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; } }
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; } }