double getAlignmentTransform(const ROMol &prbMol, const ROMol &refMol,
RDGeom::Transform3D &trans,
int prbCid, int refCid,
const MatchVectType *atomMap,
const RDNumeric::DoubleVector *weights, bool reflect,
unsigned int maxIterations) {
RDGeom::Point3DConstPtrVect refPoints, prbPoints;
const Conformer &prbCnf = prbMol.getConformer(prbCid);
const Conformer &refCnf = refMol.getConformer(refCid);
if (atomMap == 0) {
// we have to figure out the mapping between the two molecule
MatchVectType match;
if (SubstructMatch(refMol, prbMol, match)) {
MatchVectType::const_iterator mi;
for (mi = match.begin(); mi != match.end(); mi++) {
prbPoints.push_back(&prbCnf.getAtomPos(mi->first));
refPoints.push_back(&refCnf.getAtomPos(mi->second));
}
} else {
throw MolAlignException("No sub-structure match found between the probe and query mol");
}
} else {
MatchVectType::const_iterator mi;
for (mi = atomMap->begin(); mi != atomMap->end(); mi++) {
prbPoints.push_back(&prbCnf.getAtomPos(mi->first));
refPoints.push_back(&refCnf.getAtomPos(mi->second));
}
}
double ssr = RDNumeric::Alignments::AlignPoints(refPoints, prbPoints,
trans, weights, reflect, maxIterations);
ssr /= (prbPoints.size());
return sqrt(ssr);
}
ROMol *prepareMol(const ROMol &mol, const FragCatParams *fparams,
MatchVectType &aToFmap) {
PRECONDITION(fparams,"");
// get a mapping of the functional groups onto the molecule
INT_VECT fgBonds;
MatchVectType aidToFid = findFuncGroupsOnMol(mol, fparams, fgBonds);
// get the core piece of molecule (i.e. the part of the molecule
// without the functional groups). This basically the part of the molecule
// that does not contain the function group bonds given by "fgBonds"
INT_VECT cBonds;
int bid, nbds = mol.getNumBonds();
for (bid = 0; bid < nbds; bid++) {
if (std::find(fgBonds.begin(), fgBonds.end(), bid) == fgBonds.end()) {
cBonds.push_back(bid);
}
}
INT_MAP_INT aIdxMap; // a map from atom id in mol to the new atoms id in coreMol
ROMol *coreMol = Subgraphs::pathToSubmol(mol, cBonds, false, aIdxMap);
// now map the functional groups on mol to coreMol using aIdxMap
MatchVectType::iterator mati;
int newID;
for (mati = aidToFid.begin(); mati != aidToFid.end(); mati++) {
newID = aIdxMap[mati->first];
aToFmap.push_back(std::pair<int, int>(newID, mati->second));
}
return coreMol;
}
//*************************************************************************************
//
// Adds 2D coordinates to a molecule using the Depict.dll
//
// ARGUMENTS:
// mol: the molecule to be altered
// tempFilename: (OPTIONAL) the name of the temporary file
//
// RETURNS:
// 1 on success, 0 otherwise
//
// Here's the process by which this works (it's kind of contorted):
// 1) convert the mol to SMILES
// 2) use the DLL to convert the SMILES to a mol file (on disk)
// 3) parse the mol file into a temporary molecule
// 4) do a substructure match from the old molecule to the
// temp one (which may have a different atom numbering or additional
// atoms added).
// 5) Update the positions of the atoms on the old molecule.
// 6) Free the temp molecule.
//
// NOTES:
// - *FIX:* at the moment we're not doing anything to clear up the
// temp file created in this process. It'll always have the same
// name unless the user explicitly asks that we do something different.
// - To use the DLL, it's essential that the COMBICHEM_ROOT and COMBICHEM_RELEASE
// environment variables be set. If this isn't done, this whole process
// will fail.
// - See the notes above about failures when opening the DLL.
//
//*************************************************************************************
int Add2DCoordsToMolDLL(ROMol &mol,std::string tempFilename){
std::string smi=MolToSmiles(mol,true);
int tmp = SmilesToMolFileDLL(smi,tempFilename);
int res = -1;
if(tmp){
// build another mol from that mol file:
RWMol *tmpMol = MolFileToMol(tempFilename,false);
// match it up with the starting mol:
// (We need to do this because the depict.dll conversion
// to a mol file may have added Hs)
MatchVectType matchVect;
bool hasMatch=SubstructMatch(tmpMol,&mol,matchVect);
if(hasMatch){
const Conformer &conf = tmpMol->getCoformer(0);
Coformer *nconf = new Coformer(mol.getNumAtoms());
for(MatchVectType::const_iterator mvi=matchVect.begin();
mvi!=matchVect.end();mvi++){
nconf->setAtomPos(conf.getAtomPos(mvi->first));
}
confId = (int)mol.addConformer(nconf, true);
}
delete tmpMol;
}
return res;
}
bool StructCheckTautomer::applyTautomer(unsigned it) {
if (Options.FromTautomer.size() <= it || Options.ToTautomer.size() <= it) {
if (Options.Verbose)
BOOST_LOG(rdInfoLog) << "ERROR: incorrect Tautomer index it=" << it
<< "\n";
return false;
}
const ROMol &fromTautomer = *Options.FromTautomer[it];
const ROMol &toTautomer = *Options.ToTautomer[it];
if (toTautomer.getNumAtoms() != fromTautomer.getNumAtoms()) {
if (Options.Verbose)
BOOST_LOG(rdInfoLog) << "ERROR: incorrect data toTautomer.getNumAtoms() "
"!= fromTautomer.getNumAtoms()\n";
// incorrect data
// throw(.....);
return false;
}
const unsigned nta = toTautomer.getNumAtoms();
const unsigned ntb = toTautomer.getNumBonds();
MatchVectType match; // The format is (queryAtomIdx, molAtomIdx)
std::vector<unsigned> atomIdxMap(
Mol.getNumAtoms()); // matched tau atom indeces
if (!SubstructMatch(Mol, *Options.FromTautomer[it],
match)) // SSMatch(mp, from_tautomer, SINGLE_MATCH);
return false;
if (Options.Verbose)
BOOST_LOG(rdInfoLog) << "found match for from_tautomer with " << nta
<< " atoms\n";
// init
for (unsigned i = 0; i < Mol.getNumAtoms(); i++) atomIdxMap[i] = -1;
for (MatchVectType::const_iterator mit = match.begin(); mit != match.end();
mit++) {
unsigned tai = mit->first; // From and To Tautomer Atom index
unsigned mai = mit->second; // Mol Atom index
atomIdxMap[mai] = tai;
}
// scan for completely mapped bonds and replace bond order with mapped bond
// from to_tautomer
for (RDKit::BondIterator_ bond = Mol.beginBonds(); bond != Mol.endBonds();
bond++) {
unsigned ti = atomIdxMap[(*bond)->getBeginAtomIdx()];
unsigned tj = atomIdxMap[(*bond)->getEndAtomIdx()];
if (-1 == ti || -1 == tj) continue;
const Bond *tb = toTautomer.getBondBetweenAtoms(ti, tj);
if (tb && (*bond)->getBondType() != tb->getBondType()) {
(*bond)->setBondType(tb->getBondType());
}
}
// apply charge/radical fixes if any
for (unsigned i = 0; i < match.size(); i++) {
Atom &atom = *Mol.getAtomWithIdx(match[i].second);
const Atom &ta = *toTautomer.getAtomWithIdx(match[i].first);
atom.setFormalCharge(ta.getFormalCharge());
atom.setNumRadicalElectrons(ta.getNumRadicalElectrons());
}
return true;
}