Source code for schrodinger.structutils.interactions.ssbond

from schrodinger.infra import mm
from schrodinger.structutils.analyze import evaluate_asl


def get_disulfide_bonds(ct):
    """
    Find pairs of atoms involved in disulfide bonds.

    :param ct: structure
    :type  ct: Structure

    :return: list of pairs of bonded atom CYS sulfur atoms in provided ct
    :rtype: list[tuple(structure._StructureAtom, structure._StructureAtom)]
    """

    def bonded(atom1, atom2):
        """ Test if atom1 and atom2 are bonded """
        return mm.mmct_is_atom_bonded(ct, atom1, atom2) == mm.TRUE

    asl = "protein and a.pt SG and (res. CYS or res. CYX)"
    s_atoms = evaluate_asl(ct, asl)
    bond_list = []
    for atom1 in s_atoms:
        for atom2 in s_atoms:
            if atom1 < atom2 and bonded(atom1, atom2):
                bond_list.append((ct.atom[atom1], ct.atom[atom2]))

    return bond_list