void setReactantAtomPropertiesToProduct(
Atom *productAtom, const Atom& reactantAtom,
bool setImplicitProperties)
{
// which properties need to be set from the reactant?
if(productAtom->getAtomicNum()<=0) {
productAtom->setAtomicNum(reactantAtom.getAtomicNum());
productAtom->setIsAromatic(reactantAtom.getIsAromatic());
// don't copy isotope information over from dummy atoms
productAtom->setIsotope(reactantAtom.getIsotope());
// remove dummy labels (if present)
if(productAtom->hasProp(common_properties::dummyLabel)) productAtom->clearProp(common_properties::dummyLabel);
if(productAtom->hasProp(common_properties::_MolFileRLabel)) productAtom->clearProp(common_properties::_MolFileRLabel);
}
if(setImplicitProperties) {
updateImplicitAtomProperties(productAtom,&reactantAtom);
}
// One might be tempted to copy over the reactant atom's chirality into the
// product atom if chirality is not specified on the product. This would be a
// very bad idea because the order of bonds will almost certainly change on the
// atom and the chirality is referenced to bond order.
// --------- --------- --------- --------- --------- ---------
// While we're here, set the stereochemistry
// FIX: this should be free-standing, not in this function.
if(reactantAtom.getChiralTag()!=Atom::CHI_UNSPECIFIED &&
reactantAtom.getChiralTag()!=Atom::CHI_OTHER &&
productAtom->hasProp(common_properties::molInversionFlag)) {
checkProductChirality(reactantAtom.getChiralTag(), productAtom);
}
}
void setReactantAtomPropertiesToProduct(Atom *productAtom,
const Atom &reactantAtom,
bool setImplicitProperties) {
// which properties need to be set from the reactant?
if (productAtom->getAtomicNum() <= 0 ||
productAtom->hasProp(common_properties::_MolFileAtomQuery)) {
productAtom->setAtomicNum(reactantAtom.getAtomicNum());
productAtom->setIsAromatic(reactantAtom.getIsAromatic());
// don't copy isotope information over from dummy atoms
// (part of github #243) unless we're setting implicit properties,
// in which case we do need to copy them in (github #1269)
if (!setImplicitProperties) {
productAtom->setIsotope(reactantAtom.getIsotope());
}
// remove dummy labels (if present)
if (productAtom->hasProp(common_properties::dummyLabel)) {
productAtom->clearProp(common_properties::dummyLabel);
}
if (productAtom->hasProp(common_properties::_MolFileRLabel)) {
productAtom->clearProp(common_properties::_MolFileRLabel);
}
productAtom->setProp<unsigned int>(common_properties::reactantAtomIdx,
reactantAtom.getIdx());
productAtom->setProp(WAS_DUMMY, true);
} else {
// remove bookkeeping labels (if present)
if (productAtom->hasProp(WAS_DUMMY)) productAtom->clearProp(WAS_DUMMY);
}
productAtom->setProp<unsigned int>(common_properties::reactantAtomIdx,
reactantAtom.getIdx());
if (setImplicitProperties) {
updateImplicitAtomProperties(productAtom, &reactantAtom);
}
// One might be tempted to copy over the reactant atom's chirality into the
// product atom if chirality is not specified on the product. This would be a
// very bad idea because the order of bonds will almost certainly change on
// the atom and the chirality is referenced to bond order.
// --------- --------- --------- --------- --------- ---------
// While we're here, set the stereochemistry
// FIX: this should be free-standing, not in this function.
if (reactantAtom.getChiralTag() != Atom::CHI_UNSPECIFIED &&
reactantAtom.getChiralTag() != Atom::CHI_OTHER &&
productAtom->hasProp(common_properties::molInversionFlag)) {
checkProductChirality(reactantAtom.getChiralTag(), productAtom);
}
// copy over residue information if it's there. This was github #1632
if (reactantAtom.getMonomerInfo()) {
productAtom->setMonomerInfo(reactantAtom.getMonomerInfo()->copy());
}
}
