//computes a set of solitary grid points that represent the interaction between
//this ligand and the provided receptor in some way
void OBAMolecule::computeInteractionGridPoints(OBAMolecule& receptor,
MGrid& grid, double interactionDist,
double maxClusterDist,
unsigned minClusterPoints, double interactionPointRadius)
{
grid.clear();
//first construct a bounding box for the ligand while assembling a
//vector of atomic coordinates
BoundingBox ligandBox;
vector<AtomPoint> points;
points.reserve(mol.NumAtoms());
for (OBAtomIterator aitr = mol.BeginAtoms(); aitr != mol.EndAtoms(); ++aitr)
{
OBAtom* atom = *aitr;
points.push_back(AtomPoint(atom->x(), atom->y(), atom->z()));
ligandBox.update(atom->x(), atom->y(), atom->z());
}
ligandBox.extend(interactionDist);
//then identify all coordinates that are interacting
double idistSq = interactionDist * interactionDist;
OBMol& rmol = receptor.getMol();
for (OBAtomIterator aitr = rmol.BeginAtoms(); aitr != rmol.EndAtoms();
++aitr)
{
OBAtom* a = *aitr;
if (ligandBox.contains(a->x(), a->y(), a->z()))
{
for (unsigned i = 0, n = points.size(); i < n; i++)
{
if (points[i].distSq(a->x(), a->y(), a->z()) <= idistSq)
{
points[i].interactingCnt++;
}
}
}
}
//prune out non-interacting poitns
vector<AtomPoint> tmp;
tmp.reserve(points.size());
for (unsigned i = 0, n = points.size(); i < n; i++)
{
if (points[i].interactingCnt > 0)
tmp.push_back(points[i]);
}
points.swap(tmp);
tmp.clear();
//cluster these coordinates
vector<vector<unsigned> > clusters;
clusterPoints(points, maxClusterDist, clusters);
//make the cluster centers the interaction grid points
for (unsigned i = 0, n = clusters.size(); i < n; i++)
{
double xtot = 0, ytot = 0, ztot = 0;
unsigned npts = clusters[i].size();
if (npts >= minClusterPoints)
{
for (unsigned j = 0; j < npts; j++)
{
xtot += points[clusters[i][j]].x;
ytot += points[clusters[i][j]].y;
ztot += points[clusters[i][j]].z;
}
double xave = xtot / (double) npts;
double yave = ytot / (double) npts;
double zave = ztot / (double) npts;
grid.setPoint(xave, yave, zave);
if(interactionPointRadius > 0)
{
grid.markXYZSphere(xave,yave,zave,interactionPointRadius);
}
}
}
}
