Source code for schrodinger.ui.sketcher_extensions

from schrodinger.forcefield import OPLSVersion
from schrodinger.structutils import minimize
from schrodinger.thirdparty import rdkit_adapter

CONSTRAINT_FORCE_CONSTANT = 200.0
COORDINATES_LIMIT = 10000000.0


def get_2D_structure(sketcher):
    """
    :param sketcher: given sketcher instance
    :return: extracted Structure object with sketcher-generated 2D coordinates
    """
    rdmol = sketcher.getRDKitStructure()
    return rdkit_adapter.from_rdkit(rdmol)


def get_3D_structure(sketcher):
    """
    :param sketcher: given sketcher instance
    :return: extracted Structure object with sketcher-generated 3D coordinates
    :raises RuntimeError: if 3D coordinates are not available
    """
    rdmol = sketcher.getRDKitStructure()
    if rdmol.GetNumConformers() < 2:
        raise RuntimeError("No 3D coordinates available")

    # 3D coordinates should be in the second conformer
    st = rdkit_adapter.from_rdkit(rdmol, conformer=1)

    # mmffld minization has a hard time with many atoms overlapping
    # at the same position; update atoms with invalid coordinates
    # to the 2D coordinates generated by the sketcher, and freeze all others
    fixed_atom_indices = []
    st_2d = get_2D_structure(sketcher)
    for atom in st.atom:
        if any(c > COORDINATES_LIMIT for c in (atom.x, atom.y, atom.z)):
            atom.xyz = st_2d.atom[atom.index].xyz
        else:
            fixed_atom_indices.append(atom.index)

    if len(fixed_atom_indices) == st.atom_total:
        return st

    minimizer = minimize.Minimizer(ffld_version=OPLSVersion.F16,
                                   struct=st,
                                   honor_pbc=False,
                                   nonbonded_cutoff=10.0)
    for index in fixed_atom_indices:
        minimizer.addPosRestraint(index,
                                  force_constant=CONSTRAINT_FORCE_CONSTANT)
    minimizer.minimize()

    return st


def set_structure(sketcher, st):
    """
    :param sketcher: given sketcher instance
    :param st: Structure to set into the sketcher
    """
    rdmol = rdkit_adapter.to_rdkit(st, implicitH=True, sanitize=False)
    sketcher.clearStructure()
    sketcher.setStructure(rdmol)