示例#1
0
文件: Crippen.cpp 项目: giallu/rdkit
void calcCrippenDescriptors(const ROMol &mol, double &logp, double &mr,
                            bool includeHs, bool force) {
  if (!force && mol.hasProp(common_properties::_crippenLogP)) {
    mol.getProp(common_properties::_crippenLogP, logp);
    mol.getProp(common_properties::_crippenMR, mr);
    return;
  }

  // this isn't as bad as it looks, we aren't actually going
  // to harm the molecule in any way!
  ROMol *workMol = const_cast<ROMol *>(&mol);
  if (includeHs) {
    workMol = MolOps::addHs(mol, false, false);
  }
  std::vector<double> logpContribs(workMol->getNumAtoms());
  std::vector<double> mrContribs(workMol->getNumAtoms());
  getCrippenAtomContribs(*workMol, logpContribs, mrContribs, force);
  logp = 0.0;
  for (std::vector<double>::const_iterator iter = logpContribs.begin();
       iter != logpContribs.end(); ++iter) {
    logp += *iter;
  }
  mr = 0.0;
  for (std::vector<double>::const_iterator iter = mrContribs.begin();
       iter != mrContribs.end(); ++iter) {
    mr += *iter;
  }

  if (includeHs) {
    delete workMol;
  }

  mol.setProp(common_properties::_crippenLogP, logp, true);
  mol.setProp(common_properties::_crippenMR, mr, true);
};
示例#2
0
文件: MolSurf.cpp 项目: ASKCOS/rdkit
std::vector<double> calcSlogP_VSA(const ROMol &mol, std::vector<double> *bins,
                                  bool force) {
  // FIX: use force value to include caching
  std::vector<double> lbins;
  if (!bins) {
    double blist[11] = {-0.4, -0.2, 0,   0.1, 0.15, 0.2,
                        0.25, 0.3,  0.4, 0.5, 0.6};
    lbins.resize(11);
    std::copy(blist, blist + 11, lbins.begin());
  } else {
    lbins.resize(bins->size());
    std::copy(bins->begin(), bins->end(), lbins.begin());
  }
  std::vector<double> res(lbins.size() + 1, 0);

  std::vector<double> vsaContribs(mol.getNumAtoms());
  double tmp;
  getLabuteAtomContribs(mol, vsaContribs, tmp, true, force);
  std::vector<double> logpContribs(mol.getNumAtoms());
  std::vector<double> mrContribs(mol.getNumAtoms());
  getCrippenAtomContribs(mol, logpContribs, mrContribs, force);

  assignContribsToBins(vsaContribs, logpContribs, lbins, res);

  return res;
}
示例#3
0
文件: MolSurf.cpp 项目: ASKCOS/rdkit
std::vector<double> calcSMR_VSA(const ROMol &mol, std::vector<double> *bins,
                                bool force) {
  std::vector<double> lbins;
  if (!bins) {
    double blist[9] = {1.29, 1.82, 2.24, 2.45, 2.75, 3.05, 3.63, 3.8, 4.0};
    lbins.resize(9);
    std::copy(blist, blist + 9, lbins.begin());
  } else {
    lbins.resize(bins->size());
    std::copy(bins->begin(), bins->end(), lbins.begin());
  }
  std::vector<double> res(lbins.size() + 1, 0);

  std::vector<double> vsaContribs(mol.getNumAtoms());
  double tmp;
  getLabuteAtomContribs(mol, vsaContribs, tmp, true, force);
  std::vector<double> logpContribs(mol.getNumAtoms());
  std::vector<double> mrContribs(mol.getNumAtoms());
  getCrippenAtomContribs(mol, logpContribs, mrContribs, force);

  assignContribsToBins(vsaContribs, mrContribs, lbins, res);

  return res;
}