Home
last modified time | relevance | path

Searched refs:atomMap (Results 1 – 25 of 144) sorted by relevance

123456

/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ChemReactions/
H A DSanitizeRxn.cpp88 int atomMap; member
95 atomMap(0), in AtomInfo()
117 if (atomMap) { in bestGuessRLabel()
118 return atomMap; in bestGuessRLabel()
229 if (rat.atomMap == pat.atomMap) { in fixRGroups()
264 if (at.rlabel && !at.atomMap) { in fixAtomMaps()
285 if (!at.atomMap) { in fixAtomMaps()
321 int atomMap = 0; in fixHs() local
326 if (atomMap) { in fixHs()
336 int atomMap = 0; in fixHs() local
[all …]
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolAlign/
H A DtestMolAlign.cpp147 MatchVectType atomMap; in test2AtomMap() local
148 atomMap.push_back(std::pair<int, int>(18, 27)); in test2AtomMap()
149 atomMap.push_back(std::pair<int, int>(13, 23)); in test2AtomMap()
150 atomMap.push_back(std::pair<int, int>(21, 14)); in test2AtomMap()
151 atomMap.push_back(std::pair<int, int>(24, 7)); in test2AtomMap()
152 atomMap.push_back(std::pair<int, int>(9, 19)); in test2AtomMap()
153 atomMap.push_back(std::pair<int, int>(16, 30)); in test2AtomMap()
167 MatchVectType atomMap; in test3Weights() local
168 atomMap.push_back(std::pair<int, int>(18, 27)); in test3Weights()
171 atomMap.push_back(std::pair<int, int>(24, 7)); in test3Weights()
[all …]
H A DAlignMolecules.cpp24 const MatchVectType *atomMap, in getAlignmentTransform() argument
30 if (atomMap == nullptr) { in getAlignmentTransform()
49 for (mi = atomMap->begin(); mi != atomMap->end(); mi++) { in getAlignmentTransform()
61 const MatchVectType *atomMap, in alignMol() argument
66 atomMap, weights, reflect, maxIterations); in alignMol()
H A DAlignMolecules.h68 int prbCid = -1, int refCid = -1, const MatchVectType *atomMap = nullptr,
101 const MatchVectType *atomMap = nullptr,
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/cn3d/
H A Datom_set.hpp109 AtomMap atomMap; member in AtomSet
114 …bool HasTemp(void) const { return (atomMap.size()>0 && (*(atomMap.begin()->second.begin()))->HasTe… in HasTemp()
115 …bool HasOccup(void) const { return (atomMap.size()>0 && (*(atomMap.begin()->second.begin()))->HasO… in HasOccup()
116 …bool HasAlt(void) const { return (atomMap.size()>0 && (*(atomMap.begin()->second.begin()))->HasAlt… in HasAlt()
H A Datom_set.cpp188 if (atomMap.find(key) != atomMap.end()) { in BEGIN_SCOPE()
189 AtomAltList::const_iterator i_atom, e=atomMap[key].end(); in BEGIN_SCOPE()
190 for (i_atom=atomMap[key].begin(); i_atom!=e; ++i_atom) { in BEGIN_SCOPE()
195 atomMap[key].push_back(atom); in BEGIN_SCOPE()
255 AtomMap::const_iterator atomConfs = atomMap.find(MakeKey(ap)); in GetAtom()
256 if (atomConfs == atomMap.end()) { in GetAtom()
/dports/science/cdk/cdk-cdk-2.3/storage/inchi/src/main/java/org/openscience/cdk/inchi/
H A DInChIGenerator.java207 Map<IAtom, JniInchiAtom> atomMap = new HashMap<IAtom, JniInchiAtom>(); in generateInchiFromCDKAtomContainer() local
236 atomMap.put(atom, iatom); in generateInchiFromCDKAtomContainer()
275 JniInchiAtom at0 = (JniInchiAtom) atomMap.get(bond.getBegin()); in generateInchiFromCDKAtomContainer()
276 JniInchiAtom at1 = (JniInchiAtom) atomMap.get(bond.getEnd()); in generateInchiFromCDKAtomContainer()
343 JniInchiAtom at0 = (JniInchiAtom) atomMap.get(surroundingAtoms[0]); in generateInchiFromCDKAtomContainer()
344 JniInchiAtom at1 = (JniInchiAtom) atomMap.get(surroundingAtoms[1]); in generateInchiFromCDKAtomContainer()
345 JniInchiAtom at2 = (JniInchiAtom) atomMap.get(surroundingAtoms[2]); in generateInchiFromCDKAtomContainer()
346 JniInchiAtom at3 = (JniInchiAtom) atomMap.get(surroundingAtoms[3]); in generateInchiFromCDKAtomContainer()
377 at0 = (JniInchiAtom) atomMap.get(surroundingBonds[0].getEnd()); in generateInchiFromCDKAtomContainer()
381 at1 = (JniInchiAtom) atomMap.get(surroundingBonds[0].getEnd()); in generateInchiFromCDKAtomContainer()
[all …]
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Depictor/Wrap/
H A DtestDepictor.py275 atomMap = tuple(zip(refMatchVect, molMatchVect))
277 for refIdx, molIdx in atomMap:
295 … rdDepictor.GenerateDepictionMatching2DStructure(cycloheptylPyrazole, indazoleRef, atomMap=atomMap)
298 for refIdx, molIdx in atomMap:
301 msd /= len(atomMap)
311 atomMapOutOfRange = list(atomMap) + [(100, 100)]
319 cycloheptylPyrazole, indazoleRef, atomMap=atomMap, confId=1)
365 for refIdx, molIdx in atomMap:
368 msd /= len(atomMap)
397 for refIdx, molIdx in atomMap:
[all …]
H A DrdDepictor.cpp115 python::list atomMap; in GenerateDepictionMatching2DStructure() local
117 atomMap.append(python::make_tuple(pair.first, pair.second)); in GenerateDepictionMatching2DStructure()
119 return python::tuple(atomMap); in GenerateDepictionMatching2DStructure()
124 python::object atomMap, in GenerateDepictionMatching2DStructureAtomMap() argument
126 std::unique_ptr<RDKit::MatchVectType> matchVect(translateAtomMap(atomMap)); in GenerateDepictionMatching2DStructureAtomMap()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ShapeHelpers/
H A DtestShapeHelpers.cpp71 MatchVectType atomMap; in test2Compare() local
72 atomMap.push_back(std::pair<int, int>(18, 27)); in test2Compare()
73 atomMap.push_back(std::pair<int, int>(13, 23)); in test2Compare()
74 atomMap.push_back(std::pair<int, int>(21, 14)); in test2Compare()
75 atomMap.push_back(std::pair<int, int>(24, 7)); in test2Compare()
76 atomMap.push_back(std::pair<int, int>(9, 19)); in test2Compare()
77 atomMap.push_back(std::pair<int, int>(16, 30)); in test2Compare()
78 rmsd = MolAlign::alignMol(*m2, *m, 0, 0, &atomMap); in test2Compare()
/dports/science/cdk/cdk-cdk-2.3/base/data/src/main/java/org/openscience/cdk/
H A DPolymer.java173 … Map<IAtom, IAtom> atomMap = new HashMap<IAtom, IAtom>(atomCount >= 3 ? atomCount + atomCount / 3 in clone() local
183 atomMap.put(atom, cloned); in clone()
193 newAtoms[j] = atomMap.get(bond.getAtom(j)); in clone()
207 newLp.setAtom(atomMap.get(lp.getAtom())); in clone()
219 newSingleElectron.setAtom(atomMap.get(singleElectron.getAtom())); in clone()
226 clone.addStereoElement(element.map(atomMap, bondMap)); in clone()
233 replace.putAll(atomMap); in clone()
/dports/science/cdk/cdk-cdk-2.3/base/silent/src/main/java/org/openscience/cdk/silent/
H A DPolymer.java173 … Map<IAtom, IAtom> atomMap = new HashMap<IAtom, IAtom>(atomCount >= 3 ? atomCount + atomCount / 3 in clone() local
183 atomMap.put(atom, cloned); in clone()
193 newAtoms[j] = atomMap.get(bond.getAtom(j)); in clone()
207 newLp.setAtom(atomMap.get(lp.getAtom())); in clone()
219 newSingleElectron.setAtom(atomMap.get(singleElectron.getAtom())); in clone()
226 clone.addStereoElement(element.map(atomMap, bondMap)); in clone()
233 replace.putAll(atomMap); in clone()
/dports/science/rdkit/rdkit-Release_2021_03_5/rdkit/Chem/
H A DTemplateAlign.py86 atomMap = {}
90 atomMap[idx] = Geometry.Point2D(p.x, p.y)
91 molConfId = rdDepictor.Compute2DCoords(mol, clearConfs=clearConfs, coordMap=atomMap)
/dports/science/lammps/lammps-stable_29Sep2021/lib/atc/
H A DPerAtomQuantity-inl.h317 const INT_ARRAY & atomMap(atomMap_->quantity()); in set_lammps_to_quantity()
326 int idx = atomMap(i,0); in set_lammps_to_quantity()
336 int idx = atomMap(i,0); in set_lammps_to_quantity()
351 for (int i = 0; i < atomMap.nRows(); i++) { in set_lammps_to_quantity()
352 int idx = atomMap(i,0); in set_lammps_to_quantity()
362 int idx = atomMap(i,0); in set_lammps_to_quantity()
383 const INT_ARRAY & atomMap(atomMap_->quantity()); in set_quantity_to_lammps()
391 int idx = atomMap(i,0); in set_quantity_to_lammps()
400 int idx = atomMap(i,0); in set_quantity_to_lammps()
415 int idx = atomMap(i,0); in set_quantity_to_lammps()
[all …]
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/FMCS/
H A DRingMatchTableSet.h184 std::map<const Atom*, unsigned> atomMap; in makeRingGraph() local
193 ai = atomMap.find(atom1); in makeRingGraph()
194 if (atomMap.end() != ai) j1 = ai->second; in makeRingGraph()
195 ai = atomMap.find(atom2); in makeRingGraph()
196 if (atomMap.end() != ai) j2 = ai->second; in makeRingGraph()
199 atomMap[atom1] = j1; in makeRingGraph()
204 atomMap[atom2] = j2; in makeRingGraph()
/dports/science/liggghts/LIGGGHTS-PUBLIC-3.8.0-26-g6e873439/lib/atc/
H A DPerAtomQuantity-inl.h317 const INT_ARRAY & atomMap(atomMap_->quantity()); in set_lammps_to_quantity()
326 int idx = atomMap(i,0); in set_lammps_to_quantity()
336 int idx = atomMap(i,0); in set_lammps_to_quantity()
351 for (int i = 0; i < atomMap.nRows(); i++) { in set_lammps_to_quantity()
352 int idx = atomMap(i,0); in set_lammps_to_quantity()
362 int idx = atomMap(i,0); in set_lammps_to_quantity()
383 const INT_ARRAY & atomMap(atomMap_->quantity()); in set_quantity_to_lammps()
391 int idx = atomMap(i,0); in set_quantity_to_lammps()
400 int idx = atomMap(i,0); in set_quantity_to_lammps()
415 int idx = atomMap(i,0); in set_quantity_to_lammps()
[all …]
/dports/science/jmol/jmol-14.32.7/src/org/jmol/minimize/
H A DMMConstraint.java26 public void set(int steps, BS bsAtoms, int[] atomMap) { in set() argument
34 minList[j - 1] = atomMap[indexes[j]]; in set()
H A DMinimizer.java68 private int[] atomMap; field in Minimizer
192 atomMap = null; in clear()
278 constraints.get(i).set(steps, bsAtoms, atomMap); in minimize()
301 atomMap = new int[atoms.length]; in setupMinimization()
308 atomMap[i] = pt; in setupMinimization()
385 bondInfo.addLast(new MinBond(i, bondCount++, atomMap[i1], atomMap[i2], bondOrder, 0, null)); in getBonds()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/cif/
H A DMMCifValidationParser.java21 private Map<String, Integer> atomMap; field in MMCifValidationParser
55 (asResidues ? null : atomMap), modelMap); in finalizeValidations()
122 atomMap = new Hashtable<String, Integer>(); in mapAtomResIDs()
140 atomMap.put(atom, ia); in mapAtomResIDs()
H A DMMTFReader.java177 private Atom[] atomMap; // necessary because some atoms may be deleted. field in MMTFReader
229 atomMap = new Atom[fileAtomCount]; in getMMTFAtoms()
319 atomMap[iatom] = a; in getMMTFAtoms()
338 Atom a1 = atomMap[bi[pt++] + a0]; in addMMTFBonds()
339 Atom a2 = atomMap[bi[pt++] + a0]; in addMMTFBonds()
/dports/games/xblast/xblast-2.10.4/
H A Dlevel.c161 sec = DB_CreateSection (warnings, atomMap); in ParseLevel()
166 if (!ParseLevelMap (DB_GetSection (level, atomMap), sec)) { in ParseLevel()
200 ConfigLevelMap (DB_GetSection (level, atomMap)); in ConfigLevel()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/util/
H A DMolWriter.java60 int[] atomMap = new int[ms.ac]; in addMolFile() local
86 getAtomRecordMOL(iModel, ms, mol, atomMap[i] = ++n, ms.at[i], q, pTemp, in addMolFile()
96 getBondRecordMOL(mol, ++n, ms.bo[i], atomMap, asV3000, asJSON, in addMolFile()
296 private void getBondRecordMOL(SB mol, int n, Bond b, int[] atomMap, in getBondRecordMOL() argument
299 int a1 = atomMap[b.atom1.i]; in getBondRecordMOL()
300 int a2 = atomMap[b.atom2.i]; in getBondRecordMOL()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/smarter/
H A DXtalSymmetry.java749 int[] atomMap = (bondCount0 > asc.bondIndex0 && applySymmetryToBonds in applyAllSymmetry() local
854 int[] atomMap) throws Exception { in symmetryAddAtoms() argument
856 boolean addBonds = (atomMap != null); in symmetryAddAtoms()
1015 atomMap[atomSite] = special.index; in symmetryAddAtoms()
1020 atomMap[atomSite] = asc.ac; in symmetryAddAtoms()
1064 int ia1 = atomMap[atom1.atomSite]; in symmetryAddAtoms()
1065 int ia2 = atomMap[atom2.atomSite]; in symmetryAddAtoms()
1232 int[] atomMap = (addBonds ? new int[asc.ac] : null); in applySymmetryBio() local
1264 atomMap[atomSite] = asc.ac; in applySymmetryBio()
1281 int iAtom1 = atomMap[atoms[bond.atomIndex1].atomSite]; in applySymmetryBio()
[all …]
/dports/science/jdftx/jdftx-1.6.0/jdftx/electronic/
H A DSymmetries.cpp213 tempForces[atom] += (~sym[iRot].rot) * f[sp][atomMap[sp][atom][iRot]]; in symmetrize()
236 int nAtoms = atomMap[sp].size(); in symmetrizeSpherical()
249 { int atomOut = atomMap[sp][atom][iRot]; in symmetrizeSpherical()
321 { return atomMap; in getAtomMap()
621 atomMap.resize(iInfo.species.size()); in initAtomMaps()
626 atomMap[sp].resize(spInfo.atpos.size()); in initAtomMaps()
632 atomMap[sp][a1].resize(sym.size()); in initAtomMaps()
641 atomMap[sp][a1][iRot] = a2; in initAtomMaps()
646 if(shouldPrintMatrices) logPrintf(" %3u", atomMap[sp][a1][iRot]); in initAtomMaps()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/RDBoost/
H A DWrap.cpp80 const python::object &atomMap) { in translateAtomMap() argument
81 PySequenceHolder<python::object> pyAtomMap(atomMap); in translateAtomMap()

123456