rdkit/Code/GraphMol/Descriptors/PBF.cpp

//
//  Copyright (c) 2012, Institue of Cancer Research.
//  All rights reserved.
//
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//modification, are permitted provided that the following conditions are
// met:
//
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//       notice, this list of conditions and the following disclaimer.
//     * 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
//       with the distribution.
//     * Neither the name of Institue of Cancer Research.
//       nor the names of its contributors may be used to endorse or promote
//       products derived from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// For more information on the Plane of Best Fit please see http://pubs.acs.org/doi/abs/10.1021/ci300293f
//
//  If this code has been useful to you, please include the reference
//  in any work which has made use of it:

//  Plane of Best Fit: A Novel Method to Characterize the Three-Dimensionality of Molecules, Nicholas C. Firth, Nathan Brown, and Julian Blagg, Journal of Chemical Information and Modeling 2012 52 (10), 2516-2525

//
//
// Created by Nicholas Firth, November 2011
// Modified by Greg Landrum for inclusion in the RDKit distribution November 2012
// Further modified by Greg Landrum for inclusion in the RDKit core September 2016
//

#include <GraphMol/RDKitBase.h>
#include <GraphMol/MolTransforms/MolTransforms.h>

#include "PBF.h"
#include <Numerics/Matrix.h>
#include <Numerics/SquareMatrix.h>
#include <Numerics/SymmMatrix.h>
#include <boost/foreach.hpp>

#include <Eigen/Dense>

namespace RDKit {
namespace Descriptors{
namespace {

double distanceFromAPlane(const RDGeom::Point3D &pt,const std::vector<double> &plane, double denom){
  double numer=0.0;
  numer = std::abs(pt.x*plane[0]+pt.y*plane[1]+pt.z*plane[2]+plane[3]);

  return numer/denom;
}

bool getBestFitPlane(const Conformer &conf,
                    const std::vector<RDGeom::Point3D> &points,
                     std::vector<double> &plane,
                     const std::vector<double> *weights) {
  PRECONDITION((!weights || weights->size()>=points.size()),"bad weights vector");
  PRECONDITION(plane.size()>=4,"bad plane");
  RDGeom::Point3D origin(0,0,0);
  double wSum=0.0;

  for(unsigned int i=0;i<points.size();++i){
    if(weights){
      double w=(*weights)[i];
      wSum+=w;
      origin+=points[i]*w;
    } else {
      wSum+=1;
      origin+=points[i];
    }
  }
  origin /= wSum;

  Eigen::Matrix3d evects;
  Eigen::Vector3d evals;
  MolTransforms::computePrincipalAxesAndMoments(conf,evects,evals,false,weights);
  RDGeom::Point3D normal;
  normal.x=evects(0,0);
  normal.y=evects(1,0);
  normal.z=evects(2,0);

  plane[0] = normal.x;
  plane[1] = normal.y;
  plane[2] = normal.z;
  plane[3] = -1*normal.dotProduct(origin);
  return true;
}

} //end of anonymous namespace

double PBF(const ROMol& mol,int confId){
  PRECONDITION(mol.getNumConformers()>=1,"molecule has no conformers")
  unsigned int numAtoms = mol.getNumAtoms();
  if(numAtoms<4) return 0;

  const Conformer &conf = mol.getConformer(confId);
  if(!conf.is3D()) return 0 ;

  std::vector<RDGeom::Point3D> points;
  points.reserve(numAtoms);
  for(unsigned int i=0; i<numAtoms; ++i){
    points.push_back(conf.getAtomPos(i));
  }

  std::vector<double> plane(4);
  if(!getBestFitPlane(conf,points,plane,NULL)){
    // the eigenvalue calculation failed, return 0
    // FIX: throw an exception here?
    return 0.0;
  }

  double denom=0.0;
  for(unsigned int i=0; i<3; ++i){
    denom += plane[i]*plane[i];
  }
  denom = sqrt(denom);

  double res=0.0;
  for(unsigned int i=0; i<numAtoms; ++i){
    res+= distanceFromAPlane(points[i], plane, denom);
  }
  res /= numAtoms;

  return res;
}

} // end of Descriptors namespace
} // end of RDKit namespace