rdkit/Code/GraphMol/Descriptors/AUTOCORR3D.cpp

//
//  Copyright (c) 2016, Guillaume GODIN.
//  All rights reserved.
//
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// modification, are permitted provided that the following conditions are
// met:
//
//     * Redistributions of source code must retain the above copyright
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//     * Redistributions in binary form must reproduce the above
//       copyright notice, this list of conditions and the following
//       disclaimer in the documentation and/or other materials provided
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//       nor the names of its contributors may be used to endorse or promote
//       products derived from this software without specific prior written
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// Guillaume GODIN access the AutoCorrelation 3D descriptors names in Dragon TDB

#include <GraphMol/RDKitBase.h>

#include "AUTOCORR3D.h"
#include "MolData3Ddescriptors.h"

#include <math.h>
#include <Eigen/Dense>
#include <Eigen/SVD>
#include <iostream>
#include <Eigen/Core>
#include <Eigen/QR>

using namespace Eigen;
namespace RDKit {
namespace Descriptors {

namespace {

MolData3Ddescriptors moldata3D;

VectorXd getEigenVect(std::vector<double> v) {
  double* varray_ptr = &v[0];
  Map<VectorXd> V(varray_ptr, v.size());
  return V;
}

double* GetGeodesicMatrix(double* dist, int lag, int numAtoms) {
  int sizeArray = numAtoms * numAtoms;
  double* Geodesic = new double[sizeArray];
  for (int i = 0; i < sizeArray; i++) {
    if (dist[i] == lag)
      Geodesic[i] = 1.0;
    else
      Geodesic[i] = 0.0;
  }
  return Geodesic;
}

// matrix prod that mimic the v2 version
// the code is in respect to Dragon 6 descriptors.
// replace the number of "Bicount" vertex per lag by a (numAtoms * (numAtoms -
// 1))!
// provided by Kobe team!
void get3DautocorrelationDesc(double* dist3D, double* topologicaldistance,
                              int numAtoms, const ROMol& mol,
                              std::vector<double>& res) {
  Map<MatrixXd> dm(dist3D, numAtoms, numAtoms);
  Map<MatrixXd> di(topologicaldistance, numAtoms, numAtoms);

  std::vector<double> wp = moldata3D.GetRelativePol(mol);
  VectorXd Wp = getEigenVect(wp);

  std::vector<double> wm = moldata3D.GetRelativeMW(mol);
  VectorXd Wm = getEigenVect(wm);

  std::vector<double> wi = moldata3D.GetRelativeIonPol(mol);
  VectorXd Wi = getEigenVect(wi);

  std::vector<double> wv = moldata3D.GetRelativeVdW(mol);
  VectorXd Wv = getEigenVect(wv);

  std::vector<double> we = moldata3D.GetRelativeENeg(mol);
  VectorXd We = getEigenVect(we);

  std::vector<double> wu = moldata3D.GetUn(numAtoms);
  VectorXd Wu = getEigenVect(wu);

  std::vector<double> ws = moldata3D.GetIState(mol);
  VectorXd Ws = getEigenVect(ws);

  std::vector<double> wr = moldata3D.GetRelativeRcov(mol);
  VectorXd Wr = getEigenVect(wr);

  MatrixXd Bi;
  MatrixXd tmp;
  double TDBmat[8][10];
  double dtmp;

  for (int i = 0; i < 10; i++) {
    double* Bimat = GetGeodesicMatrix(topologicaldistance, i + 1, numAtoms);
    Map<MatrixXd> Bi(Bimat, numAtoms, numAtoms);
    MatrixXd RBi = Bi.cwiseProduct(dm);
    // double Bicount = (double)Bi.sum();

    tmp = Wu.transpose() * RBi * Wu;
    dtmp = (double)tmp(0);
    if (std::isnan(dtmp)) dtmp = 0.0;
    TDBmat[0][i] = dtmp;

    tmp = Wm.transpose() * RBi * Wm;
    dtmp = (double)tmp(0);
    if (std::isnan(dtmp)) dtmp = 0.0;
    TDBmat[1][i] = dtmp;

    tmp = Wv.transpose() * RBi * Wv;
    dtmp = (double)tmp(0);
    if (std::isnan(dtmp)) dtmp = 0.0;
    TDBmat[2][i] = dtmp;

    tmp = We.transpose() * RBi * We;
    dtmp = (double)tmp(0);
    if (std::isnan(dtmp)) dtmp = 0.0;
    TDBmat[3][i] = dtmp;

    tmp = Wp.transpose() * RBi * Wp;
    dtmp = (double)tmp(0);
    if (std::isnan(dtmp)) dtmp = 0.0;
    TDBmat[4][i] = dtmp;

    tmp = Wi.transpose() * RBi * Wi;
    dtmp = (double)tmp(0);
    if (std::isnan(dtmp)) dtmp = 0.0;
    TDBmat[5][i] = dtmp;

    tmp = Ws.transpose() * RBi * Ws;
    dtmp = (double)tmp(0);
    if (std::isnan(dtmp)) dtmp = 0.0;
    TDBmat[6][i] = dtmp;

    tmp = Wr.transpose() * RBi * Wr;
    dtmp = (double)tmp(0);
    if (std::isnan(dtmp)) dtmp = 0.0;
    TDBmat[7][i] = dtmp;
    delete[] Bimat;
  }

  // update the Output vector!
  for (unsigned int j = 0; j < 8; ++j) {
    for (unsigned int i = 0; i < 10; ++i) {
      res[j * 10 + i] =
          round(1000 * TDBmat[j][i] / (numAtoms * (numAtoms - 1))) / 1000;
    }
  }
}

void Get3Dauto(double* dist3D, double* topologicaldistance, int numAtoms,
               const ROMol& mol, std::vector<double>& res) {
  // AUTOCORRNAMES={"TDB01u","TDB02u","TDB03u","TDB04u","TDB05u","TDB06u","TDB07u","TDB08u","TDB09u","TDB10u","TDB01m","TDB02m","TDB03m","TDB04m","TDB05m","TDB06m","TDB07m","TDB08m","TDB09m","TDB10m","TDB01v","TDB02v","TDB03v","TDB04v","TDB05v","TDB06v","TDB07v","TDB08v","TDB09v","TDB10v","TDB01e","TDB02e","TDB03e","TDB04e","TDB05e","TDB06e","TDB07e","TDB08e","TDB09e","TDB10e","TDB01p","TDB02p","TDB03p","TDB04p","TDB05p","TDB06p","TDB07p","TDB08p","TDB09p","TDB10p","TDB01i","TDB02i","TDB03i","TDB04i","TDB05i","TDB06i","TDB07i","TDB08i","TDB09i","TDB10i","TDB01s","TDB02s","TDB03s","TDB04s","TDB05s","TDB06s","TDB07s","TDB08s","TDB09s","TDB10s","TDB01r","TDB02r","TDB03r","TDB04r","TDB05r","TDB06r","TDB07r","TDB08r","TDB09r","TDB10r"};
  get3DautocorrelationDesc(dist3D, topologicaldistance, numAtoms, mol, res);
}

}  // end of anonymous namespace

void AUTOCORR3D(const ROMol& mol, std::vector<double>& res, int confId) {
  PRECONDITION(mol.getNumConformers() >= 1, "molecule has no conformers")
  int numAtoms = mol.getNumAtoms();

  const Conformer& conf = mol.getConformer(confId);

  double* topologicaldistance =
      MolOps::getDistanceMat(mol, false);  // topological matrix
  double* dist3D =
      MolOps::get3DDistanceMat(mol, confId, false, true);  // 3D distance matrix

  res.clear();
  res.resize(80);
  Get3Dauto(dist3D, topologicaldistance, numAtoms, mol, res);
}
}  // end of Descriptors namespace
}  // end of RDKit namespace