simbad.command_line.simbad_database module¶

Script to download or update SIMBAD-related databases

class ContaminantSearchResult(pdb_code, space_group, uniprot_name, uniprot_mnemonic)[source]¶

Bases: object

A basic contabase storing class

pdb_code¶

space_group¶

uniprot_mnemonic¶

uniprot_name¶

create_contaminant_db(database, add_morda_domains, nproc=2, submit_qtype=None, submit_queue=False)[source]¶

Create a contaminant database

Parameters:	database : str The path to the database folder add_morda_domains : bool Retrospectively add morda domains to a contaminant database updated when morda was not installed nproc : int, optional The number of processors [default: 2] submit_qtype : str The cluster submission queue type - currently support SGE and LSF submit_queue : str The queue to submit to on the cluster
Raises:	RuntimeError dimple.contaminants.prepare module not available RuntimeError Windows is currently not supported

create_db_argparse()[source]¶

Argparse function database creationg

create_db_custom(custom_db, database)[source]¶

Create custom database

Parameters:	custom_db : str The path to the input database of PDB files database : str The path to the output database folder
Raises:	RuntimeError Windows is currently not supported

create_lattice_db(database)[source]¶

Create a lattice search database

Parameters:	database : str The path to the database file

create_morda_db(database, nproc=2, submit_qtype=None, submit_queue=False, chunk_size=5000)[source]¶

Create the MoRDa search database

Parameters:	database : str The path to the database folder nproc : int, optional The number of processors [default: 2] submit_qtype : str The cluster submission queue type - currently support SGE and LSF submit_queue : str The queue to submit to on the cluster chunk_size : int, optional The number of jobs to submit at the same time [default: 5000]
Raises:	RuntimeError Windows is currently not supported

download_morda()[source]¶

Download the MoRDa database

Returns:	str The path to the downloaded MoRDa database

is_valid_db_location(database)[source]¶

Validate permissions for a database

leave_timestamp(f)[source]¶

Write the current date & time to a file

main()[source]¶

SIMBAD database creation function

validate_compressed_database(dir)[source]¶

Validate an installation of a SIMBAD database