configuration package

Submodules

api.alphafold module

Module containing the AlphaFold class and the command line interface.

class api.alphafold.AlphaFold(output_pdb_path, properties=None, **kwargs)[source]

Bases: biobb_common.generic.biobb_object.BiobbObject

biobb_io AlphaFold
This class is a wrapper for downloading a PDB structure from the AlphaFold Protein Structure Database.
Wrapper for the AlphaFold Protein Structure Database for downloading a single PDB structure from its corresponding Uniprot code.
Parameters:
  • output_pdb_path (str) – Path to the output PDB file. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).
  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
    • uniprot_code (str) - (None) Uniprot code.
    • remove_tmp (bool) - (True) [WF property] Remove temporal files.
    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_io.api.alphafold import alphafold
prop = {
    'uniprot_code': 'P00489'
}
alphafold(output_pdb_path='/path/to/newStructure.pdb',
    properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

launch() → int[source]

Execute the AlphaFold api.alphafold.AlphaFold object.

api.alphafold.alphafold(output_pdb_path: str, properties: dict = None, **kwargs) → int[source]

Execute the AlphaFold class and execute the launch() method.

api.alphafold.main()[source]

Command line execution of this building block. Please check the command line documentation.

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: biobb_common.generic.biobb_object.BiobbObject

biobb_io Drugbank
This class is a wrapper for the Drugbank REST API.
Download a single component in SDF format from the Drugbank REST API.
Parameters:
  • output_sdf_path (str) –

    Path to the output SDF component file. File type: output. Sample file. Accepted formats: sdf (edam:format_3814).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
    • drugbank_id (str) - (None) Drugbank component id.
    • remove_tmp (bool) - (True) [WF property] Remove temporal files.
    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_io.api.drugbank import drugbank
prop = {
    'drugbank_id': 'DB00530'
}
drugbank(output_sdf_path='/path/to/newComponent.sdf',
        properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

launch() → int[source]

Execute the Drugbank api.drugbank.Drugbank object.

api.drugbank.drugbank(output_sdf_path: str, properties: dict = None, **kwargs) → int[source]

Execute the Drugbank class and execute the launch() method.

api.drugbank.main()[source]

Command line execution of this building block. Please check the command line documentation.

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: biobb_common.generic.biobb_object.BiobbObject

biobb_io Ligand
This class is a wrapper for downloading a PDB ligand from the Protein Data Bank.
Wrapper for the Protein Data Bank in Europe and the MMB PDB mirror for downloading a single PDB ligand.
Parameters:
  • output_pdb_path (str) –

    Path to the output PDB ligand file. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
    • ligand_code (str) - (None) RSCB PDB ligand code.
    • api_id (str) - (“pdbe”) Identifier of the PDB REST API from which the PDB structure will be downloaded. Values: pdbe (PDB in Europe REST API), mmb (MMB PDB mirror API).
    • remove_tmp (bool) - (True) [WF property] Remove temporal files.
    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_io.api.ligand import ligand
prop = {
    'ligand_code': 'CPB',
    'api_id': 'pdbe'
}
ligand(output_pdb_path='/path/to/newLigand.pdb',
        properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

launch() → int[source]

Execute the Ligand api.ligand.Ligand object.

api.ligand.ligand(output_pdb_path: str, properties: dict = None, **kwargs) → int[source]

Execute the Ligand class and execute the launch() method.

api.ligand.main()[source]

Command line execution of this building block. Please check the command line documentation.

api.memprotmd_sim module

Module containing the MemProtMDSim class and the command line interface.

class api.memprotmd_sim.MemProtMDSim(output_simulation, properties=None, **kwargs)[source]

Bases: biobb_common.generic.biobb_object.BiobbObject

biobb_io MemProtMDSim
This class is a wrapper of the MemProtMD to download a simulation using its REST API.
Wrapper for the MemProtMD DB REST API to download a simulation.
Parameters:
  • output_simulation (str) –

    Path to the output simulation in a ZIP file. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
    • pdb_code (str) - (None) RSCB PDB code.
    • remove_tmp (bool) - (True) [WF property] Remove temporal files.
    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_io.api.memprotmd_sim import memprotmd_sim
prop = {
    'pdb_code': '2VGB'
}
memprotmd_sim(output_simulation='/path/to/newSimulation.zip',
            properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

launch() → int[source]

Execute the MemProtMDSim api.memprotmd_sim.MemProtMDSim object.

api.memprotmd_sim.main()[source]

Command line execution of this building block. Please check the command line documentation.

api.memprotmd_sim.memprotmd_sim(output_simulation: str, properties: dict = None, **kwargs) → int[source]

Execute the MemProtMDSim class and execute the launch() method.

api.memprotmd_sim_list module

Module containing the MemProtMDSimList class and the command line interface.

class api.memprotmd_sim_list.MemProtMDSimList(output_simulations, properties=None, **kwargs)[source]

Bases: biobb_common.generic.biobb_object.BiobbObject

biobb_io MemProtMDSimList
This class is a wrapper of the MemProtMD to get all available membrane-protein systems from its REST API.
Wrapper for the MemProtMD DB REST API to get all available membrane-protein systems (simulations).
Parameters:
  • output_simulations (str) –

    Path to the output JSON file. File type: output. Sample file. Accepted formats: json (edam:format_3464).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
    • remove_tmp (bool) - (True) [WF property] Remove temporal files.
    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_io.api.memprotmd_sim_list import memprotmd_sim_list
prop = { }
memprotmd_sim_list(output_simulations='/path/to/newSimulationList.json',
                    properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

launch() → int[source]

Execute the MemProtMDSimList api.memprotmd_sim_list.MemProtMDSimList object.

api.memprotmd_sim_list.main()[source]

Command line execution of this building block. Please check the command line documentation.

api.memprotmd_sim_list.memprotmd_sim_list(output_simulations: str, properties: dict = None, **kwargs) → int[source]

Execute the MemProtMDSimList class and execute the launch() method.

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: biobb_common.generic.biobb_object.BiobbObject

biobb_io Pdb
This class is a wrapper for downloading a PDB structure from the Protein Data Bank.
Wrapper for the Protein Data Bank in Europe, the Protein Data Bank and the MMB PDB mirror for downloading a single PDB structure.
Parameters:
  • output_pdb_path (str) –

    Path to the output PDB file. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
    • pdb_code (str) - (None) 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.
    • api_id (str) - (“pdbe”) Identifier of the PDB REST API from which the PDB structure will be downloaded. Values: pdbe (PDB in Europe REST API), pdb (RCSB PDB REST API), mmb (MMB PDB mirror API).
    • remove_tmp (bool) - (True) [WF property] Remove temporal files.
    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_io.api.pdb import pdb
prop = {
    'pdb_code': '2VGB',
    'filter': ['ATOM', 'MODEL', 'ENDMDL'],
    'api_id': 'pdbe'
}
pdb(output_pdb_path='/path/to/newStructure.pdb',
    properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

launch() → int[source]

Execute the Pdb api.pdb.Pdb object.

api.pdb.main()[source]

Command line execution of this building block. Please check the command line documentation.

api.pdb.pdb(output_pdb_path: str, properties: dict = None, **kwargs) → int[source]

Execute the Pdb class and execute the launch() method.

api.pdb_cluster_zip module

PdbClusterZip Module

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

Bases: biobb_common.generic.biobb_object.BiobbObject

biobb_io PdbClusterZip
This class is a wrapper for downloading a PDB cluster from the Protein Data Bank.
Wrapper for the Protein Data Bank in Europe, the Protein Data Bank and the MMB PDB mirror for downloading a PDB cluster.
Parameters:
  • output_pdb_zip_path (str) –

    Path to the ZIP file containing the output PDB files. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
    • pdb_code (str) - (None) 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)
    • cluster (int) - (90) Sequence Similarity Cutoff. Values: 50 (structures having less than 50% sequence identity to each other), 70 (structures having less than 70% sequence identity to each other), 90 (structures having less than 90% sequence identity to each other), 95 (structures having less than 95% sequence identity to each other).
    • api_id (str) - (“pdbe”) Identifier of the PDB REST API from which the PDB structure will be downloaded. Values: pdbe (PDB in Europe REST API), pdb (RCSB PDB REST API), mmb (MMB PDB mirror API).
    • remove_tmp (bool) - (True) [WF property] Remove temporal files.
    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_io.api.pdb_cluster_zip import pdb_cluster_zip
prop = {
    'pdb_code': '2VGB',
    'filter': ['ATOM', 'MODEL', 'ENDMDL'],
    'cluster': 90,
    'api_id': 'pdbe'
}
pdb_cluster_zip(output_pdb_zip_path='/path/to/newStructures.zip',
                properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

launch() → int[source]

Execute the PdbClusterZip api.pdb_cluster_zip.PdbClusterZip object.

api.pdb_cluster_zip.main()[source]

Command line execution of this building block. Please check the command line documentation.

api.pdb_cluster_zip.pdb_cluster_zip(output_pdb_zip_path: str, properties: dict = None, **kwargs) → int[source]

Execute the PdbClusterZip class and execute the launch() method.

api.pdb_variants module

PdbVariants Module

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

Bases: biobb_common.generic.biobb_object.BiobbObject

biobb_io PdbVariants
This class creates a text file containing a list of all the variants mapped to a PDB code from the corresponding UNIPROT entries.
Wrapper for the UNIPROT mirror of the MMB group REST API for creating a list of all the variants mapped to a PDB code from the corresponding UNIPROT entries.
Parameters:
  • output_mutations_list_txt (str) –

    Path to the TXT file containing an ASCII comma separated values of the mutations. File type: output. Sample file. Accepted formats: txt (edam:format_2330).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
    • pdb_code (str) - (None) RSCB PDB four letter code.
    • remove_tmp (bool) - (True) [WF property] Remove temporal files.
    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the PdbVariants module from Python

from biobb_io.api.pdb_variants import pdb_variants prop = {

‘pdb_code’: ‘2VGB’

} pdb_variants(output_mutations_list_txt=’/path/to/newMutationsList.txt’,

properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

launch() → int[source]

Execute the PdbVariants api.pdb_variants.PdbVariants object.

api.pdb_variants.main()[source]

Command line execution of this building block. Please check the command line documentation.

api.pdb_variants.pdb_variants(output_mutations_list_txt: str, properties: dict = None, **kwargs) → int[source]

Execute the PdbVariants class and execute the launch() method.

api.api_binding_site module

Module containing the ApiBindingSite class and the command line interface.

class api.api_binding_site.ApiBindingSite(output_json_path, properties=None, **kwargs)[source]

Bases: biobb_common.generic.biobb_object.BiobbObject

biobb_io ApiBindingSite
This class is a wrapper for the PDBe REST API Binding Sites endpoint.
This call provides details on binding sites in the entry as per STRUCT_SITE records in PDB files, such as ligand, residues in the site, description of the site, etc.
Parameters:
  • output_json_path (str) –

    Path to the JSON file with the binding sites for the requested structure. File type: output. Sample file. Accepted formats: json (edam:format_3464).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
    • pdb_code (str) - (None) RSCB PDB code.
    • remove_tmp (bool) - (True) [WF property] Remove temporal files.
    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_io.api.api_binding_site import api_binding_site
prop = {
    'pdb_code': '4i23'
}
api_binding_site(output_json_path='/path/to/newBindingSites.json',
        properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

launch() → int[source]

Execute the ApiBindingSite api.api_binding_site.ApiBindingSite object.

api.api_binding_site.api_binding_site(output_json_path: str, properties: dict = None, **kwargs) → int[source]

Execute the ApiBindingSite class and execute the launch() method.

api.api_binding_site.main()[source]

Command line execution of this building block. Please check the command line documentation.

api.canonical_fasta module

Module containing the CanonicalFasta class and the command line interface.

class api.canonical_fasta.CanonicalFasta(output_fasta_path, properties=None, **kwargs)[source]

Bases: biobb_common.generic.biobb_object.BiobbObject

biobb_io CanonicalFasta
This class is a wrapper for downloading a FASTA structure from the Protein Data Bank.
Wrapper for the Protein Data Bank and the MMB PDB mirror for downloading a single FASTA structure.
Parameters:
  • output_fasta_path (str) –

    Path to the canonical FASTA file. File type: output. Sample file. Accepted formats: fasta (edam:format_1929).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
    • pdb_code (str) - (None) RSCB PDB code.
    • api_id (str) - (“pdbe”) Identifier of the PDB REST API from which the PDB structure will be downloaded. Values: pdbe (PDB in Europe REST API), pdb (RCSB PDB REST API), mmb (MMB PDB mirror API).
    • remove_tmp (bool) - (True) [WF property] Remove temporal files.
    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_io.api.canonical_fasta import canonical_fasta
prop = {
    'pdb_code': '4i23',
    'api_id': 'pdb'
}
canonical_fasta(output_fasta_path='/path/to/newFasta.fasta',
        properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

launch() → int[source]

Execute the CanonicalFasta api.canonical_fasta.CanonicalFasta object.

api.canonical_fasta.canonical_fasta(output_fasta_path: str, properties: dict = None, **kwargs) → int[source]

Execute the CanonicalFasta class and execute the launch() method.

api.canonical_fasta.main()[source]

Command line execution of this building block. Please check the command line documentation.

api.mmcif module

Module containing the Mmcif class and the command line interface.

class api.mmcif.Mmcif(output_mmcif_path, properties=None, **kwargs)[source]

Bases: biobb_common.generic.biobb_object.BiobbObject

biobb_io Mmcif
This class is a wrapper for downloading a MMCIF structure from the Protein Data Bank.
Wrapper for the Protein Data Bank in Europe, the Protein Data Bank and the MMB PDB mirror for downloading a single MMCIF structure.
Parameters:
  • output_mmcif_path (str) –

    Path to the output MMCIF file. File type: output. Sample file. Accepted formats: cif (edam:format_1477), mmcif (edam:format_1477).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
    • pdb_code (str) - (None) RSCB PDB code.
    • api_id (str) - (“pdbe”) Identifier of the PDB REST API from which the MMCIF structure will be downloaded. Values: pdbe (PDB in Europe REST API), pdb (RCSB PDB REST API), mmb (MMB PDB mirror API).
    • remove_tmp (bool) - (True) [WF property] Remove temporal files.
    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_io.api.mmcif import mmcif
prop = {
    'pdb_code': '2VGB',
    'api_id': 'pdbe'
}
mmcif(output_mmcif_path='/path/to/newStructure.mmcif',
    properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

launch() → int[source]

Execute the Mmcif api.mmcif.Mmcif object.

api.mmcif.main()[source]

Command line execution of this building block. Please check the command line documentation.

api.mmcif.mmcif(output_mmcif_path: str, properties: dict = None, **kwargs) → int[source]

Execute the Mmcif class and execute the launch() method.

api.ideal_sdf module

Module containing the IdealSdf class and the command line interface.

class api.ideal_sdf.IdealSdf(output_sdf_path, properties=None, **kwargs)[source]

Bases: biobb_common.generic.biobb_object.BiobbObject

biobb_io IdealSdf
This class is a wrapper for downloading an ideal SDF ligand from the Protein Data Bank.
Wrapper for the Protein Data Bank in Europe and the Protein Data Bank for downloading a single ideal SDF ligand.
Parameters:
  • output_sdf_path (str) –

    Path to the output SDF file. File type: output. Sample file. Accepted formats: sdf (edam:format_3814).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
    • ligand_code (str) - (None) RSCB PDB ligand code.
    • api_id (str) - (“pdbe”) Identifier of the PDB REST API from which the SDF structure will be downloaded. Values: pdbe (PDB in Europe REST API), pdb (RCSB PDB REST API).
    • remove_tmp (bool) - (True) [WF property] Remove temporal files.
    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_io.api.ideal_sdf import ideal_sdf
prop = {
    'ligand_code': 'HYZ',
    'api_id': 'pdbe'
}
ideal_sdf(output_sdf_path='/path/to/newStructure.sdf',
            properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

launch() → int[source]

Execute the IdealSdf api.ideal_sdf.IdealSdf object.

api.ideal_sdf.ideal_sdf(output_sdf_path: str, properties: dict = None, **kwargs) → int[source]

Execute the IdealSdf class and execute the launch() method.

api.ideal_sdf.main()[source]

Command line execution of this building block. Please check the command line documentation.

api.structure_info module

Module containing the StructureInfo class and the command line interface.

class api.structure_info.StructureInfo(output_json_path, properties=None, **kwargs)[source]

Bases: biobb_common.generic.biobb_object.BiobbObject

biobb_io StructureInfo
This class is a wrapper for getting all the available information of a structure from the Protein Data Bank.
Wrapper for the MMB PDB mirror for getting all the available information of a structure from the Protein Data Bank.
Parameters:
  • output_json_path (str) –

    Path to the output JSON file with all the structure information. File type: output. Sample file. Accepted formats: json (edam:format_3464).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –
    • pdb_code (str) - (None) RSCB PDB structure code.
    • remove_tmp (bool) - (True) [WF property] Remove temporal files.
    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_io.api.structure_info import structure_info
prop = {
    'pdb_code': '2vgb'
}
structure_info(output_json_path='/path/to/newStructure.sdf',
            properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

launch() → int[source]

Execute the StructureInfo api.structure_info.StructureInfo object.

api.structure_info.main()[source]

Command line execution of this building block. Please check the command line documentation.

api.structure_info.structure_info(output_json_path: str, properties: dict = None, **kwargs) → int[source]

Execute the StructureInfo class and execute the launch() method.