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#include <cstdlib>
#include <iostream>
#include "MolData3Ddescriptors.h"
#include <GraphMol/RDKitBase.h>
#include <boost/math/special_functions/round.hpp>
#include "GraphMol/PartialCharges/GasteigerCharges.h"
#include "GraphMol/PartialCharges/GasteigerParams.h"
using namespace std;
MolData3Ddescriptors::MolData3Ddescriptors() {}
std::vector<double> MolData3Ddescriptors::GetUn(int numAtoms) {
std::vector<double> u(numAtoms, 1.0);
return u;
}
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;
}
std::vector<double> MolData3Ddescriptors::GetRelativePol(
const RDKit::ROMol& mol) {
int numAtoms = mol.getNumAtoms();
double* relativePol = data3D.getPOL();
std::vector<double> pol(numAtoms, 0.0);
for (int i = 0; i < numAtoms; ++i) {
pol[i] = relativePol[mol.getAtomWithIdx(i)->getAtomicNum() - 1];
}
return pol;
}
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;
}
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;
}
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;
}
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;
}
std::vector<double> MolData3Ddescriptors::GetCustomAtomProp(
const RDKit::ROMol& mol, const std::string &customAtomPropName) {
int numAtoms = mol.getNumAtoms();
std::vector<double> customAtomarray(numAtoms, 0.0);
for (int i = 0; i < numAtoms; ++i) {
if (mol.getAtomWithIdx(i)->hasProp(customAtomPropName)) {
customAtomarray[i] = mol.getAtomWithIdx(i)->getProp<double>(customAtomPropName);
}
else {
customAtomarray[i] =1;
}
}
return customAtomarray;
}
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;
}
int MolData3Ddescriptors::GetPrincipalQuantumNumber(int AtomicNum) {
if (AtomicNum <= 2)
return 1;
else if (AtomicNum <= 10)
return 2;
else if (AtomicNum <= 18)
return 3;
else if (AtomicNum <= 36)
return 4;
else if (AtomicNum <= 54)
return 5;
else if (AtomicNum <= 86)
return 6;
else
return 7;
}
std::vector<double> MolData3Ddescriptors::GetIState(const RDKit::ROMol& mol) {
int numAtoms = mol.getNumAtoms();
std::vector<double> Is(numAtoms, 1.0); // values set to 1 for Hs
for (int i = 0; i < numAtoms; ++i) {
const RDKit::Atom* atom = mol.getAtomWithIdx(i);
int atNum = atom->getAtomicNum();
int degree = atom->getDegree(); // number of substituants (heavy of not?)
if (degree > 0 && atNum > 1) {
int h = atom->getTotalNumHs(
true); // caution getTotalNumHs(true) to count h !!!!
int dv = RDKit::PeriodicTable::getTable()->getNouterElecs(atNum) -
h; // number of valence (explicit with Hs)
int N = GetPrincipalQuantumNumber(atNum); // principal quantum number
double d = (double)degree - h; // degree-h
if (d > 0) {
Is[i] =
boost::math::round(1000 * (4.0 / (N * N) * dv + 1.0) / d) / 1000;
}
}
}
return Is;
}
std::vector<double> MolData3Ddescriptors::GetIStateDrag(
const RDKit::ROMol& mol) {
int numAtoms = mol.getNumAtoms();
std::vector<double> Is(numAtoms, 1.0);
for (int i = 0; i < numAtoms; ++i) {
const RDKit::Atom* atom = mol.getAtomWithIdx(i);
int atNum = atom->getAtomicNum();
int degree = atom->getDegree(); // number of substituants
if (degree > 0 && atNum > 1) {
int h = atom->getTotalNumHs(true);
int Zv = RDKit::PeriodicTable::getTable()->getNouterElecs(
atNum); // number of valence (explicit with Hs)
double dv = (double)Zv - h; // number of valence electron without Hs
int N = GetPrincipalQuantumNumber(atNum); // principal quantum number
double d = (double)degree - h; // degree-h
if (d > 0) {
Is[i] =
boost::math::round(1000 * (4.0 / (N * N) * dv + 1.0) / d) / 1000;
}
}
}
return Is;
}
// 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);
std::vector<double> accum(numAtoms, 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;
}
// 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);
std::vector<double> accum(numAtoms, 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;
}
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