schrodinger.application.desmond.fep_fragment

Module fep_fragment_group

Classes

FragmentGroup
Groups of mutating fragments, that attach to at least one common core atom

Functions

find_connnected_atoms(atom_idx, fragment, ct)
find all atom a in fragment that is connected to atom_idx atom_idx: atom index fragment: list of atom indices ct: structure return list of atom indices in fragment that is connected to atom_idx

group_connected_atoms(atoms, ct)
group connected atom in to lists of lists atoms: atom indices ct: structure return: list of sets, each atom list is a connected fragment

find_connected_fragments(atom_index, fragment_list, ct)
find all connected fragments to given atom_index

generate_connection_points(source_att, source_bridge_list, dest_att, dest_bridge_list)
source_att: source core atom index source_bridge_list: list of atoms in source fragment that is attached to source core atom dest_att: dest core atom index dest_bridge_list: list of atoms in dest fragment that is attached to source core atom return: list of attachment points ((sa, ab), (da, db) ...)

register_att_point_fragmentgroup(att_point_in_frag_group, att, conn_atoms, group_id, frag_id)
store the group_id and frag_id for attachment point att_point_in_frag_group: dictionary keyed by att_point atom pair, input and output att: core atom attachment point conn_atoms: atom is fragment bonded to att group_id: index to fragmentgroup group_id: index to fragment within a fragment group

update_visted_fragments(frag_visited, frag_id, other_frag_id, anchor_atom, connected_atoms)
update visted fragments, add other_id to list of other fragments, add attachment points frag_visited: input and output dictionary for visited fragments frag_id: id of fragment other_frag_id: id of fragment sharing anchor atom anchor_atom: anchor atom index connected_atoms: all atoms connected to the anchor atom return: Nothing

find_all_related_fragments(source_frag_id, source_frag_visited, dest_frag_visited)
find all fragments in both source and dest cts that share attachment point source_frag_id: source fragment input - hash index into source_frag_visited source_frag_visited: source fragment attachment information dest_frag_visited: dest fragment attachment information return: [sets of source fragment ids, sets of dest fragment ids]

get_mutating_fragment_groups(source_core_atoms, dest_core_atoms, source_ct, dest_ct)
given matched source and dest core atoms, cts, find all fragment groups sharing attachment anchor atoms in the core.

Variables

[hide private]

__package__ = 'schrodinger.application.desmond'

Function Details

[hide private]

get_mutating_fragment_groups(source_core_atoms, dest_core_atoms, source_ct, dest_ct)


given matched source and dest core atoms, cts, find all fragment groups sharing
    attachment anchor atoms in the core.  Two dictionaries keyed by
    source and dest attachment points are also returned to locate attachmen point
    in which fragment of which fragment group
source_core_atoms: lists of core atoms for initial molecule
dest_core_atoms: lists of core atoms for initial molecule
source_ct: structure of initial molecule
dest_ct: structure of final molecule
return: (lists FragmentGroup objects,
         dictionary of tuples (group number, source fragment number)
                    keyed by source attachment points,
         dictionary of tuples (group number, dest fragment number)
                    keyed by source attachment points,