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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
// 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::fabs(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::computePrincipalAxesAndMomentsFromGyrationMatrix(
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, nullptr)) {
// 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
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