ties.Pair

class ties.Pair(ligA, ligZ, config=None, **kwargs)[source]

Facilitates the creation of morphs. It offers functionality related to a pair of ligands (a transformation).

Parameters:

  • ligA (Ligand or string) – The ligand to be used as the starting state for the transformation.

  • ligZ (Ligand or string) – The ligand to be used as the ending point of the transformation.

  • config (Config) – The configuration object holding all settings.

__init__(ligA, ligZ, config=None, **kwargs)[source]

Please use the Config class for the documentation of the possible kwargs. Each kwarg is passed to the config class.

fixme - list all relevant kwargs here

param ligand_net_charge: integer, net charge of each ligand (has to be the same)

Methods

__init__(ligA, ligZ[, config])

Please use the Config class for the documentation of the possible kwargs.

check_json_file()

Performance optimisation in case TIES is rerun again.

make_atom_names_unique([out_ligA_filename, ...])

Ensure that each that atoms across the two ligands have unique names.

merge_frcmod_files([ligcom])

Merges the .frcmod files generated for each ligand separately, simply by adding them together.

overlap_fractions()

Calculate the size of the common area.

set_distance(value)

set_suptop(suptop, parmed_ligA, parmed_ligZ)

Attach a SuperimposedTopology object along with the ParmEd objects for the ligA and ligZ.

superimpose(**kwargs)

Please see Config class for the documentation of kwargs.