Exemplo n.º 1
0
std::vector<double> MolData3Ddescriptors::GetRelativeRcov(const RDKit::ROMol& mol){
  int numAtoms= mol.getNumAtoms();
  double* rcov=data3D.getRCOV();

  std::vector<double> wroc(numAtoms, 0.0);
  for( int i=0; i<numAtoms; ++i){

    wroc[i]=rcov[mol.getAtomWithIdx(i)->getAtomicNum()-1]/rcov[5];
  }
  return wroc;
}
Exemplo n.º 2
0
std::vector<double> MolData3Ddescriptors::GetRelativeENeg(const RDKit::ROMol& mol){
   int numAtoms= mol.getNumAtoms();
   double* relativeNeg=data3D.getNEG();

  std::vector<double> neg(numAtoms, 0.0);
  for( int i=0; i<numAtoms; ++i){

    neg[i]=relativeNeg[mol.getAtomWithIdx(i)->getAtomicNum()-1];
  }
  return neg;
}
Exemplo n.º 3
0
std::vector<double> MolData3Ddescriptors::GetRelativeMW(const RDKit::ROMol& mol){
  double* relativeMw=data3D.getMW();
  int numAtoms= mol.getNumAtoms();

  std::vector<double> pol(numAtoms, 0.0);
  for( int i=0; i<numAtoms; ++i){

    pol[i]=relativeMw[mol.getAtomWithIdx(i)->getAtomicNum()-1];
  }
  return pol;
}
Exemplo n.º 4
0
std::vector<double> MolData3Ddescriptors::GetRelativeIonPol(const RDKit::ROMol& mol){
   int numAtoms= mol.getNumAtoms();
	double* absionpol=data3D.getIonPOL();

  std::vector<double> ionpols(numAtoms, 0.0);
  for( int i=0; i<numAtoms; ++i){

    ionpols[i]=absionpol[mol.getAtomWithIdx(i)->getAtomicNum()-1];
  }
  return ionpols;
}
Exemplo n.º 5
0
std::vector<double> MolData3Ddescriptors::GetRelativeVdW(const RDKit::ROMol& mol){
   int numAtoms= mol.getNumAtoms();
   double* relativeVdW=data3D.getVDW();

  std::vector<double> vdw(numAtoms, 0.0);
  for( int i=0; i<numAtoms; ++i){

    vdw[i]=relativeVdW[mol.getAtomWithIdx(i)->getAtomicNum()-1];

  }
  return vdw;
}
Exemplo n.º 6
0
double calcSASA(const RDKit::ROMol &mol, const std::vector<double> &radii,
                int confIdx, const RDKit::QueryAtom *query,
                const SASAOpts &opts) {
  double result = internalCalcSASA(mol, radii, confIdx, opts);
  if (query) {
    result = 0.0f;
    for (ROMol::ConstQueryAtomIterator at = mol.beginQueryAtoms(query);
         at != mol.endQueryAtoms(); ++at) {
      const Atom *atom = *at;
      result += atom->getProp<double>("SASA");
    }
  }
  return result;
}
Exemplo n.º 7
0
unsigned int Compute2DCoords(RDKit::ROMol &mol, bool canonOrient,
                             bool clearConfs, python::dict &coordMap,
                             unsigned int nFlipsPerSample = 3,
                             unsigned int nSamples = 100, int sampleSeed = 100,
                             bool permuteDeg4Nodes = false,
                             double bondLength = -1.0) {
  RDGeom::INT_POINT2D_MAP cMap;
  cMap.clear();
  python::list ks = coordMap.keys();
  for (unsigned int i = 0;
       i < python::extract<unsigned int>(ks.attr("__len__")()); i++) {
    unsigned int id = python::extract<unsigned int>(ks[i]);
    if (id >= mol.getNumAtoms()) {
      throw_value_error("atom index out of range");
    }
    cMap[id] = python::extract<RDGeom::Point2D>(coordMap[id]);
  }
  double oBondLen = RDDepict::BOND_LEN;
  if (bondLength > 0) {
    RDDepict::BOND_LEN = bondLength;
  }
  unsigned int res;
  res = RDDepict::compute2DCoords(mol, &cMap, canonOrient, clearConfs,
                                  nFlipsPerSample, nSamples, sampleSeed,
                                  permuteDeg4Nodes);
  if (bondLength > 0) {
    RDDepict::BOND_LEN = oBondLen;
  }
  return res;
}
Exemplo n.º 8
0
// adaptation from EState.py 
// we need the Is value only there
std::vector<double> MolData3Ddescriptors::GetEState(const  RDKit::ROMol &mol){
  int numAtoms = mol.getNumAtoms();
 
  std::vector<double> Is =GetIState(mol);

  double tmp,p;
  double *dist =  RDKit::MolOps::getDistanceMat(mol,false,false);
  double accum[numAtoms];

    for (int i=0;i<numAtoms;i++) {
    accum[i]=0.0;
  }

  for (int i=0;i<numAtoms;i++) {
    for (int j=i+1;j<numAtoms;j++) {
       p = dist[i * numAtoms + j]+1;
       if (p < 1e6) {
        tmp = (Is[i] - Is[j]) / (p * p);
        accum[i] += tmp;
        accum[j] -= tmp;
      }
    }
  }

 for (int i=0;i<numAtoms;i++) {
    Is[i]+=accum[i];
 }

 return Is;
}
Exemplo n.º 9
0
std::string MolpherMol::MolpherMolImpl::asMolBlock(bool include_locks) const {
    RDKit::ROMol* temp = asRDMol(include_locks);
	std::ostringstream os;
	os << RDKit::MolToMolBlock(*temp) << std::endl;
    if (include_locks) {
		RDKit::STR_VECT prop_names = temp->getPropList();
		for (MolpherAtom::LockingMask lock : MolpherAtom::atom_locks) {
			std::string lock_prop_name("MOLPHER_" + MolpherAtom::lockToString(lock));
			if (std::find(prop_names.begin(), prop_names.end(), lock_prop_name) != prop_names.end()) {
				os << ">  <" << lock_prop_name << ">" << std::endl;
				os << temp->getProp<std::string>(lock_prop_name) << std::endl;
				os << std::endl;
			}
		}
		os << "$$$$" << std::endl;
    }
    delete temp;
    return os.str();
}
Exemplo n.º 10
0
std::vector<double> MolData3Ddescriptors::GetIState(const  RDKit::ROMol &mol){
  int numAtoms = mol.getNumAtoms();
  std::vector<double> Is;

  for (int i = 0; i < numAtoms; ++i) {
    const RDKit::Atom * atom= mol.getAtomWithIdx(i);
    int atNum=atom->getAtomicNum();
    int degree = atom->getDegree();
    if (degree>0 and atNum>1) {
      int h = atom->getTotalNumHs();
      int Zv = RDKit::PeriodicTable::getTable()->getNouterElecs(atNum);
      double dv =(double) Zv-h;
      dv = dv / (double) (atNum-Zv-1);
      int N =  GetPrincipalQuantumNumber(atNum);
      Is.push_back(round(1000*(4.0/(N*N)*dv+1.0)/degree)/1000);  // WHIM-P5.pdf paper 1997  => +7 & NoHydrogens is used!
    }
    else Is.push_back(0);
 }

 return Is;
}
Exemplo n.º 11
0
void testautocorrelation() {
  std::cout << "=>start test rdf\n";

  std::string pathName = getenv("RDBASE");
  std::string sdfName =
      pathName + "/Code/GraphMol/Descriptors/test_data/chlorobenzene.sdf";

  RDKit::SDMolSupplier reader(sdfName, true, false);
 
  int nDone = 0;
  while (!reader.atEnd()) {
    ++nDone;

    RDKit::ROMol *m = reader.next();
    TEST_ASSERT(m);
    std::string nm;
    m->getProp("_Name",nm);


    std::vector<double> dwhim;
//for (int i=1;i<11;i++) {
 // std::cout << "i:" << 0.005*i << "\n";
    dwhim = RDKit::Descriptors::AUTOCORR3D(*m, -1);


    for (int j=0;j<80;j++) {
      std::cout << dwhim[j] << ",";
     }
    std::cout << "\n";

//}

       
    std::cout << "=>read molecule: " << nDone  << std::endl;

    delete m;
  }

  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}
Exemplo n.º 12
0
// modification of previous code to follow documentation from Padel code
std::vector<double> MolData3Ddescriptors::GetEState2(const  RDKit::ROMol &mol){

  int numAtoms = mol.getNumAtoms();
 
  std::vector<double> Si =GetIState(mol);


// in WHIM definition it's write:
  double tmp,p,d;
  double *dist =  RDKit::MolOps::getDistanceMat(mol,false,false);
  double accum[numAtoms];

  for (int i=0;i<numAtoms;i++) {
    accum[i]=0.0;
  }


  for (int i=0;i<numAtoms;i++) {
    for (int j=i+1;j<numAtoms;j++) {
       d = dist[i * numAtoms + j];
       p = dist[i * numAtoms + j]+1;
       if (d == 1) {
        tmp = (Si[i] - Si[j]) / (p * p);
        accum[i] += tmp;
        accum[j] -= tmp;
      }
    }
  }

// add the Accum to the Si
// WHIM Si values
// electrotopological indices are scaled thus: Si'=Si + 7 => Si' > 0
// In this case, only the nonhydrogen atoms are considered,
// and the atomic electrotopological charge of each atom depends on its atom neighbor.
// So we should not use all the terms in the sum but only Adj matrix cases!

// Correct the Si adding the rescaling parameter for WHIM only
 for (int i=0;i<numAtoms;i++) {
    Si[i]+=accum[i]+7.0;
 }



 return Si;
}
Exemplo n.º 13
0
unsigned int Compute2DCoordsMimicDistmat(
    RDKit::ROMol &mol, python::object distMat, bool canonOrient,
    bool clearConfs, double weightDistMat, unsigned int nFlipsPerSample,
    unsigned int nSamples, int sampleSeed, bool permuteDeg4Nodes,
    double bondLength = -1.0) {
  PyObject *distMatPtr = distMat.ptr();
  if (!PyArray_Check(distMatPtr)) {
    throw_value_error("Argument isn't an array");
  }

  PyArrayObject *dmatrix = reinterpret_cast<PyArrayObject *>(distMatPtr);
  unsigned int nitems = PyArray_DIM(dmatrix, 0);
  unsigned int na = mol.getNumAtoms();

  if (nitems != na * (na - 1) / 2) {
    throw_value_error(
        "The array size does not match the number of atoms in the molecule");
  }
  double *inData = reinterpret_cast<double *>(PyArray_DATA(dmatrix));
  double *cData = new double[nitems];

  memcpy(static_cast<void *>(cData), static_cast<const void *>(inData),
         nitems * sizeof(double));

  DOUBLE_SMART_PTR dmat(cData);
  double oBondLen = RDDepict::BOND_LEN;
  if (bondLength > 0) {
    RDDepict::BOND_LEN = bondLength;
  }
  unsigned int res;
  res = RDDepict::compute2DCoordsMimicDistMat(
      mol, &dmat, canonOrient, clearConfs, weightDistMat, nFlipsPerSample,
      nSamples, sampleSeed, permuteDeg4Nodes);
  if (bondLength > 0) {
    RDDepict::BOND_LEN = oBondLen;
  }
  return res;
}
Exemplo n.º 14
0
std::vector<double> MolData3Ddescriptors::GetCharges(const RDKit::ROMol &mol) {
  std::vector<double> charges(mol.getNumAtoms(), 0);
  // use 12 iterations... can be more
  RDKit::computeGasteigerCharges(mol, charges, 12, true);
  return charges;
}
Exemplo n.º 15
0
void getExperimentalTorsions(const RDKit::ROMol &mol, CrystalFFDetails &details,
                             bool useExpTorsions, bool useBasicKnowledge,
                             unsigned int version, bool verbose) {
  unsigned int nb = mol.getNumBonds();
  unsigned int na = mol.getNumAtoms();
  if (!na) {
    throw ValueErrorException("molecule has no atoms");
  }

  // check that vectors are empty
  details.expTorsionAtoms.clear();
  details.expTorsionAngles.clear();
  details.improperAtoms.clear();

  unsigned int aid1, aid2, aid3, aid4;
  unsigned int bid2;

  boost::dynamic_bitset<> doneBonds(nb);

  if (useExpTorsions) {
    // we set the torsion angles with experimental data
    const ExpTorsionAngleCollection *params =
        ExpTorsionAngleCollection::getParams(version);

    // loop over patterns
    for (const auto &param : *params) {
      std::vector<MatchVectType> matches;
      SubstructMatch(mol, *(param.dp_pattern.get()), matches, false, true);

      // loop over matches
      for (std::vector<MatchVectType>::const_iterator matchIt = matches.begin();
           matchIt != matches.end(); ++matchIt) {
        // get bond indices
        aid1 = (*matchIt)[param.idx[0]].second;
        aid2 = (*matchIt)[param.idx[1]].second;
        aid3 = (*matchIt)[param.idx[2]].second;
        aid4 = (*matchIt)[param.idx[3]].second;
        // FIX: check if bond is NULL
        bid2 = mol.getBondBetweenAtoms(aid2, aid3)->getIdx();
        if (!doneBonds[bid2]) {
          doneBonds[bid2] = 1;
          std::vector<int> atoms(4);
          atoms[0] = aid1;
          atoms[1] = aid2;
          atoms[2] = aid3;
          atoms[3] = aid4;
          details.expTorsionAtoms.push_back(atoms);
          details.expTorsionAngles.push_back(
              std::make_pair(param.signs, param.V));
          if (verbose) {
            std::cout << param.smarts << ": " << aid1 << " " << aid2 << " "
                      << aid3 << " " << aid4 << ", (";
            for (unsigned int i = 0; i < param.V.size() - 1; ++i) {
              std::cout << param.V[i] << ", ";
            }
            std::cout << param.V[param.V.size() - 1] << ") " << std::endl;
          }
        }  // if not donePaths
      }    // end loop over matches

    }  // end loop over patterns
  }

  // apply basic knowledge such as flat aromatic rings, other sp2-centers,
  // straight triple bonds, etc.
  if (useBasicKnowledge) {
    boost::dynamic_bitset<> doneAtoms(na);
    ROMol::ADJ_ITER nbrIdx;
    ROMol::ADJ_ITER endNbrs;

    // inversion terms (improper torsions / out-of-plane bends / inversion)
    // loop over atoms
    for (aid2 = 0; aid2 < na; ++aid2) {
      if (!(doneAtoms[aid2])) {
        std::vector<int> atoms(4, -1);
        atoms[1] = aid2;
        const Atom *atom2 = mol.getAtomWithIdx(atoms[1]);
        int at2AtomicNum = atom2->getAtomicNum();

        // if atom is a N,O or C and SP2-hybridized
        if (((at2AtomicNum == 6) || (at2AtomicNum == 7) ||
             (at2AtomicNum == 8)) &&
            (atom2->getHybridization() == Atom::SP2)) {
          // get neighbors
          boost::tie(nbrIdx, endNbrs) = mol.getAtomNeighbors(atom2);
          // check if enough neighbours
          if (mol.getAtomDegree(atom2) != 3) {
            continue;
          }
          unsigned int i = 0;
          unsigned int isBoundToSP2O = 0;  // false
          for (; nbrIdx != endNbrs; ++nbrIdx) {
            const Atom *atomX = mol[*nbrIdx];
            atoms[i] = atomX->getIdx();
            // if the central atom is sp2 carbon and is bound to sp2 oxygen, set
            // a flag
            if (!isBoundToSP2O) {
              isBoundToSP2O =
                  ((at2AtomicNum == 6) && (atomX->getAtomicNum() == 8) &&
                   (atomX->getHybridization() == Atom::SP2));
            }
            if (!i) {
              ++i;
            }
            ++i;
          }
          atoms.push_back(at2AtomicNum);
          atoms.push_back(isBoundToSP2O);
          details.improperAtoms.push_back(atoms);
          /*if (verbose) {
            std::cout << "out-of-plane bend: " << atoms[0] << " " << atoms[1] <<
          " "
                << atoms[2] << " " << atoms[3] << std::endl;
          }*/
        }
      }  // if atom is a N,O or C and SP2-hybridized
    }

    // torsions for flat rings
    const RingInfo *rinfo =
        mol.getRingInfo();  // FIX: make sure we have ring info
    CHECK_INVARIANT(rinfo, "");
    const VECT_INT_VECT &atomRings = rinfo->atomRings();
    for (const auto &atomRing : atomRings) {
      unsigned int rSize = atomRing.size();
      // we don't need to deal with 3 membered rings
      // and we do not treat rings greater than 6
      if (rSize < 4 || rSize > 6) {
        continue;
      }
      // loop over ring atoms
      for (unsigned int i = 0; i < rSize; ++i) {
        // proper torsions
        aid1 = atomRing[i];
        aid2 = atomRing[(i + 1) % rSize];
        aid3 = atomRing[(i + 2) % rSize];
        aid4 = atomRing[(i + 3) % rSize];
        bid2 = mol.getBondBetweenAtoms(aid2, aid3)->getIdx();
        // if all 4 atoms are SP2, add torsion
        if (!(doneBonds[bid2]) &&
            (mol.getAtomWithIdx(aid1)->getHybridization() == Atom::SP2) &&
            (mol.getAtomWithIdx(aid2)->getHybridization() == Atom::SP2) &&
            (mol.getAtomWithIdx(aid3)->getHybridization() == Atom::SP2) &&
            (mol.getAtomWithIdx(aid4)->getHybridization() == Atom::SP2)) {
          doneBonds[bid2] = 1;
          std::vector<int> atoms(4);
          atoms[0] = aid1;
          atoms[1] = aid2;
          atoms[2] = aid3;
          atoms[3] = aid4;
          details.expTorsionAtoms.push_back(atoms);
          std::vector<int> signs(6, 1);
          signs[1] = -1;  // MMFF sign for m = 2
          std::vector<double> fconsts(6, 0.0);
          fconsts[1] = 100.0;  // 7.0 is MMFF force constants for aromatic rings
          details.expTorsionAngles.push_back(std::make_pair(signs, fconsts));
          /*if (verbose) {
            std::cout << "SP2 ring: " << aid1 << " " << aid2 << " " << aid3 << "
          " << aid4 << std::endl;
          }*/
        }

      }  // loop over atoms in ring
    }    // loop over rings
  }      // if useBasicKnowledge

}  // end function
Exemplo n.º 16
0
void testMORSE() {
  std::cout << "=>start test MORSE\n";

  std::string pathName = getenv("RDBASE");
  std::string sdfName =
      pathName + "/Code/GraphMol/Descriptors/test_data/PBF_egfr.sdf";

  RDKit::SDMolSupplier reader(sdfName, true, false);

  std::string fName =
      pathName + "/Code/GraphMol/Descriptors/test_data/MORSE.out";

  std::ifstream instrm(fName.c_str());

  std::string line;
  std::vector<std::vector<std::string> > data;

  while (std::getline(instrm, line)) {
    std::string phrase;
    std::vector<std::string> row;
    std::stringstream ss(line);
    while (std::getline(ss, phrase, '\t')) {
      row.push_back(phrase);
    }

    data.push_back(row);
  }

  std::cout << "=>read file\n";

  int nDone = 0;
  while (!reader.atEnd()) {
    RDKit::ROMol *m = reader.next();
    TEST_ASSERT(m);
    std::string nm;
    m->getProp("_Name", nm);

    std::vector<double> dmorse;

    RDKit::Descriptors::MORSE(*m, dmorse, -1);

    std::vector<std::string> myrow = data[nDone];
    std::string inm = myrow[0];
    TEST_ASSERT(inm == nm);

    for (int i = 0; i < dmorse.size(); i++) {
      double ref = atof(myrow[i + 1].c_str());

      if (fabs(ref) > 0.01) {
        if (fabs((ref - dmorse[i]) / ref) > 1) {
          std::cout << "value mismatch: pos" << i << " " << inm << " " << ref
                    << " " << dmorse[i] << std::endl;
        }
      }

      if (fabs(ref) < 0.01) {
        if (fabs(ref - dmorse[i]) > 0.02) {
          std::cout << "value mismatch: pos" << i << " " << inm << " " << ref
                    << " " << dmorse[i] << std::endl;
        }
      }
      if (ref > 1 && fabs(ref - dmorse[i]) / ref > 0.02) {
        std::cout << "value mismatch: pos" << i << " " << inm << " " << ref
                  << " " << dmorse[i] << std::endl;
      }
      // we're testing reasonably sized values and want to be sure that we're
      // within 2% of the reference.
      TEST_ASSERT(ref < 1 || fabs(ref - dmorse[i]) / ref < 0.02);
    }

    delete m;
    ++nDone;
  }

  BOOST_LOG(rdErrorLog) << "test on : " << nDone << " molecules done"
                        << std::endl;
}
Exemplo n.º 17
0
void canonicalizeMol(RDKit::ROMol &mol, bool normalizeCovar, bool ignoreHs) {
  ROMol::ConformerIterator ci;
  for (ci = mol.beginConformers(); ci != mol.endConformers(); ci++) {
    canonicalizeConformer(*(*ci), 0, normalizeCovar, ignoreHs);
  }
}
Exemplo n.º 18
0
void testGETAWAY() {
  std::cout << "=>start test GETAWAY\n";

  std::string pathName = getenv("RDBASE");
  std::string sdfName =
      pathName + "/Code/GraphMol/Descriptors/test_data/PBF_egfr.sdf";

  RDKit::SDMolSupplier reader(sdfName, true, false);
  std::string fName =
      pathName + "/Code/GraphMol/Descriptors/test_data/GETAWAY.new.out";

  std::ifstream instrm(fName.c_str());

  // std::string ofName =
  //     pathName + "/Code/GraphMol/Descriptors/test_data/GETAWAY.new.out";
  // std::ofstream outstrm(ofName.c_str());

  std::string line;
  std::vector<std::vector<std::string> > data;

  while (std::getline(instrm, line)) {
    std::string phrase;
    std::vector<std::string> row;
    std::stringstream ss(line);
    while (std::getline(ss, phrase, '\t')) {
      row.push_back(phrase);
    }

    data.push_back(row);
  }

  int nDone = 0;
  while (!reader.atEnd()) {
    // if (nDone > 10) {
    //   break;
    // }
    RDKit::ROMol *m = reader.next();
    TEST_ASSERT(m);
    std::string nm;
    m->getProp("_Name", nm);

    std::vector<double> dgetaway;

    RDKit::Descriptors::GETAWAY(*m, dgetaway);

    std::vector<std::string> myrow = data[nDone];
    std::string inm = myrow[0];
    TEST_ASSERT(inm == nm);
    // std::cout <<  "\n";
    // int numAtoms = m->getNumAtoms();
    // std::cout << "number of Atoms : " << numAtoms << "\n";

    // outstrm << nm << "\t";
    for (int i = 0; i < 273; i++) {
      double ref = atof(myrow[i + 1].c_str());

      if (fabs(ref) > 1) {
        if (fabs((ref - dgetaway[i]) / ref) > 0.01) {
          std::cerr << "value mismatch: pos" << i << " " << inm
                    << " dragon: " << ref << " rdkit: " << dgetaway[i]
                    << std::endl;
        }
      }
      if (fabs(ref) <= 1) {
        if (fabs(ref - dgetaway[i]) > 0.02) {
          std::cerr << "value mismatch: pos" << i << " " << inm
                    << " dragon: " << ref << " rdkit: " << dgetaway[i]
                    << std::endl;
        }
      }
      // if (i != 0) outstrm << "\t";
      // outstrm << dgetaway[i];
      TEST_ASSERT(fabs(ref - dgetaway[i]) < 0.05);
    }
    // outstrm << "\n";
    delete m;
    ++nDone;
    // if (nDone > 50) break;
  }

  BOOST_LOG(rdErrorLog) << "test on : " << nDone << " molecules done"
                        << std::endl;
}