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//
// Copyright (C) 2016 Greg Landrum
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <GraphMol/RDKitBase.h>
#include <GraphMol/MolTransforms/MolTransforms.h>
#include <Geometry/point.h>
#include "PMI.h"
#include <Eigen/Dense>
namespace RDKit {
namespace Descriptors {
namespace {
bool getMoments(const ROMol& mol, int confId, bool useAtomicMasses, double& pm1,
double& pm2, double& pm3, bool force) {
PRECONDITION(mol.getNumConformers() >= 1, "molecule has no conformers");
const char* pn1 = useAtomicMasses ? "_PMI1_mass" : "_PMI1";
const char* pn2 = useAtomicMasses ? "_PMI2_mass" : "_PMI2";
const char* pn3 = useAtomicMasses ? "_PMI3_mass" : "_PMI3";
if (!force && mol.hasProp(pn1) && mol.hasProp(pn2) && mol.hasProp(pn3)) {
mol.getProp(pn1, pm1);
mol.getProp(pn2, pm2);
mol.getProp(pn3, pm3);
return true;
}
const Conformer& conf = mol.getConformer(confId);
Eigen::Matrix3d axes;
Eigen::Vector3d moments;
bool res;
bool ignoreHs = false;
if (useAtomicMasses) {
std::vector<double> weights;
weights.resize(mol.getNumAtoms());
for (ROMol::ConstAtomIterator cai = mol.beginAtoms(); cai != mol.endAtoms();
++cai) {
weights[(*cai)->getIdx()] = (*cai)->getMass();
}
res = MolTransforms::computePrincipalAxesAndMoments(
conf, axes, moments, ignoreHs, false, &weights);
} else {
res = MolTransforms::computePrincipalAxesAndMoments(conf, axes, moments,
ignoreHs);
}
if (res) {
pm1 = moments(0);
pm2 = moments(1);
pm3 = moments(2);
mol.setProp(pn1, pm1, true);
mol.setProp(pn2, pm2, true);
mol.setProp(pn3, pm3, true);
}
return res;
}
bool getMomentsFromGyration(const ROMol& mol, int confId, bool useAtomicMasses,
double& pm1, double& pm2, double& pm3, bool force) {
PRECONDITION(mol.getNumConformers() >= 1, "molecule has no conformers");
const char* pn1 = useAtomicMasses ? "_PMI1_mass_cov" : "_PMI1_cov";
const char* pn2 = useAtomicMasses ? "_PMI2_mass_cov" : "_PMI2_cov";
const char* pn3 = useAtomicMasses ? "_PMI3_mass_cov" : "_PMI3_cov";
if (!force && mol.hasProp(pn1) && mol.hasProp(pn2) && mol.hasProp(pn3)) {
mol.getProp(pn1, pm1);
mol.getProp(pn2, pm2);
mol.getProp(pn3, pm3);
return true;
}
const Conformer& conf = mol.getConformer(confId);
Eigen::Matrix3d axes;
Eigen::Vector3d moments;
bool res;
bool ignoreHs = false;
if (useAtomicMasses) {
std::vector<double> weights;
weights.resize(mol.getNumAtoms());
for (ROMol::ConstAtomIterator cai = mol.beginAtoms(); cai != mol.endAtoms();
++cai) {
weights[(*cai)->getIdx()] = (*cai)->getMass();
}
res = MolTransforms::computePrincipalAxesAndMomentsFromGyrationMatrix(
conf, axes, moments, ignoreHs, false, &weights);
} else {
res = MolTransforms::computePrincipalAxesAndMomentsFromGyrationMatrix(
conf, axes, moments, ignoreHs);
}
if (res) {
pm1 = moments(0);
pm2 = moments(1);
pm3 = moments(2);
mol.setProp(pn1, pm1, true);
mol.setProp(pn2, pm2, true);
mol.setProp(pn3, pm3, true);
}
return res;
}
} // end of anonymous namespace
double NPR1(const ROMol& mol, int confId, bool useAtomicMasses, bool force) {
PRECONDITION(mol.getNumConformers() >= 1, "molecule has no conformers");
double pm1, pm2, pm3;
if (!getMoments(mol, confId, useAtomicMasses, pm1, pm2, pm3, force)) {
// the eigenvector calculation failed
return 0.0; // FIX: throw an exception here?
}
if (pm3 < 1e-8) return 0.0;
return pm1 / pm3;
}
double NPR2(const ROMol& mol, int confId, bool useAtomicMasses, bool force) {
PRECONDITION(mol.getNumConformers() >= 1, "molecule has no conformers");
double pm1, pm2, pm3;
if (!getMoments(mol, confId, useAtomicMasses, pm1, pm2, pm3, force)) {
// the eigenvector calculation failed
return 0.0; // FIX: throw an exception here?
}
if (pm3 < 1e-8) return 0.0;
return pm2 / pm3;
}
double PMI1(const ROMol& mol, int confId, bool useAtomicMasses, bool force) {
PRECONDITION(mol.getNumConformers() >= 1, "molecule has no conformers");
double pm1, pm2, pm3;
if (!getMoments(mol, confId, useAtomicMasses, pm1, pm2, pm3, force)) {
// the eigenvector calculation failed
return 0.0; // FIX: throw an exception here?
}
return pm1;
}
double PMI2(const ROMol& mol, int confId, bool useAtomicMasses, bool force) {
PRECONDITION(mol.getNumConformers() >= 1, "molecule has no conformers");
double pm1, pm2, pm3;
if (!getMoments(mol, confId, useAtomicMasses, pm1, pm2, pm3, force)) {
// the eigenvector calculation failed
return 0.0; // FIX: throw an exception here?
}
return pm2;
}
double PMI3(const ROMol& mol, int confId, bool useAtomicMasses, bool force) {
PRECONDITION(mol.getNumConformers() >= 1, "molecule has no conformers");
double pm1, pm2, pm3;
if (!getMoments(mol, confId, useAtomicMasses, pm1, pm2, pm3, force)) {
// the eigenvector calculation failed
return 0.0; // FIX: throw an exception here?
}
return pm3;
}
double radiusOfGyration(const ROMol& mol, int confId, bool useAtomicMasses,
bool force) {
PRECONDITION(mol.getNumConformers() >= 1, "molecule has no conformers");
double pm1, pm2, pm3;
if (!getMomentsFromGyration(mol, confId, useAtomicMasses, pm1, pm2, pm3,
force)) {
// the eigenvector calculation failed
return 0.0; // FIX: throw an exception here?
}
return sqrt(pm1 + pm2 + pm3);
}
double inertialShapeFactor(const ROMol& mol, int confId, bool useAtomicMasses,
bool force) {
PRECONDITION(mol.getNumConformers() >= 1, "molecule has no conformers");
double pm1, pm2, pm3;
if (!getMoments(mol, confId, useAtomicMasses, pm1, pm2, pm3, force)) {
// the eigenvector calculation failed
return 0.0; // FIX: throw an exception here?
}
if (pm1 < 1e-4 || pm3 < 1e-4) {
// planar or no coordinates
return 0.0;
} else {
return pm2 / (pm1 * pm3);
}
}
double eccentricity(const ROMol& mol, int confId, bool useAtomicMasses,
bool force) {
PRECONDITION(mol.getNumConformers() >= 1, "molecule has no conformers");
double pm1, pm2, pm3;
if (!getMoments(mol, confId, useAtomicMasses, pm1, pm2, pm3, force)) {
// the eigenvector calculation failed
return 0.0; // FIX: throw an exception here?
}
if (pm3 < 1e-4) {
// no coordinates
return 0.0;
} else {
return sqrt(pm3 * pm3 - pm1 * pm1) / pm3;
}
}
double asphericity(const ROMol& mol, int confId, bool useAtomicMasses,
bool force) {
PRECONDITION(mol.getNumConformers() >= 1, "molecule has no conformers");
double pm1, pm2, pm3;
if (!getMomentsFromGyration(mol, confId, useAtomicMasses, pm1, pm2, pm3,
force)) {
// the eigenvector calculation failed
return 0.0; // FIX: throw an exception here?
}
if (pm3 < 1e-4) {
// no coordinates
return 0.0;
} else {
double denom = pm1 + pm2 + pm3;
return 0.5 * (pow(pm1 - pm2, 2) + pow(pm1 - pm3, 2) + pow(pm2 - pm3, 2)) /
(denom * denom);
}
}
double spherocityIndex(const ROMol& mol, int confId, bool force) {
PRECONDITION(mol.getNumConformers() >= 1, "molecule has no conformers");
bool useAtomicMasses = false;
double pm1, pm2, pm3;
if (!getMomentsFromGyration(mol, confId, useAtomicMasses, pm1, pm2, pm3,
force)) {
// the eigenvector calculation failed
return 0.0; // FIX: throw an exception here?
}
if (pm3 < 1e-4) {
// no coordinates
return 0.0;
} else {
return 3. * pm1 / (pm1 + pm2 + pm3);
}
}
} // namespace Descriptors
} // namespace RDKit
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