clone.addStereoElement(element.map(atomMap, bondMap));
clone.addStereoElement(element.map(atomMap, bondMap));
if (se instanceof TetrahedralChirality && !((TetrahedralChirality) se).getChiralAtom().getFlag(CDKConstants.VISITED)) { this.addStereoElement(se); } else if (se instanceof DoubleBondStereochemistry && !((DoubleBondStereochemistry) se).getStereoBond().getFlag(CDKConstants.VISITED)) { this.addStereoElement(se); } else if (se instanceof ExtendedTetrahedral && !((ExtendedTetrahedral) se).focus().getFlag(CDKConstants.VISITED)) { this.addStereoElement(se);
/** * Constructs a shallow copy of the provided IAtomContainer with the same * atoms, bonds, electron containers and stereochemistry of another * AtomContainer. Removing atoms/bonds in this copy will not affect * the original, however changing the properties will. * * @param src the source atom container */ AtomContainer2(IAtomContainer src) { this(src.getAtomCount(), src.getBondCount(), src.getLonePairCount(), src.getSingleElectronCount()); for (IAtom atom : src.atoms()) addAtom(atom); for (IBond bond : src.bonds()) addBond(bond); for (ISingleElectron se : src.singleElectrons()) addSingleElectron(se); for (ILonePair lp : src.lonePairs()) addLonePair(lp); for (IStereoElement se : src.stereoElements()) addStereoElement(se); }
/** * Constructs a shallow copy of the provided IAtomContainer with the same * atoms, bonds, electron containers and stereochemistry of another * AtomContainer. Removing atoms/bonds in this copy will not affect * the original, however changing the properties will. * * @param src the source atom container */ AtomContainer2(IAtomContainer src) { this(src.getAtomCount(), src.getBondCount(), src.getLonePairCount(), src.getSingleElectronCount()); for (IAtom atom : src.atoms()) addAtom(atom); for (IBond bond : src.bonds()) addBond(bond); for (ISingleElectron se : src.singleElectrons()) addSingleElectron(se); for (ILonePair lp : src.lonePairs()) addLonePair(lp); for (IStereoElement se : src.stereoElements()) addStereoElement(se); }
if (se instanceof TetrahedralChirality && !((TetrahedralChirality) se).getChiralAtom().getFlag(CDKConstants.VISITED)) { this.addStereoElement(se); } else if (se instanceof DoubleBondStereochemistry && !((DoubleBondStereochemistry) se).getStereoBond().getFlag(CDKConstants.VISITED)) { this.addStereoElement(se); } else if (se instanceof ExtendedTetrahedral && !((ExtendedTetrahedral) se).focus().getFlag(CDKConstants.VISITED)) { this.addStereoElement(se);