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;
} // constructForceField
