ample.util.process_models module¶

class CheckModelsResult[source]¶

single_ensemble¶

check_models(pdb_structures, results)[source]¶

Examine PDB files to determine their suitablilty for running with AMPLE.

check_models_dir(models_in_dir, models_out_dir)[source]¶

Examine a directory of PDB files to determine their suitability for running with AMPLE.

check_sequences_match(ref_data, seq_data, idx_pdb, chains_match_across_pdbs, multiple)[source]¶

Check whether chains with the same index across multiple pdbs have matching sequences.

extract_and_validate_models(amoptd)[source]¶

Extract models given to AMPLE from arguments in the amoptd and validate that they are suitable

Parameters:	amoptd (dict) – AMPLE options dictionary

handle_model_import(amoptd, results)[source]¶

Handle any errors flagged up by importing models and set any options based on the type of models.

single_chain_models_with_same_sequence(hierarchy)[source]¶

Return True if hierarchy contains sequence-identical single-chain models.

split_quark_alldecoy(alldecoy, directory)[source]¶

Split a single QUARK PDB with multiple models into individual PDB files

Parameters:	alldecoy (str) – Single QUARK PDB file with multiple model entries directory (str) – Directory to extract the PDB files to
Returns:	extracted_models – List of PDB files for all models
Return type:	list