atomTypes[f].getBondOrderSum() && maxBondOrder == atomTypes[f].getMaxBondOrder… in hasPerfectConfiguration() 164 if (atomTypes.length == 0) return true; in isSaturated() 177 for (int f = 0; f < atomTypes.length; f++) { in isSaturated() 197 if (atomTypes.length == 0) return false; in isOverSaturated() 209 for (int f = 0; f < atomTypes.length; f++) { in isOverSaturated() 228 if (atomTypes.length == 0) return 0; in getCurrentMaxBondOrder() 233 for (int f = 0; f < atomTypes.length; f++) { in getCurrentMaxBondOrder() 622 if (atomTypes.length > 0) { in calculateNumberOfImplicitHydrogens() [all …]
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H A D | SmilesValencyChecker.java | 274 … IAtomType[] atomTypes = getAtomTypeFactory(atom.getBuilder()).getAtomTypes(atom.getSymbol()); in calculateNumberOfImplicitHydrogens() local 275 if (atomTypes.length == 0) { in calculateNumberOfImplicitHydrogens() 280 logger.debug("Found atomtypes: ", atomTypes.length); in calculateNumberOfImplicitHydrogens() 281 for (int f = 0; f < atomTypes.length; f++) { in calculateNumberOfImplicitHydrogens() 282 IAtomType type = atomTypes[f]; in calculateNumberOfImplicitHydrogens() 316 … IAtomType[] atomTypes = getAtomTypeFactory(atom.getBuilder()).getAtomTypes(atom.getSymbol()); in isSaturated() local 317 if (atomTypes.length == 0) { in isSaturated() 333 for (int f = 0; f < atomTypes.length; f++) { in isSaturated() 334 IAtomType type = atomTypes[f]; in isSaturated()
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/dports/biology/protomol/protomol/framework/frontend/ |
H A D | OutputPaulTrap.cpp | 120 vector<int> n(myTopology->atomTypes.size(),0); in doInitialize() 129 …Real f = myTopology->atomTypes[i].charge/myTopology->atomTypes[0].charge*myTopology->atomTypes[0].… in doInitialize() 134 myPaulQ += myTopology->atomTypes[i].charge*myTopology->atomTypes[i].charge*n[i]*(n[i]-1.0)/2.0; in doInitialize() 136 myPaulQ += myTopology->atomTypes[i].charge*myTopology->atomTypes[i].charge*n[i]; in doInitialize() 137 myPaulM += myTopology->atomTypes[i].mass*n[i]; in doInitialize() 139 myPaulQ += myTopology->atomTypes[i].charge*myTopology->atomTypes[j].charge*n[i]*n[j]; in doInitialize() 150 if(!myTopology->atomTypes.empty() && myTopology->atomTypes[0].charge < 0) in doInitialize() 281 if(!pos.write(myLowXYZ,myTopology->atoms,myTopology->atomTypes)) in doWrite()
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H A D | buildTopology.cpp | 59 topo->atomTypes.clear(); in buildTopology() 84 atomLookUpTable[tempatomtype.name] = topo->atomTypes.size(); in buildTopology() 85 topo->atomTypes.push_back(tempatomtype); in buildTopology() 155 string bond1(topo->atomTypes[topo->atoms[atom1].type].name); in buildTopology() 156 string bond2(topo->atomTypes[topo->atoms[atom2].type].name); in buildTopology() 228 string angle1(topo->atomTypes[topo->atoms[atom1].type].name); in buildTopology() 229 string angle2(topo->atomTypes[topo->atoms[atom2].type].name); in buildTopology() 230 string angle3(topo->atomTypes[topo->atoms[atom3].type].name); in buildTopology() 511 unsigned int sizeAtomTypes = topo->atomTypes.size(); in buildTopology() 802 ((topo->atomTypes[topo->atoms[mol[0]].type].symbolName == h && in buildMoleculeTable() [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ReducedGraphs/Wrap/ |
H A D | rdReducedGraphs.cpp | 29 python::object atomTypes) { in GenerateMolExtendedReducedGraphHelper() argument 30 if (atomTypes) { in GenerateMolExtendedReducedGraphHelper() 38 python::object atomTypes, in GenerateErGFingerprintForReducedGraphHelper() argument 42 if (atomTypes) { in GenerateErGFingerprintForReducedGraphHelper() 56 python::object atomTypes, in GetErGFingerprintHelper() argument 59 if (atomTypes) { in GetErGFingerprintHelper()
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/dports/science/avogadrolibs/avogadrolibs-1.94.0/avogadro/io/ |
H A D | gromacsformat.cpp | 89 AtomTypeMap atomTypes; in read() local 162 AtomTypeMap::const_iterator it = atomTypes.find(value); in read() 163 if (it == atomTypes.end()) { in read() 164 atomTypes.insert(std::make_pair(value, customElementCounter++)); in read() 165 it = atomTypes.find(value); in read() 193 if (!atomTypes.empty()) { in read() 195 for (AtomTypeMap::const_iterator it = atomTypes.begin(), in read() 196 itEnd = atomTypes.end(); in read()
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/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/avogadro/io/ |
H A D | gromacsformat.cpp | 89 AtomTypeMap atomTypes; in read() local 162 AtomTypeMap::const_iterator it = atomTypes.find(value); in read() 163 if (it == atomTypes.end()) { in read() 164 atomTypes.insert(std::make_pair(value, customElementCounter++)); in read() 165 it = atomTypes.find(value); in read() 193 if (!atomTypes.empty()) { in read() 195 for (AtomTypeMap::const_iterator it = atomTypes.begin(), in read() 196 itEnd = atomTypes.end(); in read()
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/dports/biology/protomol/protomol/framework/forces/ |
H A D | PaulTrapExtendedForce.h | 239 const unsigned int numberOfTypes = topo->atomTypes.size(); in initialize() 244 if(topo->atomTypes[i].charge < 0.0) in initialize() 246 else if(topo->atomTypes[i].charge > 0.0) in initialize() 256 …Real f = topo->atomTypes[i].charge/topo->atomTypes[0].charge*topo->atomTypes[0].mass/topo->atomTyp… in initialize() 279 q += topo->atomTypes[i].charge*topo->atomTypes[i].charge*n[i]*(n[i]-1.0)/2.0; in initialize() 281 q += topo->atomTypes[i].charge*topo->atomTypes[i].charge*n[i]; in initialize() 282 m += topo->atomTypes[i].mass*n[i]; in initialize() 284 q += topo->atomTypes[i].charge*topo->atomTypes[j].charge*n[i]*n[j]; in initialize() 323 …Real c = topo->atomTypes[i].mass*1e-3*Constant::SI::KCAL*Constant::SI::TIME_FS*Constant::SI::TIME_… in initialize()
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/dports/biology/protomol/protomol/applications/iSGProtomol-app/io/ |
H A D | TRANSReader.cpp | 273 trans.atomTypes.push_back(TRANS::AtomType(numIdentities, numStages, myTypes[Index])); in read() 277 trans.atomTypes[Index].mass[toInt(j[3]) - 1] = toReal(j[1]); in read() 278 trans.atomTypes[Index].charge[toInt(j[3]) - 1] = toReal(j[2]); in read() 279 trans.atomTypes[Index].stage[toInt(j[3]) - 1] = toInt(j[4]); in read() 305 trans.atomTypes.push_back(TRANS::AtomType(numIdentities, numStages, myTypes[Index])); in read() 312 trans.atomTypes[Index].old_charge[o][n][s] = toReal(j[4]); in read() 313 trans.atomTypes[Index].new_charge[o][n][s] = toReal(j[5]); in read() 335 trans.atomTypes.push_back(TRANS::AtomType(numIdentities, numStages, myTypes[Index])); in read() 343 trans.atomTypes[Index].old_charge[o][n][s] = toReal(j[4]); in read() 344 trans.atomTypes[Index].new_charge[o][n][s] = toReal(j[5]); in read() [all …]
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/dports/biology/protomol/protomol/framework/io/ |
H A D | XYZTrajectoryWriter.cpp | 40 … XYZTrajectoryWriter::open(const std::vector<Atom>& atoms, const std::vector<AtomType>& atomTypes){ in open() argument 41 setNames(atoms,atomTypes); in open() 61 …onst std::string& filename,const std::vector<Atom>& atoms, const std::vector<AtomType>& atomTypes){ in open() argument 62 setNames(atoms,atomTypes); in open() 128 const std::vector<AtomType>& atomTypes){ in write() argument 129 setNames(atoms,atomTypes); in write() 180 …ZTrajectoryWriter::setNames(const std::vector<Atom>& atoms,const std::vector<AtomType>& atomTypes){ in setNames() argument 183 myAtomTypes = &atomTypes; in setNames()
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H A D | XYZTrajectoryWriter.h | 46 bool open(const std::vector<Atom>& atoms, const std::vector<AtomType>& atomTypes); 50 …nst std::string& filename, const std::vector<Atom>& atoms, const std::vector<AtomType>& atomTypes); 55 …onst Vector3DBlock& coords, const std::vector<Atom>& atoms,const std::vector<AtomType>& atomTypes); 59 void setNames(const std::vector<Atom>& atoms,const std::vector<AtomType>& atomTypes);
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/dports/biology/protomol/protomol/applications/iSGProtomol-app/frontend/ |
H A D | buildISGTopology.cpp | 55 topo->atomTypes.clear(); in buildISGTopology() 80 atomLookUpTable[tempatomtype.name] = topo->atomTypes.size(); in buildISGTopology() 81 topo->atomTypes.push_back(tempatomtype); in buildISGTopology() 154 string bond1(topo->atomTypes[topo->atoms[atom1].type].name); in buildISGTopology() 155 string bond2(topo->atomTypes[topo->atoms[atom2].type].name); in buildISGTopology() 220 string angle1(topo->atomTypes[topo->atoms[atom1].type].name); in buildISGTopology() 221 string angle2(topo->atomTypes[topo->atoms[atom2].type].name); in buildISGTopology() 222 string angle3(topo->atomTypes[topo->atoms[atom3].type].name); in buildISGTopology() 524 unsigned int sizeAtomTypes = topo->atomTypes.size(); in buildISGTopology() 866 ((topo->atomTypes[topo->atoms[mol[0]].type].symbolName == h && in buildMoleculeTable() [all …]
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/dports/math/vtk8/VTK-8.2.0/Domains/Chemistry/ |
H A D | vtkProteinRibbonFilter.cxx | 107 vtkStringArray *atomTypes = in RequestData() local 112 if (!atomTypes || !atomType) in RequestData() 156 this->SetColorByAtom(atomsColors, atomTypes); in RequestData() 157 this->SetColorByStructure(atomsColors, atomTypes, atom_ss, in RequestData() 169 vtkStdString type = atomTypes->GetValue(i); in RequestData() 244 vtkStringArray* atomTypes) in SetColorByAtom() argument 247 unsigned int len = atomTypes->GetNumberOfValues(); in SetColorByAtom() 251 if(this->ElementColors.find(atomTypes->GetValue(i)) != this->ElementColors.end()) in SetColorByAtom() 253 colors[i] = this->ElementColors[atomTypes->GetValue(i)]; in SetColorByAtom() 264 vtkStringArray* atomTypes, in SetColorByStructure() argument [all …]
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/dports/math/vtk9/VTK-9.1.0/Domains/Chemistry/ |
H A D | vtkProteinRibbonFilter.cxx | 108 vtkStringArray* atomTypes = in RequestData() local 113 if (!atomTypes || !atomType) in RequestData() 156 this->SetColorByAtom(atomsColors, atomTypes); in RequestData() 158 atomsColors, atomTypes, atom_ss, ToColor3ubFromHex3(0xFF0080), ToColor3ubFromHex3(0xFFC800)); in RequestData() 168 vtkStdString type = atomTypes->GetValue(i); in RequestData() 238 std::vector<vtkColor3ub>& colors, vtkStringArray* atomTypes) in SetColorByAtom() argument 241 unsigned int len = atomTypes->GetNumberOfValues(); in SetColorByAtom() 245 if (this->ElementColors.find(atomTypes->GetValue(i)) != this->ElementColors.end()) in SetColorByAtom() 247 colors[i] = this->ElementColors[atomTypes->GetValue(i)]; in SetColorByAtom() 257 vtkStringArray* atomTypes, vtkUnsignedCharArray* ss, const vtkColor3ub& helixColor, in SetColorByStructure() argument [all …]
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/dports/math/vtk6/VTK-6.2.0/Domains/Chemistry/ |
H A D | vtkProteinRibbonFilter.cxx | 109 vtkStringArray *atomTypes = in RequestData() local 114 if (!atomTypes || !atomType) in RequestData() 158 this->SetColorByAtom(atomsColors, atomTypes); in RequestData() 159 this->SetColorByStructure(atomsColors, atomTypes, atom_ss, in RequestData() 171 vtkStdString type = atomTypes->GetValue(i); in RequestData() 246 vtkStringArray* atomTypes) in SetColorByAtom() argument 249 unsigned int len = atomTypes->GetNumberOfValues(); in SetColorByAtom() 253 if(this->ElementColors.find(atomTypes->GetValue(i)) != this->ElementColors.end()) in SetColorByAtom() 255 colors[i] = this->ElementColors[atomTypes->GetValue(i)]; in SetColorByAtom() 266 vtkStringArray* atomTypes, in SetColorByStructure() argument [all …]
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/dports/science/cdk/cdk-cdk-2.3/misc/extra/src/main/java/org/openscience/cdk/validate/ |
H A D | BasicValidator.java | 229 IAtomType[] atomTypes = structgenATF.getAtomTypes(atom.getSymbol()); in validateMaxBondOrder() local 232 for (int j = 0; j < atomTypes.length; j++) { in validateMaxBondOrder() 233 … if (!BondManipulator.isHigherOrder(bond.getOrder(), atomTypes[j].getMaxBondOrder())) { in validateMaxBondOrder() 236 failedOn = atomTypes[j]; in validateMaxBondOrder() 299 IAtomType[] atomTypes = structgenATF.getAtomTypes(atom.getSymbol()); in validateBondOrderSum() local 300 if (atomTypes.length == 0) { in validateBondOrderSum() 307 for (int j = 0; j < atomTypes.length; j++) { in validateBondOrderSum() 308 IAtomType type = atomTypes[j]; in validateBondOrderSum() 314 failedOn = atomTypes[j]; in validateBondOrderSum()
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/dports/science/gabedit/GabeditSrc251_300720/src/MolecularMechanics/ |
H A D | MolecularMechanics.c | 723 a1Type = atomTypes[a1]; in setStretchParameters() 724 a2Type = atomTypes[a2]; in setStretchParameters() 803 a1Type = atomTypes[a1]; in setBendParameters() 804 a2Type = atomTypes[a2]; in setBendParameters() 805 a3Type = atomTypes[a3]; in setBendParameters() 879 a1Type = atomTypes[a1]; in setDihedralParameters() 880 a2Type = atomTypes[a2]; in setDihedralParameters() 881 a3Type = atomTypes[a3]; in setDihedralParameters() 882 a4Type = atomTypes[a4]; in setDihedralParameters() 951 a1Type = atomTypes[a1]; in setImproperTorionParameters() [all …]
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H A D | CreatePersonalMMFile.c | 199 amberParameters->atomTypes[i].name, in saveParametersAtomTypes() 200 amberParameters->atomTypes[i].symbol, in saveParametersAtomTypes() 201 amberParameters->atomTypes[i].number+1, in saveParametersAtomTypes() 202 amberParameters->atomTypes[i].masse, in saveParametersAtomTypes() 203 amberParameters->atomTypes[i].polarisability, in saveParametersAtomTypes() 204 amberParameters->atomTypes[i].description in saveParametersAtomTypes()
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