подсказка про лиганд в гомологичном моделировании

Added by Andrey Golovin over 6 years ago

ищем modlib/modeller/automodel/automodel.py
там есть что-то такое:

    def nonstd_restraints(self, aln):
        """Create restraints on HETATM and BLK residues.""" 
        # Select all HETATM residues plus any ATOM residues that have
        # no defined topology (generally speaking, BLK residues)
        allatoms = selection(self)
        selhet = allatoms.only_het_residues() | allatoms.only_no_topology()

        rsrgrp = physical.xy_distance
        self.het_std_restraints(aln, selhet, 10.0, 2.3, rsrgrp)
        self.het_het_restraints(aln, selhet, 7.0, 2.3, rsrgrp)
        self.het_internal_restraints(aln, selhet, rsrgrp)

    def het_std_restraints(self, aln, selhet, ca_distance, bond_distance,
        """Constrain each atom in a HETATM or BLK residue by its distance to all
           protein atoms within C{bond_distance} (these interactions are also
           removed from the nonbonded list) and also less strongly to all
           protein CA atoms that are within C{ca_distance}. The former
           maintains any protein-HETATM bonding, and the latter maintains
           the residue in roughly the right position.""" 


осталось перезадать некоторые функции :)