struct reaccs_molecule_t *molToReaccs(const ROMol &mol) {
std::string molB = MolToMolBlock(mol, true);
Utils::LocaleSwitcher ls;
struct reaccs_molecule_t *res = MolStr2Mol((char *)molB.c_str());
POSTCONDITION(res, "could not build a molecule");
return res;
}
//! returns an RXN block for a reaction
std::string ChemicalReactionToRxnBlock(const ChemicalReaction &rxn, bool separateAgents){
std::ostringstream res;
res<<"$RXN\n\n RDKit\n\n";
if(separateAgents){
res<<std::setw(3)<<rxn.getNumReactantTemplates()
<<std::setw(3)<<rxn.getNumProductTemplates()
<<std::setw(3)<<rxn.getNumAgentTemplates()<<"\n";
}
else{
res<<std::setw(3)<<(rxn.getNumReactantTemplates()+rxn.getNumAgentTemplates())
<<std::setw(3)<<rxn.getNumProductTemplates()<<"\n";
}
for(MOL_SPTR_VECT::const_iterator iter=rxn.beginReactantTemplates();
iter != rxn.endReactantTemplates();++iter){
// to write the mol block, we need ring information:
MolOps::findSSSR(**iter);
res<<"$MOL\n";
res << MolToMolBlock(**iter,true,-1,false);
}
if(!separateAgents){
for(MOL_SPTR_VECT::const_iterator iter=rxn.beginAgentTemplates();
iter != rxn.endAgentTemplates();++iter){
// to write the mol block, we need ring information:
MolOps::findSSSR(**iter);
res<<"$MOL\n";
res << MolToMolBlock(**iter,true,-1,false);
}
}
for(MOL_SPTR_VECT::const_iterator iter=rxn.beginProductTemplates();
iter != rxn.endProductTemplates();++iter){
// to write the mol block, we need ring information:
MolOps::findSSSR(**iter);
res<<"$MOL\n";
res << MolToMolBlock(**iter,true,-1,false);
}
if(separateAgents){
for(MOL_SPTR_VECT::const_iterator iter=rxn.beginAgentTemplates();
iter != rxn.endAgentTemplates();++iter){
// to write the mol block, we need ring information:
MolOps::findSSSR(**iter);
res<<"$MOL\n";
res << MolToMolBlock(**iter,true,-1,false);
}
}
return res.str();
};
void SDWriter::write(const ROMol &mol, int confId) {
PRECONDITION(dp_ostream,"no output stream");
// write the molecule
(*dp_ostream) << MolToMolBlock(mol, true, confId, df_kekulize, df_forceV3000);
// now write the properties
STR_VECT_CI pi;
if (d_props.size() > 0) {
// check if we have any properties the user specified to write out
// in which loop over them and write them out
for (pi = d_props.begin(); pi != d_props.end(); pi++) {
if (mol.hasProp(*pi)) {
writeProperty(mol, (*pi));
}
}
}
else {
// if use did not specify any properties, write all non computed properties
// out to the file
STR_VECT properties = mol.getPropList();
STR_VECT compLst;
if (mol.hasProp(detail::computedPropName)) {
mol.getProp(detail::computedPropName, compLst);
}
STR_VECT_CI pi;
for (pi = properties.begin(); pi != properties.end(); pi++) {
// ignore any of the following properties
if ( ((*pi) == detail::computedPropName) ||
((*pi) == "_Name") ||
((*pi) == "_MolFileInfo") ||
((*pi) == "_MolFileComments") ||
((*pi) == "_MolFileChiralFlag")) {
continue;
}
// check if this property is not computed
if (std::find(compLst.begin(), compLst.end(), (*pi)) == compLst.end()) {
writeProperty(mol, (*pi));
}
}
}
// add the $$$$ that marks the end of a molecule
(*dp_ostream) << "$$$$\n";
++d_molid;
}
