| /dports/science/openbabel/openbabel-3.1.1/src/depict/ |
| H A D | depict.cpp | 698 vector3 begin = beginAtom->GetVector(); in DrawWobblyBond()
702 if (HasLabel(beginAtom)) in DrawWobblyBond()
736 vector3 begin = beginAtom->GetVector(); in DrawWedge()
740 if (HasLabel(beginAtom)) in DrawWedge()
760 vector3 begin = beginAtom->GetVector(); in DrawHash()
764 if (HasLabel(beginAtom)) in DrawHash()
796 if (HasLabel(beginAtom)) in DrawSimpleBond()
843 if (HasLabel(beginAtom)) in DrawSimpleBond()
883 if (HasLabel(beginAtom)) in DrawRingBond()
889 if (HasLabel(beginAtom)) in DrawRingBond()
[all …]
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| /dports/science/molsketch/Molsketch-0.7.2/libmolsketch/actions/ |
| H A D | ringaction.cpp | 96 Q_CHECK_PTR(bond->beginAtom()); in alignRingWithBond()
103 QPointF bondNormal = normalized(bond->endAtom()->pos() - bond->beginAtom()->pos()); in alignRingWithBond()
112 … double triSign = triangleSign(bond->beginAtom()->scenePos(), bond->endAtom()->scenePos(), pos); in alignRingWithBond()
114 …qreal bondLengthScale = QLineF(bond->beginAtom()->pos(), bond->endAtom()->pos()).length()/40.; // … in alignRingWithBond()
128 hintMoleculeItems.setPos(bond->beginAtom()->scenePos()); in alignRingWithBond()
224 …newMolecule->addBond(atomMapping[bond->beginAtom()], atomMapping[bond->endAtom()], bond->bondType(… in getRingAtoms()
262 foreach(Bond* otherBond, bond->beginAtom()->bonds() + bond->endAtom()->bonds()) in addAromaticity()
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| /dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ |
| H A D | FindStereo.cpp | 34 const auto beginAtom = bond->getBeginAtom(); in getStereoInfo() local
37 if (beginAtom->getDegree() < 2 || endAtom->getDegree() < 2 || in getStereoInfo()
38 beginAtom->getDegree() > 3 || endAtom->getDegree() > 3) { in getStereoInfo()
49 boost::make_iterator_range(mol.getAtomBonds(beginAtom))) { in getStereoInfo()
56 nbr->getOtherAtomIdx(beginAtom->getIdx())); in getStereoInfo()
59 if (beginAtom->getDegree() == 2) { in getStereoInfo()
195 const auto beginAtom = bond->getBeginAtom(); in isBondPotentialStereoBond() local
197 beginAtom->getTotalDegree() - beginAtom->getTotalNumHs(true); in isBondPotentialStereoBond()
201 if (begHeavyDegree > 1 && beginAtom->getDegree() < 4 && endHeavyDegree > 1 && in isBondPotentialStereoBond()
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| H A D | RWMol.h | 127 unsigned int addBond(Atom *beginAtom, Atom *endAtom,
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| /dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/FMCS/ |
| H A D | Graph.h | 35 void addBond(unsigned bond, unsigned beginAtom, unsigned endAtom) { in addBond() argument
38 boost::tie(which, res) = boost::add_edge(beginAtom, endAtom, *this); in addBond()
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| /dports/science/molsketch/Molsketch-0.7.2/libmolsketch/ |
| H A D | bond.cpp | 133 auto beginExtent = getExtentForStereoBond(beginAtom(), outerLines, false), in drawHashBond()
181 auto beginExtent = getExtentForStereoBond(beginAtom(), outerLines, false), in drawWedgeBond()
252 if (b->beginAtom() != a) in effectiveBondLine()
321 qreal beginAngle = findIdealAngle(beginAtom(), this, false), in bondPath()
347 qreal beginAngle = findIdealAngle(beginAtom(), this, false), in bondPath()
354 beginAngle = findIdealAngle(beginAtom(), this, true); in bondPath()
568 Atom* Bond::beginAtom() const in beginAtom() function in Molsketch::Bond
604 return qMakePair(beginAtom(), endAtom()); in atoms()
762 qreal beginAngle = findIdealAngle(beginAtom(), this, false), in outline()
799 qreal beginAngle = findIdealAngle(beginAtom(), this, false), in outline()
[all …]
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| H A D | molecule.cpp | 120 Atom *begin = bond->beginAtom(), *end = bond->endAtom();
161 if (atoms.contains(bond->beginAtom()) in clone()
168 addBond(new Bond(*bond, oldToNewAtoms[bond->beginAtom()], in clone()
188 Bond* newBond = new Bond(*bond, atomMap[bond->beginAtom()], atomMap[bond->endAtom()]); in combineMolecules()
232 Bond* bondX = bondBetween(bond->beginAtom(), bond->endAtom()); in addBond()
241 bond->setAtoms(bond->beginAtom(), bond->endAtom()); // updates pos and atom shapes in addBond()
433 …if (((bond->beginAtom() == atomA) || (bond->beginAtom() == atomB )) && ((bond->endAtom() == atomA)… in bondBetween()
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| H A D | bond.h | 99 Atom* beginAtom() const;
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| H A D | commands.h | 214 … : setItemPropertiesCommand(bond, qMakePair(bond->endAtom(), bond->beginAtom()), text, parent ) {}
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| H A D | molscene.cpp | 259 (partiallySelectedMolecules[bond->molecule()] += bond->beginAtom()) += bond->endAtom(); in copy()
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| /dports/science/openbabel/openbabel-3.1.1/src/formats/json/ |
| H A D | pubchemjsonformat.cpp | 308 OBAtom *beginAtom = pmol->GetAtomById(oAid1s[i].GetUint()); in ReadMolecule() local
310 if (beginAtom && endAtom) { in ReadMolecule()
312 pbond->SetBegin(beginAtom); in ReadMolecule()
335 beginAtom->AddBond(pbond); in ReadMolecule()
353 OBAtom *beginAtom = pmol->GetAtomById(oAid1s[i].GetUint()); in ReadMolecule() local
355 if (beginAtom && endAtom) { in ReadMolecule()
357 pbond->SetBegin(beginAtom); in ReadMolecule()
360 beginAtom->AddBond(pbond); in ReadMolecule()
426 if (beginAtom && endAtom) { in ReadMolecule()
427 OBBond *pbond = pmol->GetBond(beginAtom, endAtom); in ReadMolecule()
[all …]
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| /dports/science/rdkit/rdkit-Release_2021_03_5/Code/JavaWrappers/ |
| H A D | RWMol_doc.i | 123 %javamethodmodifiers RDKit::RWMol::addBond ( Atom * beginAtom, Atom * endAtom, Bond::Bond…
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| /dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ChemTransforms/ |
| H A D | ChemTransforms.cpp | 489 auto beginAtom = newBond->getBeginAtom(); in replaceCore() local
494 beginAtom->getIdx()); in replaceCore()
496 MolOps::setTerminalAtomCoords(*newMol, beginAtom->getIdx(), in replaceCore()
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| /dports/science/rdkit/rdkit-Release_2021_03_5/rdkit/Chem/Draw/ |
| H A D | __init__.py | 760 beginAtom = amap[mol.GetBondWithIdx(b).GetBeginAtomIdx()]
762 envSubmol.append(submol.GetBondBetweenAtoms(beginAtom, endAtom).GetIdx())
909 beginAtom = amap[mol.GetBondWithIdx(b).GetBeginAtomIdx()]
911 envSubmol.append(submol.GetBondBetweenAtoms(beginAtom, endAtom).GetIdx())
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| /dports/science/gromacs/gromacs-2021.4/src/gromacs/mdrun/ |
| H A D | tpi.cpp | 140 const int beginAtom) in reactionFieldExclusionCorrection() argument
144 for (int i = beginAtom; i < mdatoms.homenr; i++) in reactionFieldExclusionCorrection()
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| /dports/science/molsketch/Molsketch-0.7.2/obabeliface/ |
| H A D | obabeliface.cpp | 104 Atom* a1 = bond->beginAtom(); in toOBMolecule()
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| /dports/science/openbabel/openbabel-3.1.1/src/ |
| H A D | canon.cpp | 1709 OBAtom *beginAtom = mol->GetAtomById(config.begin); in CanonicalLabels() local
1711 if (!beginAtom || !endAtom) in CanonicalLabels()
1714 OBBond *bond = mol->GetBond(beginAtom, endAtom); in CanonicalLabels()
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