configuration package

Submodules

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.memprotmd_sim_search module

Module containing the MemProtMDSimSearch class and the command line interface.

class api.memprotmd_sim_search.MemProtMDSimSearch(output_simulations, properties=None, **kwargs)[source]

Bases: biobb_common.generic.biobb_object.BiobbObject

biobb_io MemProtMDSimSearch
This class is a wrapper of the MemProtMD to perform advanced searches in the MemProtMD DB using its REST API.
Wrapper for the MemProtMD DB REST API to perform advanced searches.
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) –
    • collection_name (str) - (“refs”) Name of the collection to query.
    • keyword (str) - (None) String to search for in the database metadata. Examples are families like gpcr or porin. Values: porin, outer membrane protein, membrane protein, gpcr (7-transmembrane domain receptors transducing extracellular signals into cells), ion channels, rhodopsin (The most famous GPCRs), abc, mip (Major Intrinsic Protein (MIP)/FNT superfamily: specific for the transport of water and small neutral solutes), ligand-gated (Ligand-dependent signal conversion from chemical signals to electric signals), ammonia (Regulating transepithelial ammonia secretion), mapeg (Eicosanoid and Glutathione metabolism proteins), transmembrane (Heme biosynthesis), protein, kinase (Tyrosine-protein kinases: regulate central nervous system; gene transcription and cell differentiation), glycoprotein (Expression of TCR complex), immunoglobulin (Recognition; binding and adhesion process of cells), integrin (Bridges for cell-cell and cell-extracellular matrix interaction), bnip3 (BNip3 protein family: protect cell from apoptosis), bcl-2 (Regulating cell-death; either induce apoptotic or inhibit apoptosis), atpase (ATPase regulators; P-P-bond hydrolysis-driven transporter), cytochrome (Terminal oxidase enzyme in electron transfer chain), nadp (Transmembrane proteins with NAD(P)-binding Rossmann-fold domains: monoamine oxidase; deaminates norepinephrine; epinephrine; serotonin and dopamine), a4 (Amyloid beta A4 protein; involved in alzheimer’s diseases), lysosome (Lysosome-associated membrane glycoprotein: specific to lysosomes; CD107), necrosis (Tumor necrosis factor recepto: binding with TNF and NGF; interacting with a variety of signal molecules; highly associated with apoptosis), oxidoreductase (DHODH; biosynthesis of orotate), ceramidase (Neutral/alkaline ceramidase: converting sphingolipid to sphingosine), dehydrogenase (Aldehyde dehydrogenase:ALDH; Oxidation of aldehydes), mitochondrial, plastid.
    • 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_search import memprotmd_sim_search
prop = {
    'collection_name': 'refs',
    'keyword': 'porin'
}
memprotmd_sim_search(output_simulations='/path/to/newSimulationSearch.json',
                    properties=prop).launch()
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

launch() → int[source]

Execute the MemProtMDSimSearch api.memprotmd_sim_search.MemProtMDSimSearch object.

api.memprotmd_sim_search.main()[source]

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

Execute the MemProtMDSimSearch 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.