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 AlphaFoldThis 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:
- wrapped_software:
- name: AlphaFold Protein Structure Database
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
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 DrugbankThis 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:
- wrapped_software:
- name: Drugbank
- license: Creative Commons
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
- output_sdf_path (str) –
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 LigandThis 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) - (“mmb”) 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': 'mmb' } ligand(output_pdb_path='/path/to/newLigand.pdb', properties=prop)
- Info:
- wrapped_software:
- name: Protein Data Bank
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
- output_pdb_path (str) –
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 MemProtMDSimThis 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:
- wrapped_software:
- name: MemProtMD DB
- license: Creative Commons
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
MemProtMDSim
api.memprotmd_sim.MemProtMDSim object.
- output_simulation (str) –
-
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 thelaunch()
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 MemProtMDSimListThis 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:
- wrapped_software:
- name: MemProtMD DB
- license: Creative Commons
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
MemProtMDSimList
api.memprotmd_sim_list.MemProtMDSimList object.
- output_simulations (str) –
-
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 thelaunch()
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 MemProtMDSimSearchThis 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:
- wrapped_software:
- name: MemProtMD DB
- license: Creative Commons
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
MemProtMDSimSearch
api.memprotmd_sim_search.MemProtMDSimSearch object.
- output_simulations (str) –
-
api.memprotmd_sim_search.
main
()[source]¶ Command line execution of this building block. Please check the command line documentation.
-
api.memprotmd_sim_search.
memprotmd_sim_search
(output_simulations: str, properties: dict = None, **kwargs) → int[source]¶ Execute the
MemProtMDSimSearch
class and execute thelaunch()
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 PdbThis 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:
- wrapped_software:
- name: Protein Data Bank
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
- output_pdb_path (str) –
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 PdbClusterZipThis 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:
- wrapped_software:
- name: Protein Data Bank
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
PdbClusterZip
api.pdb_cluster_zip.PdbClusterZip object.
- output_pdb_zip_path (str) –
-
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 thelaunch()
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 PdbVariantsThis 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:
- wrapped_software:
- name: UNIPROT
- license: Creative Commons
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
PdbVariants
api.pdb_variants.PdbVariants object.
- output_mutations_list_txt (str) –
-
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 thelaunch()
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 ApiBindingSiteThis 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:
- wrapped_software:
- name: PDBe REST API
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
ApiBindingSite
api.api_binding_site.ApiBindingSite object.
- output_json_path (str) –
-
api.api_binding_site.
api_binding_site
(output_json_path: str, properties: dict = None, **kwargs) → int[source]¶ Execute the
ApiBindingSite
class and execute thelaunch()
method.
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 CanonicalFastaThis 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:
- wrapped_software:
- name: Protein Data Bank
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
CanonicalFasta
api.canonical_fasta.CanonicalFasta object.
- output_fasta_path (str) –
-
api.canonical_fasta.
canonical_fasta
(output_fasta_path: str, properties: dict = None, **kwargs) → int[source]¶ Execute the
CanonicalFasta
class and execute thelaunch()
method.
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 MmcifThis 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:
- wrapped_software:
- name: Protein Data Bank
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
- output_mmcif_path (str) –
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 IdealSdfThis 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:
- wrapped_software:
- name: Protein Data Bank
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
- output_sdf_path (str) –
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 StructureInfoThis 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:
- wrapped_software:
- name: Protein Data Bank
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
StructureInfo
api.structure_info.StructureInfo object.
- output_json_path (str) –
-
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 thelaunch()
method.