ties.topology_superimposer

The main module responsible for the superimposition.

Functions

assign_coords_from_pdb(atoms, pdb_atoms)	Match the atoms from the ParmEd object based on a .pdb file and overwrite the coordinates from ParmEd. :param atoms: internal Atom representation (fixme: refer to it here in docu), will have their coordinates overwritten. :param pdb_atoms: atoms loaded with ParmEd with the coordinates to be used.
best_rmsd_match(suptops)
calculate_rmsd(atom_pairs)
extract_best_suptop(suptops, ignore_coords)
generate_nxg_from_list(atoms)	Helper function.
get_atoms_bonds_from_ac(ac_file)
get_atoms_bonds_from_mol2(ref_filename, ...)	Use Parmed to load the files.
get_largest(lists)	return a list of largest solutions
get_starting_configurations(left_atoms, ...)	Minimise the number of starting configurations to optimise the process speed.
is_mirror_of_one(suptop, suptops, ignore_coords)	"Mirror" in the sense that it is an alternative topological way to traverse the molecule.
log(*args)
long_merge(suptop1, suptop2)	Carry out a merge and apply all checks.
remove_candidates_subgraphs(...)
resolve_sup_top_multiple_match(sup_tops)
seen(suptop, suptops)
solve_one_combination(one_atom_species, ...)
solve_partial_overlaps(candidate_suptop, suptops)
sub_graph_of(candidate_suptop, suptops)
sup_top_correct_chirality(sup_tops, ...)
superimpose_topologies(top1_nodes, top2_nodes)	The main function that manages the entire process.

Classes

Atom(name, atom_type[, charge, use_general_type])
AtomPair(left_node, right_node)	An atom pair for networkx.
SuperimposedTopology([topology1, topology2, ...])	SuperimposedTopology contains in the minimal case two sets of nodes S1 and S2, which are paired together and represent a strongly connected component.