Ensembler module for ab initio decoys
AbinitioEnsembler(**kwargs)[source]¶Bases: ample.ensembler._ensembler.Ensembler
Ensemble creator using on multiple models with identical sequences most likely created using Rosetta or Quark ab initio modelling
Methods
cluster_models([models, cluster_method, …]) |
Wrapper function to run clustering of models dependent on the method |
edit_side_chains(raw_ensemble[, …]) |
Mutate side chains for the supplied all-atom ensembles |
generate_ensembles_from_amoptd(models, amoptd) |
Generate ensembles from data in supplied ample data dictionary. |
parse_cluster_method(cluster_method) |
Return the cluster_method_type, cluster_score_type, cluster_exe from a generic cluster_method |
scwrl_models(models, work_dir, scwrl_exe) |
Add side chains to the models with Scwrl |
subclusterer_factory(subcluster_program) |
Return an instantiated subclusterer based on the given program |
| ensemble_from_subcluster | |
| generate_ensembles | |
| subcluster_models | |
| subcluster_models_fixed_radii | |
| subcluster_models_floating_radii | |
| superpose_models |
cluster_models(models=None, cluster_method=’spicker’, num_clusters=1, cluster_dir=None, max_cluster_size=200)[source]¶Wrapper function to run clustering of models dependent on the method
generate_ensembles(models, cluster_dir=None, cluster_method=None, ensembles_directory=None, ensemble_max_models=None, num_clusters=None, percent_truncation=None, side_chain_treatments=[‘polyAla’], subcluster_radius_thresholds=[1, 3], subcluster_program=None, truncation_method=None, truncation_pruning=None, use_scwrl=False)[source]¶generate_ensembles_from_amoptd(models, amoptd)[source]¶Generate ensembles from data in supplied ample data dictionary.
parse_cluster_method(cluster_method)[source]¶Return the cluster_method_type, cluster_score_type, cluster_exe from a generic cluster_method
subcluster_models(truncation, subcluster_program=None, radius_thresholds=None, ensemble_max_models=None)[source]¶subcluster_models_fixed_radii(truncation, subcluster_program=None, ensemble_max_models=None, radius_thresholds=None)[source]¶