rdkit/Code/DistGeom/DistGeomUtils.cpp

// $Id$
//
//  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(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;
  }
}