Пример #1
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;
}
Пример #2
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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;
}
Пример #3
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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;
}
Пример #4
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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;
}
Пример #5
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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;
}
Пример #6
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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;
}
Пример #7
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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;
}
Пример #8
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// 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;
}
Пример #9
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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;
}
Пример #10
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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;
}
Пример #11
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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;
}
Пример #12
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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