biobb-io 5.0.1__tar.gz → 5.1.1__tar.gz

{biobb_io-5.0.1 → biobb_io-5.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: biobb_io
-Version: 5.0.1
+Version: 5.1.1
 Summary: Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks.
 Home-page: https://github.com/bioexcel/biobb_io
 Author: Biobb developers
@@ -17,14 +17,26 @@ Classifier: Operating System :: Unix
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: biobb_common==5.0.0
+Requires-Dist: biobb_common==5.1.1
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license-file
+Dynamic: project-url
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 [![](https://img.shields.io/github/v/tag/bioexcel/biobb_io?label=Version)](https://GitHub.com/bioexcel/biobb_io/tags/)
 [![](https://img.shields.io/pypi/v/biobb-io.svg?label=Pypi)](https://pypi.python.org/pypi/biobb-io/)
 [![](https://img.shields.io/conda/vn/bioconda/biobb_io?label=Conda)](https://anaconda.org/bioconda/biobb_io)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_io?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_io)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_io?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:5.0.1--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:5.1.1--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_io)
 [![](https://img.shields.io/pypi/pyversions/biobb-io.svg?label=Python%20Versions)](https://pypi.org/project/biobb-io/)
@@ -62,7 +74,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb-io.readthedocs.io/en/latest/).
 
 ### Version
-v5.0.1 2024.2
+v5.1.1 2025.1
 
 ### Installation
 Using PIP:
@@ -71,7 +83,7 @@ Using PIP:
 
 * Installation:
 
-        pip install "biobb_io==5.0.1"
+        pip install "biobb_io==5.1.1"
 
 * Usage: [Python API documentation](https://biobb-io.readthedocs.io/en/latest/modules.html)
 
@@ -79,7 +91,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_io==5.0.1"
+        conda install -c bioconda "biobb_io==5.1.1"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-io.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-io.readthedocs.io/en/latest/command_line.html)
@@ -88,12 +100,12 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_io:5.0.1--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_io:5.1.1--pyhdfd78af_0
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_io:5.0.1--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_io:5.1.1--pyhdfd78af_0 <command>
 
 
 The command list and specification can be found at the [Command Line documentation](https://biobb-io.readthedocs.io/en/latest/command_line.html).
@@ -105,7 +117,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:5.0.1--pyhdfd78af_0
+        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:5.1.1--pyhdfd78af_0
 
 
 * Usage:
@@ -118,10 +130,10 @@ Using SINGULARITY:
 The command list and specification can be found at the [Command Line documentation](https://biobb-io.readthedocs.io/en/latest/command_line.html).
 
 ### Copyright & Licensing
-This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
+This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU Horizon Europe [101093290](https://cordis.europa.eu/project/id/101093290), EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
 
-* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)
-* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
+* (c) 2015-2025 [Barcelona Supercomputing Center](https://www.bsc.es/)
+* (c) 2015-2025 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
 
 Licensed under the
 [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.

{biobb_io-5.0.1 → biobb_io-5.1.1}/README.md

@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_io?label=Conda)](https://anaconda.org/bioconda/biobb_io)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_io?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_io)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_io?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:5.0.1--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:5.1.1--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_io)
 [![](https://img.shields.io/pypi/pyversions/biobb-io.svg?label=Python%20Versions)](https://pypi.org/project/biobb-io/)
@@ -41,7 +41,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb-io.readthedocs.io/en/latest/).
 
 ### Version
-v5.0.1 2024.2
+v5.1.1 2025.1
 
 ### Installation
 Using PIP:
@@ -50,7 +50,7 @@ Using PIP:
 
 * Installation:
 
-        pip install "biobb_io==5.0.1"
+        pip install "biobb_io==5.1.1"
 
 * Usage: [Python API documentation](https://biobb-io.readthedocs.io/en/latest/modules.html)
 
@@ -58,7 +58,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_io==5.0.1"
+        conda install -c bioconda "biobb_io==5.1.1"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-io.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-io.readthedocs.io/en/latest/command_line.html)
@@ -67,12 +67,12 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_io:5.0.1--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_io:5.1.1--pyhdfd78af_0
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_io:5.0.1--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_io:5.1.1--pyhdfd78af_0 <command>
 
 
 The command list and specification can be found at the [Command Line documentation](https://biobb-io.readthedocs.io/en/latest/command_line.html).
@@ -84,7 +84,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:5.0.1--pyhdfd78af_0
+        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:5.1.1--pyhdfd78af_0
 
 
 * Usage:
@@ -97,10 +97,10 @@ Using SINGULARITY:
 The command list and specification can be found at the [Command Line documentation](https://biobb-io.readthedocs.io/en/latest/command_line.html).
 
 ### Copyright & Licensing
-This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
+This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU Horizon Europe [101093290](https://cordis.europa.eu/project/id/101093290), EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
 
-* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)
-* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
+* (c) 2015-2025 [Barcelona Supercomputing Center](https://www.bsc.es/)
+* (c) 2015-2025 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
 
 Licensed under the
 [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.

{biobb_io-5.0.1 → biobb_io-5.1.1}/biobb_io/__init__.py

@@ -2,4 +2,4 @@ from . import api
 
 name = "biobb_io"
 __all__ = ["api"]
-__version__ = "5.0.1"
+__version__ = "5.1.1"

{biobb_io-5.0.1 → biobb_io-5.1.1}/biobb_io/api/__init__.py

@@ -12,6 +12,7 @@ from . import (
     pdb_cluster_zip,
     pdb_variants,
     structure_info,
+    mddb
 )
 
 name = "api"
@@ -29,4 +30,5 @@ __all__ = [
     "mmcif",
     "ideal_sdf",
     "structure_info",
+    "mddb"
 ]

{biobb_io-5.0.1 → biobb_io-5.1.1}/biobb_io/api/alphafold.py

@@ -2,10 +2,7 @@
 
 """Module containing the AlphaFold class and the command line interface."""
 
-import argparse
 from typing import Optional
-
-from biobb_common.configuration import settings
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools.file_utils import launchlogger
 
@@ -113,41 +110,11 @@ class AlphaFold(BiobbObject):
 def alphafold(output_pdb_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`AlphaFold <api.alphafold.AlphaFold>` class and
     execute the :meth:`launch() <api.alphafold.AlphaFold.launch>` method."""
+    return AlphaFold(**dict(locals())).launch()
 
-    return AlphaFold(
-        output_pdb_path=output_pdb_path, properties=properties, **kwargs
-    ).launch()
-
-
-def main():
-    """Command line execution of this building block. Please check the command line documentation."""
-    parser = argparse.ArgumentParser(
-        description="This class is a wrapper for downloading a PDB structure from the Protein Data Bank.",
-        formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
-    )
-    parser.add_argument(
-        "-c",
-        "--config",
-        required=False,
-        help="This file can be a YAML file, JSON file or JSON string",
-    )
-
-    # Specific args of each building block
-    required_args = parser.add_argument_group("required arguments")
-    required_args.add_argument(
-        "-o",
-        "--output_pdb_path",
-        required=True,
-        help="Path to the output PDB file. Accepted formats: pdb.",
-    )
-
-    args = parser.parse_args()
-    config = args.config if args.config else None
-    properties = settings.ConfReader(config=config).get_prop_dic()
-
-    # Specific call of each building block
-    alphafold(output_pdb_path=args.output_pdb_path, properties=properties)
 
+alphafold.__doc__ = AlphaFold.__doc__
+main = AlphaFold.get_main(alphafold, "This class is a wrapper for downloading a PDB structure from the Protein Data Bank.")
 
 if __name__ == "__main__":
     main()

{biobb_io-5.0.1 → biobb_io-5.1.1}/biobb_io/api/api_binding_site.py

@@ -2,11 +2,8 @@
 
 """Module containing the ApiBindingSite class and the command line interface."""
 
-import argparse
 import json
 from typing import Optional
-
-from biobb_common.configuration import settings
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools import file_utils as fu
 from biobb_common.tools.file_utils import launchlogger
@@ -125,41 +122,11 @@ def api_binding_site(
 ) -> int:
     """Execute the :class:`ApiBindingSite <api.api_binding_site.ApiBindingSite>` class and
     execute the :meth:`launch() <api.api_binding_site.ApiBindingSite.launch>` method."""
+    return ApiBindingSite(**dict(locals())).launch()
 
-    return ApiBindingSite(
-        output_json_path=output_json_path, properties=properties, **kwargs
-    ).launch()
-
-
-def main():
-    """Command line execution of this building block. Please check the command line documentation."""
-    parser = argparse.ArgumentParser(
-        description="This class is a wrapper for the PDBe REST API Binding Sites endpoint",
-        formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
-    )
-    parser.add_argument(
-        "-c",
-        "--config",
-        required=False,
-        help="This file can be a YAML file, JSON file or JSON string",
-    )
-
-    # Specific args of each building block
-    required_args = parser.add_argument_group("required arguments")
-    required_args.add_argument(
-        "-o",
-        "--output_json_path",
-        required=True,
-        help="Path to the JSON file with the binding sites for the requested structure. Accepted formats: json.",
-    )
-
-    args = parser.parse_args()
-    config = args.config if args.config else None
-    properties = settings.ConfReader(config=config).get_prop_dic()
-
-    # Specific call of each building block
-    api_binding_site(output_json_path=args.output_json_path, properties=properties)
 
+api_binding_site.__doc__ = ApiBindingSite.__doc__
+main = ApiBindingSite.get_main(api_binding_site, "This class is a wrapper for the PDBe REST API Binding Sites endpoint")
 
 if __name__ == "__main__":
     main()

{biobb_io-5.0.1 → biobb_io-5.1.1}/biobb_io/api/canonical_fasta.py

@@ -2,10 +2,7 @@
 
 """Module containing the CanonicalFasta class and the command line interface."""
 
-import argparse
 from typing import Optional
-
-from biobb_common.configuration import settings
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools.file_utils import launchlogger
 
@@ -115,41 +112,11 @@ def canonical_fasta(
 ) -> int:
     """Execute the :class:`CanonicalFasta <api.canonical_fasta.CanonicalFasta>` class and
     execute the :meth:`launch() <api.canonical_fasta.CanonicalFasta.launch>` method."""
+    return CanonicalFasta(**dict(locals())).launch()
 
-    return CanonicalFasta(
-        output_fasta_path=output_fasta_path, properties=properties, **kwargs
-    ).launch()
-
-
-def main():
-    """Command line execution of this building block. Please check the command line documentation."""
-    parser = argparse.ArgumentParser(
-        description="This class is a wrapper for downloading a FASTA structure from the Protein Data Bank.",
-        formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
-    )
-    parser.add_argument(
-        "-c",
-        "--config",
-        required=False,
-        help="This file can be a YAML file, JSON file or JSON string",
-    )
-
-    # Specific args of each building block
-    required_args = parser.add_argument_group("required arguments")
-    required_args.add_argument(
-        "-o",
-        "--output_fasta_path",
-        required=True,
-        help="Path to the canonical FASTA file. Accepted formats: fasta.",
-    )
-
-    args = parser.parse_args()
-    config = args.config if args.config else None
-    properties = settings.ConfReader(config=config).get_prop_dic()
-
-    # Specific call of each building block
-    canonical_fasta(output_fasta_path=args.output_fasta_path, properties=properties)
 
+canonical_fasta.__doc__ = CanonicalFasta.__doc__
+main = CanonicalFasta.get_main(canonical_fasta, "This class is a wrapper for downloading a FASTA structure from the Protein Data Bank.")
 
 if __name__ == "__main__":
     main()

{biobb_io-5.0.1 → biobb_io-5.1.1}/biobb_io/api/common.py

@@ -4,6 +4,7 @@ import json
 import os
 import re
 import urllib.request
+import urllib.parse
 from pathlib import Path, PurePath
 
 import requests
@@ -20,14 +21,12 @@ def check_output_path(path, argument, optional, out_log, classname) -> str:
     file_extension = PurePath(path).suffix
     if not is_valid_file(file_extension[1:], argument):
         fu.log(
-            classname
-            + ": Format %s in %s file is not compatible"
+            classname + ": Format %s in %s file is not compatible"
             % (file_extension[1:], argument),
             out_log,
         )
         raise SystemExit(
-            classname
-            + ": Format %s in %s file is not compatible"
+            classname + ": Format %s in %s file is not compatible"
             % (file_extension[1:], argument)
         )
     return path
@@ -45,6 +44,8 @@ def is_valid_file(ext, argument):
         "output_json_path": ["json"],
         "output_fasta_path": ["fasta"],
         "output_mmcif_path": ["mmcif", "cif"],
+        "output_top_path": ["pdb"],
+        "output_trj_path": ["mdcrd", "trr", "xtc"]
     }
     return ext in formats[argument]
 
@@ -84,6 +85,60 @@ def download_af(uniprot_code, out_log=None, global_log=None, classname=None):
     return r.content.decode("utf-8")
 
 
+def download_mddb_top(project_id, node_id, selection, out_log=None, global_log=None, classname=None):
+    """
+    Returns:
+        String: Content of the pdb file.
+    """
+
+    url = "https://" + node_id + ".mddbr.eu/api/rest/v1/projects/" + project_id + "/structure?selection=" + urllib.parse.quote(str(selection))
+
+    fu.log("Downloading %s topology from: %s" % (project_id, url), out_log, global_log)
+
+    r = requests.get(url)
+    if r.status_code == 404:
+        fu.log(classname + ": Incorrect url, check project_id, node_id and selection: %s" % (url), out_log)
+        raise SystemExit(classname + ": Incorrect url, check project_id, node_id and selection: %s" % (url))
+
+    return r.content.decode("utf-8")
+
+
+def download_mddb_trj(project_id, node_id, trj_format, frames, selection, out_log=None, global_log=None, classname=None):
+    """
+    Returns:
+        String: Content of the trajectory file.
+    """
+
+    url = "https://" + node_id + ".mddbr.eu/api/rest/v1/projects/" + project_id + "/trajectory?format=" + trj_format + "&frames=" + frames + "&selection=" + urllib.parse.quote(str(selection))
+
+    fu.log("Downloading %s trajectory from: %s" % (project_id, url), out_log, global_log)
+
+    r = requests.get(url)
+    if r.status_code == 404:
+        fu.log(classname + ": Incorrect url, check project_id, node_id, trj_format, frames and selection: %s" % (url), out_log)
+        raise SystemExit(classname + ": Incorrect url, check project_id, node_id, trj_format, frames and selection: %s" % (url))
+
+    return r.content
+
+
+def download_mddb_file(project_id, node_id, file_name, out_log=None, global_log=None, classname=None):
+    """
+    Returns:
+        String: Content of the trajectory file.
+    """
+
+    url = "https://" + node_id + ".mddbr.eu/api/rest/v1/projects/" + project_id + "/files/" + file_name
+
+    fu.log("Downloading %s file from: %s" % (project_id, url), out_log, global_log)
+
+    r = requests.get(url)
+    if r.status_code == 404:
+        fu.log(classname + ": Incorrect url, check project_id, node_id, trj_format, frames and selection: %s" % (url), out_log)
+        raise SystemExit(classname + ": Incorrect url, check project_id, node_id, trj_format, frames and selection: %s" % (url))
+
+    return r.content
+
+
 def download_mmcif(pdb_code, api_id, out_log=None, global_log=None):
     """
     Returns:
@@ -112,9 +167,7 @@ def download_ligand(ligand_code, api_id, out_log=None, global_log=None):
         text = requests.get(url, verify=True).content.decode("utf-8")
     elif api_id == "pdbe":
         url = (
-            "https://www.ebi.ac.uk/pdbe/static/files/pdbechem_v2/"
-            + ligand_code.upper()
-            + "_ideal.pdb"
+            "https://www.ebi.ac.uk/pdbe/static/files/pdbechem_v2/" + ligand_code.upper() + "_ideal.pdb"
         )
         text = urllib.request.urlopen(url).read().decode("utf-8")
 
@@ -173,16 +226,12 @@ def download_ideal_sdf(ligand_code, api_id, out_log=None, global_log=None):
 
     if api_id == "pdb":
         url = (
-            "https://files.rcsb.org/ligands/download/"
-            + ligand_code.upper()
-            + "_ideal.sdf"
+            "https://files.rcsb.org/ligands/download/" + ligand_code.upper() + "_ideal.sdf"
         )
         text = requests.get(url, verify=True).content.decode("utf-8")
     elif api_id == "pdbe":
         url = (
-            "https://www.ebi.ac.uk/pdbe/static/files/pdbechem_v2/"
-            + ligand_code.upper()
-            + "_ideal.sdf"
+            "https://www.ebi.ac.uk/pdbe/static/files/pdbechem_v2/" + ligand_code.upper() + "_ideal.sdf"
         )
         text = urllib.request.urlopen(url).read().decode("utf-8")
 
@@ -230,6 +279,13 @@ def write_pdb(pdb_string, output_pdb_path, filt=None, out_log=None, global_log=N
             output_pdb_file.write(pdb_string)
 
 
+def write_bin(bin_string, output_bin_path, out_log=None, global_log=None):
+    """Writes a BIN"""
+    fu.log("Writting bin to: %s" % (output_bin_path), out_log, global_log)
+    with open(output_bin_path, "wb") as output_bin_file:
+        output_bin_file.write(bin_string)
+
+
 def write_mmcif(mmcif_string, output_mmcif_path, out_log=None, global_log=None):
     """Writes a mmcif"""
     fu.log("Writting mmcif to: %s" % (output_mmcif_path), out_log, global_log)
@@ -268,22 +324,11 @@ def get_cluster_pdb_codes(pdb_code, cluster, out_log=None, global_log=None):
 
     if out_log:
         out_log.info(
-            "Cluster: "
-            + str(cluster)
-            + " of pdb_code: "
-            + pdb_code
-            + "\n List: "
-            + str(pdb_codes)
+            "Cluster: " + str(cluster) + " of pdb_code: " + pdb_code + "\n List: " + str(pdb_codes)
         )
     if global_log:
         global_log.info(
-            fu.get_logs_prefix()
-            + "Cluster: "
-            + str(cluster)
-            + " of pdb_code: "
-            + pdb_code
-            + "\n List: "
-            + str(pdb_codes)
+            fu.get_logs_prefix() + "Cluster: " + str(cluster) + " of pdb_code: " + pdb_code + "\n List: " + str(pdb_codes)
         )
 
     return pdb_codes
@@ -395,9 +440,7 @@ def get_memprotmd_sim(pdb_code, output_file, out_log=None, global_log=None):
     fu.log("Getting simulation file from pdb code %s" % (pdb_code), out_log, global_log)
 
     url = (
-        "http://memprotmd.bioch.ox.ac.uk/data/memprotmd/simulations/"
-        + pdb_code
-        + "_default_dppc/files/run/at.zip"
+        "http://memprotmd.bioch.ox.ac.uk/data/memprotmd/simulations/" + pdb_code + "_default_dppc/files/run/at.zip"
     )
     response = requests.get(url)
 

{biobb_io-5.0.1 → biobb_io-5.1.1}/biobb_io/api/ideal_sdf.py

@@ -2,10 +2,7 @@
 
 """Module containing the IdealSdf class and the command line interface."""
 
-import argparse
 from typing import Optional
-
-from biobb_common.configuration import settings
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools.file_utils import launchlogger
 
@@ -113,41 +110,11 @@ class IdealSdf(BiobbObject):
 def ideal_sdf(output_sdf_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`IdealSdf <api.ideal_sdf.IdealSdf>` class and
     execute the :meth:`launch() <api.ideal_sdf.IdealSdf.launch>` method."""
+    return IdealSdf(**dict(locals())).launch()
 
-    return IdealSdf(
-        output_sdf_path=output_sdf_path, properties=properties, **kwargs
-    ).launch()
-
-
-def main():
-    """Command line execution of this building block. Please check the command line documentation."""
-    parser = argparse.ArgumentParser(
-        description="This class is a wrapper for downloading an ideal SDF ligand from the Protein Data Bank.",
-        formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
-    )
-    parser.add_argument(
-        "-c",
-        "--config",
-        required=False,
-        help="This file can be a YAML file, JSON file or JSON string",
-    )
-
-    # Specific args of each building block
-    required_args = parser.add_argument_group("required arguments")
-    required_args.add_argument(
-        "-o",
-        "--output_sdf_path",
-        required=True,
-        help="Path to the output SDF file. Accepted formats: sdf.",
-    )
-
-    args = parser.parse_args()
-    config = args.config if args.config else None
-    properties = settings.ConfReader(config=config).get_prop_dic()
-
-    # Specific call of each building block
-    ideal_sdf(output_sdf_path=args.output_sdf_path, properties=properties)
 
+ideal_sdf.__doc__ = IdealSdf.__doc__
+main = IdealSdf.get_main(ideal_sdf, "This class is a wrapper for downloading an ideal SDF ligand from the Protein Data Bank.")
 
 if __name__ == "__main__":
     main()