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Searched refs:atomTypes (Results 1 – 25 of 108) sorted by relevance

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/dports/science/openbabel/openbabel-3.1.1/src/
H A Dtautomer.cpp278 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()
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/dports/science/cdk/cdk-cdk-2.3/base/core/src/main/java/org/openscience/cdk/config/
H A DAtomTypeFactory.java98 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()
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H A DOWLBasedAtomTypeConfigurator.java60 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()
H A DCDKBasedAtomTypeConfigurator.java64 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()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ReducedGraphs/
H A DReducedGraphs.cpp117 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()
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H A DReducedGraphs.h36 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,
/dports/biology/protomol/protomol/applications/iSGProtomol-app/integrators/
H A DModifierISG.cpp310 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()
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/dports/science/cdk/cdk-cdk-2.3/base/valencycheck/src/main/java/org/openscience/cdk/tools/
H A DSaturationChecker.java89 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()
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H A DSmilesValencyChecker.java274 … 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()
/dports/biology/protomol/protomol/framework/frontend/
H A DOutputPaulTrap.cpp120 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()
H A DbuildTopology.cpp59 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ReducedGraphs/Wrap/
H A DrdReducedGraphs.cpp29 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()
/dports/science/avogadrolibs/avogadrolibs-1.94.0/avogadro/io/
H A Dgromacsformat.cpp89 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()
/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/avogadro/io/
H A Dgromacsformat.cpp89 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()
/dports/biology/protomol/protomol/framework/forces/
H A DPaulTrapExtendedForce.h239 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()
/dports/biology/protomol/protomol/applications/iSGProtomol-app/io/
H A DTRANSReader.cpp273 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()
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/dports/biology/protomol/protomol/framework/io/
H A DXYZTrajectoryWriter.cpp40 … 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()
H A DXYZTrajectoryWriter.h46 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);
/dports/biology/protomol/protomol/applications/iSGProtomol-app/frontend/
H A DbuildISGTopology.cpp55 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()
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/dports/math/vtk8/VTK-8.2.0/Domains/Chemistry/
H A DvtkProteinRibbonFilter.cxx107 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
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/dports/math/vtk9/VTK-9.1.0/Domains/Chemistry/
H A DvtkProteinRibbonFilter.cxx108 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
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/dports/math/vtk6/VTK-6.2.0/Domains/Chemistry/
H A DvtkProteinRibbonFilter.cxx109 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
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/dports/science/cdk/cdk-cdk-2.3/misc/extra/src/main/java/org/openscience/cdk/validate/
H A DBasicValidator.java229 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()
/dports/science/gabedit/GabeditSrc251_300720/src/MolecularMechanics/
H A DMolecularMechanics.c723 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()
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H A DCreatePersonalMMFile.c199 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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