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.
cluster_script
(amoptd, python_path=’ccp4-python’)[source]¶Create the script for ensembling on a cluster
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cluster_table_data
(clusters, cluster_num, side_chain_treatments, header=True)[source]¶Generate a table containing the cluster data
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collate_cluster_data
(ensembles_data)[source]¶Collate the cluster data into a dictionary structure
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create_ensembles
(amoptd)[source]¶Create the ensembles using the values in the amoptd dictionary
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ensemble_summary
(ensembles_data)[source]¶Print a summary of the ensembling process
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ensembler_factory
(amoptd)[source]¶Return an ensembler object for the required ensembles
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import_ensembles
(amoptd)[source]¶Import ensembles using their file paths
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reorder_models
(models, ordered_list_file)[source]¶Reorder the list of models from a list of models (possibly in a different directory)
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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.
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