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;
}
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,
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;
}