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// $Id: DistGeomUtils.cpp 1528 2010-09-26 17:04:37Z glandrum $
//
// Copyright (C) 2004-2008 Greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include "BoundsMatrix.h"
#include "DistGeomUtils.h"
#include "DistViolationContrib.h"
#include "ChiralViolationContrib.h"
#include "FourthDimContrib.h"
#include <Numerics/Matrix.h>
#include <Numerics/SymmMatrix.h>
#include <Numerics/Vector.h>
#include <RDGeneral/Invariant.h>
#include <Numerics/EigenSolvers/PowerEigenSolver.h>
#include <RDGeneral/utils.h>
#include <ForceField/ForceField.h>
namespace DistGeom {
const double EIGVAL_TOL=0.001;
double pickRandomDistMat(const BoundsMatrix &mmat,
RDNumeric::SymmMatrix<double> &distMat,
int seed) {
// make sure the sizes match up
unsigned int npt = mmat.numRows();
CHECK_INVARIANT(npt == distMat.numRows(), "Size mismatch");
RDKit::rng_type &generator = RDKit::getRandomGenerator();
if (seed > 0) {
generator.seed(seed);
}
double largestVal=-1.0;
double *ddata = distMat.getData();
for (unsigned int i = 1; i < npt; i++) {
unsigned int id = i*(i+1)/2;
for (unsigned int j = 0; j < i; j++) {
double ub = mmat.getUpperBound(i,j);
double lb = mmat.getLowerBound(i,j);
CHECK_INVARIANT(ub >= lb, "");
double rval = RDKit::getRandomVal();
double d = lb + (rval)*(ub - lb);
ddata[id+j] = d;
if(d>largestVal){
largestVal=d;
}
}
}
return largestVal;
}
bool computeInitialCoords(const RDNumeric::SymmMatrix<double> &distMat,
RDGeom::PointPtrVect &positions, bool randNegEig,
unsigned int numZeroFail) {
unsigned int N = distMat.numRows();
unsigned int nPt = positions.size();
CHECK_INVARIANT(nPt == N, "Size mismatch");
unsigned int dim = positions.front()->dimension();
const double *data = distMat.getData();
RDNumeric::SymmMatrix<double> sqMat(N), T(N, 0.0);
RDNumeric::DoubleMatrix eigVecs(dim,N);
RDNumeric::DoubleVector eigVals(dim);
double *sqDat = sqMat.getData();
unsigned int dSize = distMat.getDataSize();
double sumSqD2 = 0.0;
for (unsigned int i = 0; i < dSize; i++) {
sqDat[i] = data[i]*data[i];
sumSqD2 += sqDat[i];
}
sumSqD2 /= (N*N);
RDNumeric::DoubleVector sqD0i(N, 0.0);
double *sqD0iData = sqD0i.getData();
for (unsigned int i = 0; i < N; i++) {
for (unsigned int j = 0; j < N; j++) {
sqD0iData[i] += sqMat.getVal(i,j);
}
sqD0iData[i] /= N;
sqD0iData[i] -= sumSqD2;
if ((sqD0iData[i] < EIGVAL_TOL) && (N > 3)){
return false;
}
}
for (unsigned int i = 0; i < N; i++) {
for (unsigned int j = 0; j <= i; j++) {
double val = 0.5*(sqD0iData[i] + sqD0iData[j] - sqMat.getVal(i,j));
T.setVal(i,j, val);
}
}
unsigned int nEigs = (dim < N) ? dim : N;
RDNumeric::EigenSolvers::powerEigenSolver(nEigs, T, eigVals, eigVecs,
(int)(sumSqD2*N));
double *eigData = eigVals.getData();
bool foundNeg = false;
unsigned int zeroEigs = 0;
for (unsigned int i = 0; i < dim; i++) {
if (eigData[i] > EIGVAL_TOL) {
eigData[i] = sqrt(eigData[i]);
} else if (fabs(eigData[i]) < EIGVAL_TOL) {
eigData[i] = 0.0;
zeroEigs++;
} else {
foundNeg = true;
}
}
if ((foundNeg) && (!randNegEig) ) {
return false;
}
if ((zeroEigs >= numZeroFail) && (N > 3)) {
return false;
}
for (unsigned int i = 0; i < N; i++) {
RDGeom::Point *pt = positions[i];
for (unsigned int j = 0; j < dim; ++j) {
if (eigData[j] >= 0.0) {
(*pt)[j] = eigData[j]*eigVecs.getVal(j,i);
} else {
(*pt)[j] = 1.0 - 2.0*RDKit::getRandomVal();
}
}
}
return true;
}
bool computeRandomCoords(RDGeom::PointPtrVect &positions, double boxSize){
CHECK_INVARIANT(boxSize>0.0, "bad boxSize");
for(RDGeom::PointPtrVect::iterator ptIt=positions.begin();
ptIt!=positions.end();++ptIt){
RDGeom::Point *pt = *ptIt;
for (unsigned int i = 0; i<pt->dimension(); ++i) {
(*pt)[i]=boxSize*(RDKit::getRandomVal()-0.5);
}
}
return true;
}
ForceFields::ForceField *constructForceField(const BoundsMatrix &mmat,
RDGeom::PointPtrVect &positions,
const VECT_CHIRALSET & csets,
double weightChiral,
double weightFourthDim,
std::map< std::pair<int,int>,double> *extraWeights,
double basinSizeTol) {
unsigned int N = mmat.numRows();
CHECK_INVARIANT(N == positions.size(), "");
ForceFields::ForceField *field=new ForceFields::ForceField(positions[0]->dimension());
for(unsigned int i=0; i < N; i++){
field->positions().push_back(positions[i]);
}
for (unsigned int i = 1; i < N; i++) {
for (unsigned int j = 0; j < i; j++) {
double w = 1.0;
double l = mmat.getLowerBound(i,j);
double u = mmat.getUpperBound(i,j);
bool includeIt=false;
if(extraWeights){
std::map< std::pair<int,int>,double>::const_iterator mapIt;
mapIt = extraWeights->find(std::make_pair<int,int>(i,j));
if(mapIt != extraWeights->end()){
w = mapIt->second;
includeIt=true;
}
}
if(u-l <= basinSizeTol) {
includeIt=true;
}
if(includeIt){
DistViolationContrib *contrib = new DistViolationContrib(field, i, j, u, l, w);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
}
}
// now add chiral constraints
if (weightChiral > 1.e-8) {
for (VECT_CHIRALSET::const_iterator csi = csets.begin();
csi != csets.end(); csi++) {
ChiralViolationContrib *contrib = new ChiralViolationContrib(field, csi->get(),
weightChiral);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
}
// finally the contribution from the fourth dimension if we need to
if ((field->dimension() == 4) && (weightFourthDim > 1.e-8)) {
for (unsigned int i = 1; i < N; i++) {
FourthDimContrib *contrib = new FourthDimContrib(field,i,weightFourthDim);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
}
return field;
}
}
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