configuration package

Submodules

api.ligand module

Module containing the Ligand class and the command line interface.

class api.ligand.Ligand(output_pdb_path, properties=None, **kwargs)[source]

Bases: object

Wrapper class for the PDB REST API. This class is a wrapper for the MMB PDB mirror.

Parameters:
  • output_pdb_path (str) – Path to the output PDB ligand file. File type: output. Sample file. Accepted formats: pdb.
  • properties (dic) –
    - ligand_code (str) - (“12D”) RSCB PDB ligand code.
    - remove_tmp (bool) - (True) [WF property] Remove temporal files.
    - restart (bool) - (False) [WF property] Do not execute if output files exist.
launch() → int[source]

Writes the PDB file content of the first ligand_code to output_pdb_path.

api.ligand.main()[source]

Command line interface.

api.pdb module

Module containing the Pdb class and the command line interface.

class api.pdb.Pdb(output_pdb_path, properties=None, **kwargs)[source]

Bases: object

Wrapper class for the PDB REST API. This class is a wrapper for the PDB download page.

Parameters:
  • output_pdb_path (str) –

    Path to the output PDB file. File type: output. Sample file. Accepted formats: pdb.

  • properties (dic) –
    - pdb_code (str) - (“1ubq”) RSCB PDB code.
    - filter (str) - ([“ATOM”, “MODEL”, “ENDMDL”]) Array of groups to be kept. If value is None or False no filter will be applied. All the possible values are defined in the official PDB specification (http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html)
    - url (str) - (“https://files.rcsb.org/download/”) URL of the PDB REST API. Another option for this parameter is the MMB PDB mirror API (“http://mmb.irbbarcelona.org/api/pdb/”).
    - remove_tmp (bool) - (True) [WF property] Remove temporal files.
    - restart (bool) - (False) [WF property] Do not execute if output files exist.
launch() → int[source]

Writes the PDB file content of the first pdb_code to output_pdb_path.

api.pdb.main()[source]

Command line interface.

api.pdb_variants module

MmbPdbVariants Module

class api.pdb_variants.MmbPdbVariants(output_mutations_list_txt, properties=None, **kwargs)[source]

Bases: object

Wrapper class for the MMB group UNIPROT REST API. This class is a wrapper for the UNIPROT mirror of the MMB PDB mirror.

Parameters:
  • output_mutations_list_txt (str) – Path to the TXT file containing an ASCII comma separated values of the mutations. File type: output. Accepted formats: txt.
  • properties (dic) –
    - pdb_code (str): (“2vgb”) RSCB PDB four letter code. ie: “2ki5”.
    - url (str) - (“https://files.rcsb.org/download/”) URL of the PDB REST API. Another option for this parameter is the MMB PDB mirror API (“http://mmb.irbbarcelona.org/api/pdb/”).
    - remove_tmp (bool) - (True) [WF property] Remove temporal files.
    - restart (bool) - (False) [WF property] Do not execute if output files exist.
launch() → int[source]

Writes the variants of the selected pdb_code to output_mutations_list_txt

api.pdb_variants.main()[source]

api.pdb_cluster_zip module

MmbPdbClusterZip Module

class api.pdb_cluster_zip.MmbPdbClusterZip(output_pdb_zip_path, properties=None, **kwargs)[source]

Bases: object

Wrapper class for the MMB PDB mirror.

Parameters:
  • output_pdb_zip_path (str) –

    Path to the ZIP or PDB file containing the output PDB files. File type: output. Sample file. Accepted formats: pdb, zip.

  • properties (dic) –
    - pdb_code (str) - (“2vgb”) RSCB PDB code. ie: “2VGB”
    - filter (str) - ([“ATOM”, “MODEL”, “ENDMDL”]) Array of groups to be kept. If value is None or False no filter will be applied. All the possible values are defined in the official PDB specification (http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html)
    - cluster (str) - (90) Cluster number for the biobb_io.api.MmbPdb.get_pdb_cluster_zip() method.
    - url (str) - (“https://files.rcsb.org/download/”) URL of the PDB REST API. Another option for this parameter is the MMB PDB mirror API (“http://mmb.irbbarcelona.org/api/pdb/”).
    - remove_tmp (bool) - (True) [WF property] Remove temporal files.
    - restart (bool) - (False) [WF property] Do not execute if output files exist.
launch() → int[source]

Writes each PDB file content of each pdb_code in the cluster to a pdb_file then creates a zip_file output_pdb_zip_path.

api.pdb_cluster_zip.main()[source]

api.drugbank module

Module containing the Drugbank class and the command line interface.

class api.drugbank.Drugbank(output_sdf_path, properties=None, **kwargs)[source]

Bases: object

Download a component in SDF format from the Drugbank.

Parameters:
  • output_sdf_path (str) –

    Path to the output SDF component file. File type: output. Sample file. Accepted formats: sdf.

  • properties (dic) –
    - drugbank_id (str) - (“DB00530”) Drugbank component id.
    - remove_tmp (bool) - (True) [WF property] Remove temporal files.
    - restart (bool) - (False) [WF property] Do not execute if output files exist.
launch() → int[source]

Writes the SDF content of the first drugbank_id to output_sdf_path.

api.drugbank.main()[source]

Command line interface.