void alignMolConformers(ROMol &mol, const std::vector<unsigned int> *atomIds,
const std::vector<unsigned int> *confIds,
const RDNumeric::DoubleVector *weights, bool reflect,
unsigned int maxIters, std::vector<double> *RMSlist) {
if (mol.getNumConformers() == 0) {
// nothing to be done ;
return;
}
RDGeom::Point3DConstPtrVect refPoints, prbPoints;
int cid = -1;
if ((confIds != 0) && (confIds->size() > 0)) {
cid = confIds->front();
}
const Conformer &refCnf = mol.getConformer(cid);
_fillAtomPositions(refPoints, refCnf, atomIds);
// now loop throught the remaininf conformations and transform them
RDGeom::Transform3D trans;
double ssd;
if (confIds == 0) {
unsigned int i = 0;
ROMol::ConformerIterator cnfi;
// Conformer *conf;
for (cnfi = mol.beginConformers(); cnfi != mol.endConformers(); cnfi++) {
// conf = (*cnfi);
i += 1;
if (i == 1) {
continue;
}
_fillAtomPositions(prbPoints, *(*cnfi), atomIds);
ssd = RDNumeric::Alignments::AlignPoints(refPoints, prbPoints, trans,
weights, reflect, maxIters);
if (RMSlist) {
ssd /= (prbPoints.size());
RMSlist->push_back(sqrt(ssd));
}
MolTransforms::transformConformer(*(*cnfi), trans);
}
} else {
std::vector<unsigned int>::const_iterator cai;
unsigned int i = 0;
for (cai = confIds->begin(); cai != confIds->end(); cai++) {
i += 1;
if (i == 1) {
continue;
}
Conformer &conf = mol.getConformer(*cai);
_fillAtomPositions(prbPoints, conf, atomIds);
ssd = RDNumeric::Alignments::AlignPoints(refPoints, prbPoints, trans,
weights, reflect, maxIters);
if (RMSlist) {
ssd /= (prbPoints.size());
RMSlist->push_back(sqrt(ssd));
}
MolTransforms::transformConformer(conf, trans);
}
}
}
std::string MolToTPLText(const ROMol &mol,std::string partialChargeProp,bool writeFirstConfTwice){
if(!mol.getNumConformers()){
BOOST_LOG(rdErrorLog)<<"Cannot write molecules with no conformers to TPL files\n";
return "";
}
std::ostringstream res;
std::string tempStr;
res << "BioCAD format, all rights reserved"<<std::endl;
res << "Output from RDKit"<<std::endl;
if(!mol.hasProp("_Name")){
BOOST_LOG(rdWarningLog)<<"Molecule has no name; arbitrary name assigned.\n";
tempStr = "Unnamed molecule";
} else {
mol.getProp("_Name",tempStr);
}
res << "NAME "<<tempStr<<std::endl;
res << "PROP 7 1"<<std::endl;
res << mol.getNumAtoms() << " " << mol.getNumBonds() << std::endl;
ROMol::ConstConformerIterator confIt=mol.beginConformers();
// write the atoms:
for(unsigned int i=0;i<mol.getNumAtoms();++i){
TPLWriter::writeAtom(mol,i,confIt,res,partialChargeProp);
}
// write the bonds:
for(unsigned int i=0;i<mol.getNumBonds();++i){
TPLWriter::writeBond(mol,i,confIt,res);
}
// write the additional conformations:
res << "CONFS "<< mol.getNumConformers()-1<<std::endl;
if(!writeFirstConfTwice) ++confIt;
while(confIt!=mol.endConformers()){
std::stringstream tmpStrm;
std::string confName;
tmpStrm<<"conformer_"<<(*confIt)->getId();
confName = tmpStrm.str();
res << "NAME " << confName << std::endl;
for(unsigned int i=0;i<mol.getNumAtoms();++i){
const RDGeom::Point3D &pos=(*confIt)->getAtomPos(i);
res << " " << 100.*pos.x << " " << 100.*pos.y << " " << 100.*pos.z << std::endl;
}
++confIt;
if(confIt!=mol.endConformers()){
res << std::endl;
}
}
return res.str();
}
bool getMolAtomPoints(const ROMol &mol,
std::vector<RDGeom::Point3D> &atomPoint,
bool twod) {
bool non_zero_z = false;
atomPoint.resize(mol.getNumAtoms());
// take X,Y,Z coordinates of each atom
if (0 != mol.getNumConformers())
for (RDKit::ROMol::ConstConformerIterator cnfi = mol.beginConformers();
cnfi != mol.endConformers(); cnfi++) {
const Conformer &conf = **cnfi; // mol.getConformer(confId);
if (twod || conf.is3D()) {
for (unsigned i = 0; i < mol.getNumAtoms(); i++) {
atomPoint[i] = conf.getAtomPos(i);
if (fabs(atomPoint[i].z) >= 1.e-7) non_zero_z = true;
}
break;
}
}
if (atomPoint.empty()) { // compute XYZ
// TODO:
// ???? ..........
}
return non_zero_z;
}
