C++ MatchVectType::push_back方法代码示例

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 test2AtomMap() {
  std::string rdbase = getenv("RDBASE");
  std::string fname1 = rdbase + "/Code/GraphMol/MolAlign/test_data/1oir.mol";
  ROMol *m1 = MolFileToMol(fname1);
  std::string fname2 = rdbase + "/Code/GraphMol/MolAlign/test_data/1oir_conf.mol";
  ROMol *m2 = MolFileToMol(fname2);
  MatchVectType atomMap;
  atomMap.push_back(std::pair<int, int>(18, 27));
  atomMap.push_back(std::pair<int, int>(13, 23));
  atomMap.push_back(std::pair<int, int>(21, 14));
  atomMap.push_back(std::pair<int, int>(24, 7));
  atomMap.push_back(std::pair<int, int>(9, 19));
  atomMap.push_back(std::pair<int, int>(16, 30));
  double rmsd = MolAlign::alignMol(*m2, *m1, 0, 0, &atomMap);
  TEST_ASSERT(RDKit::feq(rmsd, 0.8525));
  delete m1;
  delete m2;
  
}

void test3Weights() {
  std::string rdbase = getenv("RDBASE");
  std::string fname1 = rdbase + "/Code/GraphMol/MolAlign/test_data/1oir.mol";
  ROMol *m1 = MolFileToMol(fname1);
  std::string fname2 = rdbase + "/Code/GraphMol/MolAlign/test_data/1oir_conf.mol";
  ROMol *m2 = MolFileToMol(fname2);
  MatchVectType atomMap;
  atomMap.push_back(std::pair<int, int>(18, 27));
  atomMap.push_back(std::pair<int, int>(13, 23));
  atomMap.push_back(std::pair<int, int>(21, 14));
  atomMap.push_back(std::pair<int, int>(24, 7));
  atomMap.push_back(std::pair<int, int>(9, 19));
  atomMap.push_back(std::pair<int, int>(16, 30));
  
  RDNumeric::DoubleVector wts(6);
  wts.setVal(0, 1.0); wts.setVal(1, 1.0);
  wts.setVal(2, 1.0); wts.setVal(3, 1.0);
  wts.setVal(4, 1.0); wts.setVal(5, 2.0);
  double rmsd = MolAlign::alignMol(*m2, *m1, 0, 0, &atomMap, &wts);
  TEST_ASSERT(RDKit::feq(rmsd, 0.9513));
  delete m1;
  delete m2;
}

void testCrippenO3AConstraints() {
  ROMol *m = SmilesToMol("n1ccc(cc1)-c1ccccc1");
  TEST_ASSERT(m);
  ROMol *m1 = MolOps::addHs(*m);
  delete m;
  TEST_ASSERT(m1);
  DGeomHelpers::EmbedMolecule(*m1);
  MMFF::sanitizeMMFFMol((RWMol &)(*m1));
  MMFF::MMFFMolProperties mp(*m1);
  TEST_ASSERT(mp.isValid());
  ForceFields::ForceField *field = MMFF::constructForceField(*m1, &mp);
  field->initialize();
  field->minimize();
  RWMol *patt = SmartsToMol("nccc-cccc");
  MatchVectType matchVect;
  TEST_ASSERT(SubstructMatch(*m1, (ROMol &)*patt, matchVect));
  unsigned int nIdx = matchVect[0].second;
  unsigned int cIdx = matchVect[matchVect.size() - 1].second;
  MolTransforms::setDihedralDeg(m1->getConformer(), matchVect[2].second,
    matchVect[3].second, matchVect[4].second, matchVect[5].second, 0.0);
  ROMol m2(*m1);
  MolAlign::randomTransform(m2);
  ROMol m3(m2);
  unsigned int prbNAtoms = m2.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(m2, prbLogpContribs,
    prbMRContribs, true, &prbAtomTypes, &prbAtomTypeLabels);
  MolAlign::O3A *o3a = new MolAlign::O3A(m2, *m1,
    &prbLogpContribs, &prbLogpContribs, MolAlign::O3A::CRIPPEN);
  TEST_ASSERT(o3a);
  o3a->align();
  delete o3a;
  double d = (m2.getConformer().getAtomPos(cIdx)
    - m1->getConformer().getAtomPos(cIdx)).length();
  TEST_ASSERT(feq(d, 0.0, 1));
  MatchVectType constraintMap;
  constraintMap.push_back(std::make_pair(cIdx, nIdx));
  o3a = new MolAlign::O3A(m3, *m1, &prbLogpContribs, &prbLogpContribs,
    MolAlign::O3A::CRIPPEN, -1, -1, false, 50, 0, &constraintMap);
  TEST_ASSERT(o3a);
  o3a->align();
  delete o3a;
  d = (m3.getConformer().getAtomPos(cIdx)
    - m1->getConformer().getAtomPos(cIdx)).length();
  TEST_ASSERT(feq(d, 7.0, 1.0));
  delete m1;
}

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 *_translateAtomMap(python::object atomMap) {
    PySequenceHolder<python::object> aMapSeq(atomMap);
    MatchVectType *aMap;
    aMap = 0;
    unsigned int i, nAtms = aMapSeq.size();
    if (nAtms > 0) {
        aMap = new MatchVectType;
        for (i = 0; i < nAtms; ++i) {
            PySequenceHolder<int> item(aMapSeq[i]);
            if (item.size() != 2) {
                delete aMap;
                aMap = 0;
                throw_value_error("Incorrect format for atomMap");
            }
            aMap->push_back(std::pair<int, int>(item[0], item[1]));
        }
    }
    return aMap;
}

  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;
  }