schrodinger.application.desmond.int_match.AlchemicalInteractions

Class AlchemicalInteractions

Dictionaries for matched, unmatched and to be deleted interactions Atom is keyed by "m", "wt_dummy" and "mut_dummy" Each of the bond, angle, dihe, impt, pair and excl is a dictionary with keys: m: matched interactions unmatched: interactions that cannot be matched in the other molecule keep: interactions involving dummy atoms and they are kept in non-interacting state dela: interactions that need to be turned off in non-interacting state because there are dummy atoms involved del: interactions that is deleted because a bond is cleaved in non-interacting state delc: interactions that need to be turned off because a bond between core atoms is missing in the other molecule, not used for pair and excl Restraint dictionaries are keyed only by "wt" and "mut"

Instance Methods

[hide private]

__init__(self, incl_param=True)

print_all(self)

print_1(self, dict)

update_atoms(self, wt_core, mut_core, frag_groups)
Generate core, dummy atom lists wt_core: list of core atoms in 1st molecule mut_core: list core atoms in 2nd molecule frag_groups: list of FragmentGroup objects

update_bonds(self, bond_match, wt_param, mut_param)
Generate un/matched and to be deleted lists for bond

update_angles(self, angle_match, wt_param, mut_param, wt_angles_kept, mut_angles_kept, wt_angle_delete_att, mut_angle_delete_att)
Generate un/matched and to be deleted lists for bond

update_restraints(self, wt_dihe_rest, mut_dihe_rest, wt_impt_rest, mut_impt_rest)
Generate lists of restraints because of some atoms are turned into dummies

update_conf_restraints(self, wt_dihe_rest, mut_dihe_rest)
dihedral restraint for decoupled stages because some bonds are deleted

update_bonds(self, bond_match, wt_param, mut_param)

Generate un/matched and to be deleted lists for bond

bond_match: MatchedInteractions object for bond wt_param: dictionary of parameters keyed by bonds mut_param: dictionary of parameter keyed by bonds

update_angles(self, angle_match, wt_param, mut_param, wt_angles_kept, mut_angles_kept, wt_angle_delete_att, mut_angle_delete_att)

Generate un/matched and to be deleted lists for bond

angle_match: MatchedInteractions object for angle wt_param: dictionary of parameters keyed by angles mut_param: dictionary of parameter keyed by angles wt_angles_kept: angles involving dummy atoms to be kept in decoupled state for initial molecule mut_angles_kept: angles involving dummy atoms to be kept in decoupled state for final molecule wt_angle_delete_att: angles need to be turned off in decoupled state for initial molecule mut_angle_delete_att: angles need to be turned off in decoupled state for final molecule

update_restraints(self, wt_dihe_rest, mut_dihe_rest, wt_impt_rest, mut_impt_rest)

Generate lists of restraints because of some atoms are turned into dummies

wt_dihe_rest: input dihedral restraints for initial molecule mut_dihe_rest: input dihedral restraints for final molecule wt_impt_rest: input improper restraints for initial molecule mut_impt_rest: input improper restraints for final molecule

update_conf_restraints(self, wt_dihe_rest, mut_dihe_rest)

dihedral restraint for decoupled stages because some bonds are deleted

wt_dihe_rest: input restraint terms for initial molecule mut_dihe_rest: input restraint terms for final molecule