Searched refs:bondA (Results 1 – 5 of 5) sorted by relevance
72 bondA = int(bonds[i])74 atomA = ligresidue.getAtom(atommap[bondA])78 atomB.bonds.append(atommap[bondA])
504 OBBond *bondA = &*bitA; in ReadMolecule() local505 if (!bondA->IsAromatic()) continue; in ReadMolecule()507 OBAtom *carbon = bondA->GetNbrAtom(oxygenOrSulfur); in ReadMolecule()513 if (&*bitB == bondA || !bitB->IsAromatic()) continue; in ReadMolecule()524 bondA->SetAromatic(false); in ReadMolecule()
908 private static boolean hasCommonAtom(IBond bondA, IBond bondB) { in hasCommonAtom() argument909 return bondA.contains(bondB.getBegin()) || bondA.contains(bondB.getEnd()); in hasCommonAtom()920 private static String getCommonSymbol(IBond bondA, IBond bondB) { in getCommonSymbol() argument923 if (bondA.contains(bondB.getBegin())) { in getCommonSymbol()925 } else if (bondA.contains(bondB.getEnd())) { in getCommonSymbol()
308 IBond bondA = newBondList.get(i); in getContainers() local310 IAtom atomA1 = bondA.getAtom(ato); in getContainers()
731 const real bondA = iparams[type].constr.dA; in bshakef() local733 dvdl += shaked->scaled_lagrange_multiplier[ll] * dt_2 * (bondB - bondA); in bshakef()