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);
};
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;
}
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;
}