void setDihedralRad(Conformer &conf, unsigned int iAtomId, unsigned int jAtomId,
unsigned int kAtomId, unsigned int lAtomId, double value) {
RDGeom::POINT3D_VECT &pos = conf.getPositions();
URANGE_CHECK(iAtomId, pos.size());
URANGE_CHECK(jAtomId, pos.size());
URANGE_CHECK(kAtomId, pos.size());
URANGE_CHECK(lAtomId, pos.size());
ROMol &mol = conf.getOwningMol();
Bond *bondIJ = mol.getBondBetweenAtoms(iAtomId, jAtomId);
if (!bondIJ) 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");
Bond *bondKL = mol.getBondBetweenAtoms(kAtomId, lAtomId);
if (!bondKL) throw ValueErrorException("atoms k and l must be bonded");
if (queryIsBondInRing(bondJK))
throw ValueErrorException("bond (j,k) must not belong to a ring");
RDGeom::Point3D rIJ = pos[jAtomId] - pos[iAtomId];
double rIJSqLength = rIJ.lengthSq();
if (rIJSqLength <= 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");
RDGeom::Point3D rKL = pos[lAtomId] - pos[kAtomId];
double rKLSqLength = rKL.lengthSq();
if (rKLSqLength <= 1.e-16)
throw ValueErrorException("atoms k and l have identical 3D coordinates");
RDGeom::Point3D nIJK = rIJ.crossProduct(rJK);
double nIJKSqLength = nIJK.lengthSq();
RDGeom::Point3D nJKL = rJK.crossProduct(rKL);
double nJKLSqLength = nJKL.lengthSq();
RDGeom::Point3D m = nIJK.crossProduct(rJK);
// we only need to rotate by delta with respect to the current dihedral value
value -= -atan2(m.dotProduct(nJKL) / sqrt(nJKLSqLength * m.lengthSq()),
nIJK.dotProduct(nJKL) / sqrt(nIJKSqLength * nJKLSqLength));
// our rotation axis is the (j,k) bond
RDGeom::Point3D &rotAxisBegin = pos[jAtomId];
RDGeom::Point3D &rotAxisEnd = pos[kAtomId];
RDGeom::Point3D rotAxis = rotAxisEnd - rotAxisBegin;
rotAxis.normalize();
// get all atoms bonded to k 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;
}
}
RDGeom::Point3D computeCentroid(const Conformer &conf, bool ignoreHs) {
RDGeom::Point3D res(0.0, 0.0, 0.0);
const ROMol &mol = conf.getOwningMol();
ROMol::ConstAtomIterator cai;
unsigned int nAtms = 0;
for (cai = mol.beginAtoms(); cai != mol.endAtoms(); cai++) {
if (((*cai)->getAtomicNum() == 1) && (ignoreHs)) {
continue;
}
res += conf.getAtomPos((*cai)->getIdx());
nAtms++;
}
res /= nAtms;
return res;
}
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;
}
}
void EncodeShape(const Conformer &conf, RDGeom::UniformGrid3D &grid,
const RDGeom::Transform3D *trans, double vdwScale,
double stepSize, int maxLayers, bool ignoreHs) {
const ROMol &mol = conf.getOwningMol();
ROMol::ConstAtomIterator ai;
double rad;
unsigned int aid, anum;
for (ai = mol.beginAtoms(); ai != mol.endAtoms(); ai++) {
anum = (*ai)->getAtomicNum();
if ((anum == 1) && (ignoreHs)) { //ignore hydrigens
continue;
}
aid = (*ai)->getIdx();
RDGeom::Point3D loc = conf.getAtomPos(aid);
rad = PeriodicTable::getTable()->getRvdw(anum);
if (trans) {
trans->TransformPoint(loc);
}
grid.setSphereOccupancy(loc, vdwScale*rad, stepSize, maxLayers);
}
}
void setBondLength(Conformer &conf,
unsigned int iAtomId, unsigned int jAtomId, double value) {
RDGeom::POINT3D_VECT &pos = conf.getPositions();
RANGE_CHECK(0, iAtomId, pos.size() - 1);
RANGE_CHECK(0, jAtomId, pos.size() - 1);
ROMol &mol = conf.getOwningMol();
Bond *bond = mol.getBondBetweenAtoms(iAtomId, jAtomId);
if(!bond) throw ValueErrorException("atoms i and j must be bonded");
if(queryIsBondInRing(bond)) throw ValueErrorException("bond (i,j) must not belong to a ring");
RDGeom::Point3D v = pos[iAtomId] - pos[jAtomId];
double origValue = v.length();
if(origValue <= 1.e-8) throw ValueErrorException("atoms i and j have identical 3D coordinates");
// get all atoms bonded to j
std::list<unsigned int> alist;
_toBeMovedIdxList(mol, iAtomId, jAtomId, alist);
v *= (value / origValue - 1.);
for (std::list<unsigned int>::iterator it = alist.begin(); it != alist.end(); ++it) {
pos[*it] -= v;
}
}
