示例#1
0
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;
  }
}
示例#2
0
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;
  }
}