void runSDFile(std::string fileName,int checkEvery=10){
SDMolSupplier suppl(fileName,false);
RWMol *mol;
mol = (RWMol *)suppl.next();
while(mol){
std::string name;
mol->getProp("_Name",name);
std::cerr << "Mol: " << name << std::endl;
try{
MolOps::sanitizeMol(*mol);
} catch (...) {
std::cerr << " sanitization failed" << std::endl;
delete mol;
mol = 0;
}
if(mol){
ROMol *mol2=MolOps::addHs(*mol,false,true);
delete mol;
runMol(mol2,checkEvery,false);
delete mol2;
}
mol = (RWMol *)suppl.next();
}
}
int main(int argc, char *argv[]) {
RDLog::InitLogs();
std::string fname;
if (argc > 1) {
fname = argv[1];
} else {
BOOST_LOG(rdErrorLog) << "Pass in the list of smiles\n";
}
std::ifstream inStream(fname.c_str());
const int MAX_LINE_LEN = 256;
char inLine[MAX_LINE_LEN];
std::string tmpstr;
std::string smi;
inStream.getline(inLine, MAX_LINE_LEN, '\n');
tmpstr = inLine;
// MolOps molop;
while (tmpstr.size() > 0) {
getSmiles(tmpstr, smi);
RWMol *m = SmilesToMol(smi, 0, 0);
try {
// testKekule(*m);
MolOps::sanitizeMol(*m);
int nar;
m->getProp(common_properties::numArom, nar);
BOOST_LOG(rdInfoLog) << nar << "\n";
// MolOps::setHybridization(*m);
delete m;
} catch (MolSanitizeException) {
BOOST_LOG(rdErrorLog) << smi << "\n";
delete m;
}
inStream.getline(inLine, MAX_LINE_LEN, '\n');
tmpstr = inLine;
}
return 1;
}
// ------------------------------------------------------------------
//
// Enumerates the library around a template and returns the result.
//
//
// ------------------------------------------------------------------
RWMOL_SPTR_VECT enumerateLibrary(RWMol *templateMol,
VECT_RWMOL_SPTR_VECT &sidechains,
bool orientSidechains){
PRECONDITION(templateMol,"bad molecule");
RWMOL_SPTR_VECT res,tmp;
res.push_back(RWMOL_SPTR(new RWMol(*templateMol)));
// if there's no attachment point on the molecule or no
// sidechains, return now:
if(!templateMol->hasProp(common_properties::maxAttachIdx) || sidechains.size()==0 )
return res;
int maxIdx;
templateMol->getProp(common_properties::maxAttachIdx,maxIdx);
tmp.clear();
// loop over the sidechains and attach them
for(unsigned int i=0;i<sidechains.size();i++){
int tgtMark=CONNECT_BOOKMARK_START+i;
// here's another boundary condition
if(tgtMark>maxIdx) break;
/// loop over all atoms with the appropriate mark
// This means that if a mol has two attachment points with the
// same name (e.g. two Xa's) they'll always have the same
// sidechain attached to them. This is a feature.
RWMOL_SPTR_VECT::iterator sidechainIt;
for(sidechainIt=sidechains[i].begin();
sidechainIt!=sidechains[i].end();
sidechainIt++){
// we've got our sidechain, find the atom it attaches from
if( (*sidechainIt)->hasAtomBookmark(CONNECT_BOOKMARK_START) ){
//
// NOTE: If there's more than one marked atom in the sidechain,
/// we'll only use the first for the moment.
//
int sidechainAtomIdx = (*sidechainIt)->getAtomWithBookmark(CONNECT_BOOKMARK_START)->getIdx();
// now add the sidechain to each molecule
RWMOL_SPTR_VECT::iterator templMolIt;
// loop over all the mols we've generated to this point
for(templMolIt=res.begin();templMolIt!=res.end();templMolIt++){
RWMol *templ = new RWMol(**templMolIt);
std::string name,tmpStr;
if(templ->hasProp(common_properties::_Name)){
templ->getProp(common_properties::_Name,tmpStr);
name = name + " " + tmpStr;
}
while(templ->hasAtomBookmark(tgtMark)){
// this is the atom we'll be replacing in the template
Atom *at = templ->getAtomWithBookmark(tgtMark);
// copy and transform the sidechain:
RWMol *sidechain;
if(orientSidechains){
sidechain = new RWMol(*(sidechainIt->get()));
orientSidechain(templ,sidechain,
at->getIdx(),sidechainAtomIdx);
} else {
sidechain = sidechainIt->get();
}
// FIX: need to use the actual bond order here:
molAddSidechain(templ,sidechain,
at->getIdx(),sidechainAtomIdx,
Bond::SINGLE);
if(sidechain->hasProp(common_properties::_Name)){
sidechain->getProp(common_properties::_Name,tmpStr);
name = name + " " + tmpStr;
}
templ->clearAtomBookmark(tgtMark,at);
if(orientSidechains){
delete sidechain;
}
}
//std::cout << templ << "> " << MolToSmiles(*templ) << std::endl;
if(name != "") templ->setProp(common_properties::_Name,name);
tmp.push_back(RWMOL_SPTR(templ));
}
}
}
//
// if we just made any molecules, free up the memory used by the
// existing result set and move the molecules we just generated
// over
if(tmp.size()){
#if 0
RWMOL_SPTR_VECT::iterator tmpMolIt;
for(tmpMolIt=res.begin();tmpMolIt!=res.end();tmpMolIt++){
delete *tmpMolIt;
}
#endif
res = tmp;
tmp.clear();
}
}
return res;
}
