double getAngleRad(Conformer &conf,
unsigned int iAtomId, unsigned int jAtomId, unsigned int kAtomId) {
RDGeom::POINT3D_VECT &pos = conf.getPositions();
RANGE_CHECK(0, iAtomId, pos.size() - 1);
RANGE_CHECK(0, jAtomId, pos.size() - 1);
RANGE_CHECK(0, kAtomId, pos.size() - 1);
RDGeom::Point3D rJI = pos[iAtomId] - pos[jAtomId];
double rJISqLength = rJI.lengthSq();
if(rJISqLength <= 1.e-16) throw ValueErrorException("atoms i and j have identical 3D coordinates");
RDGeom::Point3D rJK = pos[kAtomId] - pos[jAtomId];
double rJKSqLength = rJK.lengthSq();
if(rJKSqLength <= 1.e-16) throw ValueErrorException("atoms j and k have identical 3D coordinates");
return rJI.angleTo(rJK);
}
void setAngleRad(Conformer &conf, unsigned int iAtomId, unsigned int jAtomId,
unsigned int kAtomId, double value) {
RDGeom::POINT3D_VECT &pos = conf.getPositions();
URANGE_CHECK(iAtomId, pos.size());
URANGE_CHECK(jAtomId, pos.size());
URANGE_CHECK(kAtomId, pos.size());
ROMol &mol = conf.getOwningMol();
Bond *bondJI = mol.getBondBetweenAtoms(jAtomId, iAtomId);
if (!bondJI) throw ValueErrorException("atoms i and j must be bonded");
Bond *bondJK = mol.getBondBetweenAtoms(jAtomId, kAtomId);
if (!bondJK) throw ValueErrorException("atoms j and k must be bonded");
if (queryIsBondInRing(bondJI) && queryIsBondInRing(bondJK))
throw ValueErrorException(
"bonds (i,j) and (j,k) must not both belong to a ring");
RDGeom::Point3D rJI = pos[iAtomId] - pos[jAtomId];
double rJISqLength = rJI.lengthSq();
if (rJISqLength <= 1.e-16)
throw ValueErrorException("atoms i and j have identical 3D coordinates");
RDGeom::Point3D rJK = pos[kAtomId] - pos[jAtomId];
double rJKSqLength = rJK.lengthSq();
if (rJKSqLength <= 1.e-16)
throw ValueErrorException("atoms j and k have identical 3D coordinates");
// we only need to rotate by delta with respect to the current angle value
value -= rJI.angleTo(rJK);
RDGeom::Point3D &rotAxisBegin = pos[jAtomId];
// our rotation axis is the normal to the plane of atoms i, j, k
RDGeom::Point3D rotAxisEnd = rJI.crossProduct(rJK) + pos[jAtomId];
RDGeom::Point3D rotAxis = rotAxisEnd - rotAxisBegin;
rotAxis.normalize();
// get all atoms bonded to j and loop through them
std::list<unsigned int> alist;
_toBeMovedIdxList(mol, jAtomId, kAtomId, alist);
for (std::list<unsigned int>::iterator it = alist.begin(); it != alist.end();
++it) {
// translate atom so that it coincides with the origin of rotation
pos[*it] -= rotAxisBegin;
// rotate around our rotation axis
RDGeom::Transform3D rotByAngle;
rotByAngle.SetRotation(value, rotAxis);
rotByAngle.TransformPoint(pos[*it]);
// translate atom back
pos[*it] += rotAxisBegin;
}
}
bool isLinearArrangement(const RDGeom::Point3D &v1, const RDGeom::Point3D &v2,
double tol = 0.035) { // tolerance of 2 degrees
return fabs(v2.angleTo(v1) - M_PI) < tol;
}