示例#1
0
double pickRandomDistMat(const BoundsMatrix &mmat,
                         RDNumeric::SymmMatrix<double> &distMat,
                         RDKit::double_source_type &rng) {
  // make sure the sizes match up
  unsigned int npt = mmat.numRows();
  CHECK_INVARIANT(npt == distMat.numRows(), "Size mismatch");

  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 = rng();
      // std::cerr<<i<<"-"<<j<<": "<<rval<<std::endl;
      double d = lb + (rval) * (ub - lb);
      ddata[id + j] = d;
      if (d > largestVal) {
        largestVal = d;
      }
    }
  }
  return largestVal;
}
示例#2
0
  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;
  }
示例#3
0
bool computeInitialCoords(const RDNumeric::SymmMatrix<double> &distMat,
                          RDGeom::PointPtrVect &positions,
                          RDKit::double_source_type &rng, 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 {
        // std::cerr<<"!!! "<<i<<"-"<<j<<": "<<eigData[j]<<std::endl;
        (*pt)[j] = 1.0 - 2.0 * rng();
      }
    }
  }
  return true;
}