/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ChemReactions/ |
H A D | SanitizeRxn.cpp | 88 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 D | testMolAlign.cpp | 147 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 D | AlignMolecules.cpp | 24 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 D | AlignMolecules.h | 68 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 D | atom_set.hpp | 109 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 D | atom_set.cpp | 188 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 D | InChIGenerator.java | 207 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 D | testDepictor.py | 275 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 D | rdDepictor.cpp | 115 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 D | testShapeHelpers.cpp | 71 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 D | Polymer.java | 173 … 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 D | Polymer.java | 173 … 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 D | TemplateAlign.py | 86 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 D | PerAtomQuantity-inl.h | 317 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 D | RingMatchTableSet.h | 184 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 D | PerAtomQuantity-inl.h | 317 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 D | MMConstraint.java | 26 public void set(int steps, BS bsAtoms, int[] atomMap) { in set() argument 34 minList[j - 1] = atomMap[indexes[j]]; in set()
|
H A D | Minimizer.java | 68 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 D | MMCifValidationParser.java | 21 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 D | MMTFReader.java | 177 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 D | level.c | 161 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 D | MolWriter.java | 60 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 D | XtalSymmetry.java | 749 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 D | Symmetries.cpp | 213 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 D | Wrap.cpp | 80 const python::object &atomMap) { in translateAtomMap() argument 81 PySequenceHolder<python::object> pyAtomMap(atomMap); in translateAtomMap()
|