fast_forward.universe_handler module

class fast_forward.universe_handler.Residue(resname, resid)[source]

Bases: object

Helper class for a residue.

class fast_forward.universe_handler.ResidueIter[source]

Bases: object

Helper class mimicking to iterate over the residues of an mdanlaysis universe.

add_residue(resname, resid)[source]
res_iter()[source]
class fast_forward.universe_handler.UniverseHandler(mol_names, *args, **kwargs)[source]

Bases: Universe

Wrapper around mda.Universe which allows for some smart selections and exposes some useful properties.

generate_molecule_graphs()[source]

Generate molecular graphs from the topology information. The molecular graphs contain the elements, bond order, and if the molecule is aromatic or charged.

mass_to_element(mass)[source]
property molecule_graphs
property n_atoms
property n_residues
pbc_complete()[source]
res_iter()[source]
property resids
shift_united_atom_carbons(association_dict)[source]

Given an atomgroup shift it’s coordinates to where the center of geometry would be if hydrogens were included.

fast_forward.universe_handler.res_as_mol(universe)[source]

For a universe without moltype/molnum info, promotes residues to molecules.

Changes universe in place. Does nothing if moltype/molnum info is already available.