Ensembler subpackage¶

The AMPLE ensembler sub-package

This sub-package contains the source to apply AMPLE’s cluster-and-truncate approach to protein structure models. It contains a series of different modules to apply varying cluster and truncation algorithms to those models.

add_argparse_options(parser=None)[source]¶

Function to add the ensemble-specific options

Parameters:	parser : argparse.ArgumentParser standalone : bool, optional Define if the parser is standalone [default: False]

cluster_script(amoptd, python_path=’ccp4-python’)[source]¶

Create the script for ensembling on a cluster

Parameters:	amoptd : dict An AMPLE option dictionary python_path : str, optional The path to the CCP4 python executable
Returns:	str The path to the cluster script

cluster_table_data(clusters, cluster_num, side_chain_treatments)[source]¶

Generate a table containing the cluster data

Parameters:	clusters : list, tuple A list of cluster dictionaries cluster_num : int The cluster number of interest side_chain_treatments : list, tuple A list of side chain treatments
Returns:	list A list of table data lines

collate_cluster_data(ensembles_data)[source]¶

Collate the cluster data into a dictionary structure

Parameters:	ensembles_data : list, tuple A list of ensembles’ data dictionaries
Returns:	A dictionary with the collated data

create_ensembles(amoptd)[source]¶

Create the ensembles using the values in the amoptd dictionary

Parameters:	amoptd : dict An AMPLE option dictionary

ensemble_summary(ensembles_data)[source]¶

Print a summary of the ensembling process

Parameters:	ensembles_data : list, tuple A list of ensembles’ data dictionaries
Returns:	str

ensembler_factory(amoptd)[source]¶

Return an ensembler object for the required ensembles

Parameters:	amoptd : dict An AMPLE option dictionary
Returns:	:obj:`HomologEnsembler`, :obj:`SingleModelEnsembler`, or :obj:`AbinitioEnsembler` Instantiated ensembler object

import_ensembles(amoptd)[source]¶

Import ensembles using their file paths

Parameters:	amoptd : dict An AMPLE option dictionary
Returns:	list A list of absolute files paths of the ensembles

reorder_models(models, ordered_list_file)[source]¶

Reorder the list of models from a list of models (possibly in a different directory)

Parameters:	models : list, tuple A list of model file paths ordered_list_file : str The path to a file with a model order list
Returns:	list The model list reordered

set_phaser_rms_from_subcluster_score(optd)[source]¶

Set the phaser_rms for each ensemble based on its score

sort_ensembles(ensemble_pdbs, ensembles_data=None, keys=None, prioritise=True)[source]¶

Sort AMPLE ensemble data.

Parameters:	ensemble_pdbs: list, tuple A list of ensemble file paths ensembles_data : list, tuple, optional A list of ensembles’ data dictionaries keys : list, tuple, optional A list of keys in ensembles_data by which we sort. The key order must be high > middle > low! prioritise : bool, optional Favour ensembles in truncation level 20-50% [default: True]
Returns:	list A sorted list of the ensemble pdb file paths
Raises:	RuntimeError Not enough ensembles provided