void testMMFFO3AConstraintsAndLocalOnly() {
std::string rdbase = getenv("RDBASE");
std::string sdf = rdbase + "/Code/GraphMol/MolAlign/test_data/ref_e2.sdf";
SDMolSupplier supplier(sdf, true, false);
const int refNum = 23;
const int prbNum = 32;
ROMol *refMol = supplier[refNum];
ROMol *prbMol = supplier[prbNum];
unsigned int refNAtoms = refMol->getNumAtoms();
std::vector<double> refLogpContribs(refNAtoms);
std::vector<double> refMRContribs(refNAtoms);
std::vector<unsigned int> refAtomTypes(refNAtoms);
std::vector<std::string> refAtomTypeLabels(refNAtoms);
Descriptors::getCrippenAtomContribs(*refMol, refLogpContribs,
refMRContribs, true, &refAtomTypes, &refAtomTypeLabels);
unsigned int prbNAtoms = prbMol->getNumAtoms();
std::vector<double> prbLogpContribs(prbNAtoms);
std::vector<double> prbMRContribs(prbNAtoms);
std::vector<unsigned int> prbAtomTypes(prbNAtoms);
std::vector<std::string> prbAtomTypeLabels(prbNAtoms);
Descriptors::getCrippenAtomContribs(*prbMol, prbLogpContribs,
prbMRContribs, true, &prbAtomTypes, &prbAtomTypeLabels);
RWMol *patt = SmartsToMol("S");
MatchVectType matchVect;
TEST_ASSERT(SubstructMatch(*refMol, (ROMol &)*patt, matchVect));
delete patt;
unsigned int refSIdx = matchVect[0].second;
matchVect.clear();
patt = SmartsToMol("O");
TEST_ASSERT(SubstructMatch(*prbMol, (ROMol &)*patt, matchVect));
delete patt;
unsigned int prbOIdx = matchVect[0].second;
std::vector<double> distOS(2);
distOS[0] = 2.7;
distOS[1] = 0.4;
std::vector<double> weights(2);
weights[0] = 0.1;
weights[1] = 100.0;
for (unsigned int i = 0; i < 2; ++i) {
MatchVectType constraintMap;
constraintMap.push_back(std::make_pair(prbOIdx, refSIdx));
RDNumeric::DoubleVector constraintWeights(1);
constraintWeights[0] = weights[i];
MolAlign::O3A *o3a = new MolAlign::O3A(*prbMol, *refMol,
&prbLogpContribs, &refLogpContribs, MolAlign::O3A::CRIPPEN,
-1, -1, false, 50, 0, &constraintMap, &constraintWeights);
TEST_ASSERT(o3a);
o3a->align();
delete o3a;
o3a = new MolAlign::O3A(*prbMol, *refMol, &prbLogpContribs,
&refLogpContribs, MolAlign::O3A::CRIPPEN, -1, -1,
false, 50, MolAlign::O3_LOCAL_ONLY);
TEST_ASSERT(o3a);
o3a->align();
delete o3a;
double d = (prbMol->getConformer().getAtomPos(prbOIdx)
- refMol->getConformer().getAtomPos(refSIdx)).length();
TEST_ASSERT(feq(d, distOS[i], 0.1));
}
}
void testCrippenO3AConstraintsAndLocalOnly() {
std::string rdbase = getenv("RDBASE");
std::string sdf = rdbase + "/Code/GraphMol/MolAlign/test_data/ref_e2.sdf";
SDMolSupplier supplier(sdf, true, false);
const int refNum = 23;
const int prbNum = 32;
ROMol *refMol = supplier[refNum];
ROMol *prbMol = supplier[prbNum];
MMFF::MMFFMolProperties refMP(*refMol);
TEST_ASSERT(refMP.isValid());
MMFF::MMFFMolProperties prbMP(*prbMol);
TEST_ASSERT(prbMP.isValid());
RWMol *patt = SmartsToMol("S");
MatchVectType matchVect;
TEST_ASSERT(SubstructMatch(*refMol, (ROMol &)*patt, matchVect));
delete patt;
unsigned int refSIdx = matchVect[0].second;
matchVect.clear();
patt = SmartsToMol("O");
TEST_ASSERT(SubstructMatch(*prbMol, (ROMol &)*patt, matchVect));
delete patt;
unsigned int prbOIdx = matchVect[0].second;
std::vector<double> distOS(2);
distOS[0] = 3.2;
distOS[1] = 0.3;
std::vector<double> weights(2);
weights[0] = 10.0;
weights[1] = 100.0;
for (unsigned int i = 0; i < 2; ++i) {
MatchVectType constraintMap;
constraintMap.push_back(std::make_pair(prbOIdx, refSIdx));
RDNumeric::DoubleVector constraintWeights(1);
constraintWeights[0] = weights[i];
MolAlign::O3A *o3a = new MolAlign::O3A(*prbMol, *refMol, &prbMP, &refMP,
MolAlign::O3A::MMFF94, -1, -1, false, 50, 0, &constraintMap, &constraintWeights);
TEST_ASSERT(o3a);
o3a->align();
delete o3a;
o3a = new MolAlign::O3A(*prbMol, *refMol, &prbMP, &refMP,
MolAlign::O3A::MMFF94, -1, -1, false, 50, MolAlign::O3_LOCAL_ONLY);
TEST_ASSERT(o3a);
o3a->align();
delete o3a;
double d = (prbMol->getConformer().getAtomPos(prbOIdx)
- refMol->getConformer().getAtomPos(refSIdx)).length();
TEST_ASSERT(feq(d, distOS[i], 0.1));
}
}
MatchVectType findFuncGroupsOnMol(const ROMol &mol,
const FragCatParams *params,
INT_VECT &fgBonds) {
PRECONDITION(params,"bad params");
fgBonds.clear();
std::pair<int, int> amat;
MatchVectType aidFgrps;
std::vector<MatchVectType> fgpMatches;
std::vector<MatchVectType>::const_iterator mati;
MatchVectType::const_iterator mi;
int aid;
//const ROMol *fgrp;
INT_VECT_CI bi;
aidFgrps.clear();
int fid = 0;
const MOL_SPTR_VECT &fgrps = params->getFuncGroups();
MOL_SPTR_VECT::const_iterator fgci;
for (fgci = fgrps.begin(); fgci != fgrps.end(); fgci++) {
const ROMol *fgrp = fgci->get();
std::string fname;
(*fgci)->getProp(common_properties::_Name, fname);
//std::cout << "Groups number: " << fname << "\n";
//(*fgci)->debugMol(std::cout);
//mol->debugMol(std::cout);
// match this functional group onto the molecule
SubstructMatch(mol, *fgrp, fgpMatches);
// loop over all the matches we get for this fgroup
for (mati = fgpMatches.begin(); mati != fgpMatches.end(); mati++) {
//FIX: we will assume that the first atom in fgrp is always the connection
// atom
amat = mati->front();
aid = amat.second; //FIX: is this correct - the second entry in the pair is the atom ID from mol
// grab the list of atom Ids from mol that match the functional group
INT_VECT bondIds, maids;
for (mi = mati->begin(); mi != mati->end(); mi++) {
maids.push_back(mi->second);
}
// create a list of bond IDs from these atom ID
// these are the bond in mol that are part of portion that matches the
// functional group
bondIds = Subgraphs::bondListFromAtomList(mol, maids);
// now check if all these bonds have been covered as part of larger
// functional group that was dealt with earlier
// FIX: obviously we assume here that the function groups in params
// come in decreasing order of size.
bool allDone = true;
for (bi = bondIds.begin(); bi != bondIds.end(); bi++) {
if (std::find(fgBonds.begin(), fgBonds.end(), (*bi)) == fgBonds.end()) {
allDone = false;
fgBonds.push_back(*bi);
}
}
if (!allDone) {
// this functional group mapping onto mol is not part of a larger func
// group mapping so record it
aidFgrps.push_back(std::pair<int, int>(aid, fid));
}
}
fid++;
}
return aidFgrps;
}