ROMol *TDTMolSupplier::parseMol(std::string inLine){
PRECONDITION(dp_inStream,"no stream");
Utils::LocaleSwitcher ls;
std::size_t startP=inLine.find("<");
std::size_t endP=inLine.find_last_of(">");
std::string smiles = inLine.substr(startP+1,endP-startP-1);
ROMol *res = SmilesToMol(smiles,0,df_sanitize);
if(res && res->getNumAtoms()>0){
// -----------
// Process the properties:
d_line++;
std::getline(*dp_inStream,inLine);
while(!dp_inStream->eof() && inLine.find("|")!=0){
endP=inLine.find("<");
std::string propName = inLine.substr(0,endP);
boost::trim_if(propName,boost::is_any_of(" \t"));
startP = endP+1;
if(propName=="2D" && d_confId2D>=0){
std::string rest=inLine.substr(startP,inLine.size()-startP);
std::vector<double> coords;
TDTParseUtils::ParseNumberList(rest,coords,dp_inStream);
Conformer *conf=new Conformer(res->getNumAtoms());
conf->setId(d_confId2D);
conf->set3D(false);
for(unsigned int atIdx=0;atIdx<res->getNumAtoms();atIdx++){
if(2*atIdx+1 < coords.size()){
conf->setAtomPos(atIdx,RDGeom::Point3D(coords[2*atIdx],coords[2*atIdx+1],0.0));
} else {
// we're going to let this slide... but maybe we should do something else?
}
}
res->addConformer(conf,false);
} else if(propName=="3D" && d_confId3D>=0){
std::string rest=inLine.substr(startP,inLine.size()-startP);
std::vector<double> coords;
TDTParseUtils::ParseNumberList(rest,coords,dp_inStream);
Conformer *conf=new Conformer(res->getNumAtoms());
conf->setId(d_confId3D);
conf->set3D(true);
for(unsigned int atIdx=0;atIdx<res->getNumAtoms();atIdx++){
if(3*atIdx+2 < coords.size()){
conf->setAtomPos(atIdx,RDGeom::Point3D(coords[3*atIdx],
coords[3*atIdx+1],
coords[3*atIdx+2]));
} else {
// we're going to let this slide... but maybe we should do something else?
}
}
res->addConformer(conf,false);
} else {
endP=inLine.find_last_of(">");
if(endP==std::string::npos){
std::ostringstream errout;
errout << "no end tag found for property" << propName;
throw FileParseException(errout.str());
} else {
std::string propVal = inLine.substr(startP,endP-startP);
res->setProp(propName,propVal);
if(propName==d_nameProp) res->setProp("_Name",propVal);
}
}
std::getline(*dp_inStream,inLine);
}
}
return res;
}
ROMol *SmilesMolSupplier::processLine(std::string inLine) {
ROMol *res = NULL;
try {
// -----------
// tokenize the input line:
// -----------
boost::char_separator<char> sep(d_delim.c_str(), "",
boost::keep_empty_tokens);
tokenizer tokens(inLine, sep);
STR_VECT recs;
for (tokenizer::iterator tokIter = tokens.begin(); tokIter != tokens.end();
++tokIter) {
std::string rec = strip(*tokIter);
recs.push_back(rec);
}
if (recs.size() <= static_cast<unsigned int>(d_smi)) {
std::ostringstream errout;
errout << "ERROR: line #" << d_line << "does not contain enough tokens\n";
throw FileParseException(errout.str());
}
// -----------
// get the smiles and create a molecule
// -----------
res = SmilesToMol(recs[d_smi], 0, df_sanitize);
if (!res) {
std::stringstream errout;
errout << "Cannot create molecule from : '" << recs[d_smi] << "'";
throw SmilesParseException(errout.str());
}
// -----------
// get the name (if there's a name column)
// -----------
if (d_name == -1) {
// if no name defaults it to the line number we read it from string
std::ostringstream tstr;
tstr << d_line;
std::string mname = tstr.str();
res->setProp(common_properties::_Name, mname);
} else {
if (d_name >= static_cast<int>(recs.size())) {
BOOST_LOG(rdWarningLog) << "WARNING: no name column found on line "
<< d_line << std::endl;
} else {
res->setProp(common_properties::_Name, recs[d_name]);
}
}
// -----------
// read in the properties
// -----------
unsigned int iprop = 0;
for (unsigned int col = 0; col < recs.size(); col++) {
if (static_cast<int>(col) == d_smi || static_cast<int>(col) == d_name)
continue;
std::string pname, pval;
if (d_props.size() > col) {
pname = d_props[col];
} else {
pname = "Column_";
std::stringstream ss;
ss << col;
pname += ss.str();
}
pval = recs[col];
res->setProp(pname, pval);
iprop++;
}
} catch (const SmilesParseException &pe) {
// Couldn't parse the passed in smiles
// Simply print out a message
BOOST_LOG(rdErrorLog) << "ERROR: Smiles parse error on line " << d_line
<< "\n";
BOOST_LOG(rdErrorLog) << "ERROR: " << pe.message() << "\n";
res = NULL;
} catch (const MolSanitizeException &se) {
// We couldn't sanitize the molecule
// write out an error message
BOOST_LOG(rdErrorLog) << "ERROR: Could not sanitize molecule on line "
<< d_line << std::endl;
BOOST_LOG(rdErrorLog) << "ERROR: " << se.message() << "\n";
res = NULL;
} catch (...) {
// write out an error message
BOOST_LOG(rdErrorLog) << "ERROR: Could not process molecule on line "
<< d_line << std::endl;
res = NULL;
}
return res;
}
