swamp.mr.searchmodel module

class SearchModel(id, ensemble_code, workdir, ermsd=0.1, nsearch=1, disable_check=True, mod='unmod', model='ensemble', pdb_fname_input=None, logger=None)

Bases: abc.ABC

Class with methods to prepare the search model before MR and data structures to keep all useful information

Parameters:

• workdir (str) – working directory where the search model will be prepared
• id (str) – unique identifier for the search model to be added
• ensemble_code (str) – the ensemble’s SWAMP library id to be used as search model
• ermsd (float) – the eRMSD to be used with phaser to place the search model (default 0.1)
• nsearch (int) – number of copies to search with phaser
• disable_check (bool) – passed to phaser.InputMR_AUTO.setENSE_DISA_CHEC (default True)
• mod (str) – indicate how to prepare the search model (default ‘unmod’)
• model (str) – indicate if the search model is an ensemble or a centroid (default ‘ensemble’)
• logger (SwampLogger) – logging interface for the MR pipeline (default None)

Variables:

• error (bool) – if True an error has occurred while preparing the search model
• modified_model_list (list) – a list with the file names of the modified models to be merged into the new ensemble

create_pdbfile()

Create the pdb file to be used as a search model on run

static extract_core(pdbout, workdir, model_list)

Extract the core structural alignment of a given ensemble

Parameters:

• pdbout (str) – the pdb file name of the resulting ensemble to output
• workdir (str) – the working directory where temporary files will be created
• model_list (list) – a list with the pdb file names of the models that make the ensemble

idealhelix_fname

File name of the ideal helix to be used to extend the solution

model_dir

Directory with the models that formed the original search model (if it was an ensemble)

model_list

A list with all the models in the original search model

modified_pdbfname

The file name of the search model after running prepare()

pdbfname

The PDB file name of the search model

phaser_info

A dictionary with all the information necessary to use with add_searchmodel()

prepare()

Prepare the pdbfname with the searchmodel using the indicated mod before MR

static split_models(pdbin, directory, strip_hetatm=True)

Method to split an ensemble into its model components

Parameters:

• pdbin (str) – input pdb file name
• directory (str) – directory where the models of the ensemble will be dumped
• strip_hetatm (bool) – if set, the hetatm will be ommited from the output models (default True)

Returns:

a list with the output file names listed (list)

static transfer_flags_pdb(pdb_ref, pdb_file, flags_to_transfer=('CRYST1', 'SCALE', 'REMARK'), overwrite=True)

Transfer PDB flags between two given pdb files

Parameters:

• pdb_ref (str) – pdb file with the reference flags to be transferred
• pdb_file (str) – pdb file where the flags will be transferred
• flags_to_transfer (tuple) – set of flags that need to be transferred
• overwrite (bool) – if False, pdb_file original flags will be kept (default True)

static truncate_polyALA(pdbin, pdbout)

Method to truncate a given pdb into poly-ala

Parameters:

• pdbin (str) – input pdb file name
• pdbout (str) – output pdb file name