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//
// Copyright (c) 2012, Institue of Cancer Research.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
//modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// 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
//
#include "PBFRDKit.h"
#include <Numerics/Matrix.h>
#include <Numerics/SquareMatrix.h>
#include <Numerics/SymmMatrix.h>
#include <boost/foreach.hpp>
#include <Eigen/Dense>
using namespace RDKit;
void getSmallestEigenVector(double fSumXX,double fSumXY,double fSumXZ,
double fSumYY,double fSumYZ,double fSumZZ,
double &x,double &y, double &z);
double distanceFromAPlane(const RDGeom::Point3D &pt,const std::vector<double> &plane, double denom){
double numer=0.0;
numer = std::fabs(pt.x*plane[0]+pt.y*plane[1]+pt.z*plane[2]+plane[3]);
return numer/denom;
}
bool getBestFitPlane(const std::vector<RDGeom::Point3D> &points,
std::vector<double> &plane,
const std::vector<double> *weights) {
PRECONDITION((!weights || weights->size()>=points.size()),"bad weights vector");
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;
double sumXX=0,sumXY=0,sumXZ=0,sumYY=0,sumYZ=0,sumZZ=0;
for(unsigned int i=0;i<points.size();++i){
RDGeom::Point3D delta=points[i]-origin;
if(weights){
double w=(*weights)[i];
delta *= w;
}
sumXX += delta.x*delta.x;
sumXY += delta.x*delta.y;
sumXZ += delta.x*delta.z;
sumYY += delta.y*delta.y;
sumYZ += delta.y*delta.z;
sumZZ += delta.z*delta.z;
}
sumXX/=wSum;
sumXY/=wSum;
sumXZ/=wSum;
sumYY/=wSum;
sumYZ/=wSum;
sumZZ/=wSum;
Eigen::Matrix3d mat;
mat << sumXX, sumXY, sumXZ,
sumXY, sumYY, sumYZ,
sumXZ, sumYZ, sumZZ;
Eigen::SelfAdjointEigenSolver<Eigen::Matrix3d> eigensolver(mat);
if(eigensolver.info()!=Eigen::Success){
BOOST_LOG(rdErrorLog)<<"eigenvalue calculation did not converge"<<std::endl;
return 0.0;
}
RDGeom::Point3D normal;
normal.x=eigensolver.eigenvectors()(0,0);
normal.y=eigensolver.eigenvectors()(1,0);
normal.z=eigensolver.eigenvectors()(2,0);
plane[0] = normal.x;
plane[1] = normal.y;
plane[2] = normal.z;
plane[3] = -1*normal.dotProduct(origin);
}
double PBFRD(ROMol& mol,int confId){
PRECONDITION(mol.getNumConformers()>=1,"molecule has no conformers")
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);
getBestFitPlane(points,plane,0);
double denom=0.0;
for(unsigned int i=0; i<3; ++i){
denom += plane[i]*plane[i];
}
denom = pow(denom,0.5);
double res=0.0;
for(unsigned int i=0; i<numAtoms; ++i){
res+= distanceFromAPlane(points[i], plane, denom);
}
res /= numAtoms;
return res;
}
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