biobb-io 5.1.0__py3-none-any.whl → 5.1.1__py3-none-any.whl

biobb_io/__init__.py

@@ -2,4 +2,4 @@ from . import api
 
 name = "biobb_io"
 __all__ = ["api"]
-__version__ = "5.1.0"
+__version__ = "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
 
@@ -113,43 +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()
-
-    alphafold.__doc__ = AlphaFold.__doc__
-
-
-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/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
@@ -125,43 +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()
-
-    api_binding_site.__doc__ = ApiBindingSite.__doc__
-
-
-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/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
 
@@ -115,43 +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()
-
-    canonical_fasta.__doc__ = CanonicalFasta.__doc__
-
-
-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/api/common.py

@@ -121,6 +121,24 @@ def download_mddb_trj(project_id, node_id, trj_format, frames, selection, out_lo
     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:

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
 
@@ -113,43 +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()
-
-    ideal_sdf.__doc__ = IdealSdf.__doc__
-
-
-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()

biobb_io/api/ligand.py

@@ -2,10 +2,7 @@
 
 """Module containing the Ligand 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
 
@@ -113,43 +110,11 @@ class Ligand(BiobbObject):
 def ligand(output_pdb_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`Ligand <api.ligand.Ligand>` class and
     execute the :meth:`launch() <api.ligand.Ligand.launch>` method."""
+    return Ligand(**dict(locals())).launch()
 
-    return Ligand(
-        output_pdb_path=output_pdb_path, properties=properties, **kwargs
-    ).launch()
-
-    ligand.__doc__ = Ligand.__doc__
-
-
-def main():
-    """Command line execution of this building block. Please check the command line documentation."""
-    parser = argparse.ArgumentParser(
-        description="Wrapper for the Protein Data Bank in Europe (https://www.ebi.ac.uk/pdbe/) and the MMB PDB mirror (http://mmb.irbbarcelona.org/api/) for downloading a single PDB ligand.",
-        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 ligand 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
-    ligand(output_pdb_path=args.output_pdb_path, properties=properties)
 
+ligand.__doc__ = Ligand.__doc__
+main = Ligand.get_main(ligand, "Wrapper for the Protein Data Bank in Europe (https://www.ebi.ac.uk/pdbe/) and the MMB PDB mirror (http://mmb.irbbarcelona.org/api/) for downloading a single PDB ligand.")
 
 if __name__ == "__main__":
     main()

biobb_io/api/mddb.py

@@ -2,10 +2,7 @@
 
 """Module containing the MDDB 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
 
@@ -15,7 +12,8 @@ from biobb_io.api.common import (
     download_mddb_top,
     write_pdb,
     download_mddb_trj,
-    write_bin
+    write_bin,
+    download_mddb_file
 )
 
 
@@ -34,6 +32,7 @@ class MDDB(BiobbObject):
             * **trj_format** (*str*) - ("xtc") Trajectory format. Values: mdcrd (AMBER trajectory format), trr (Trajectory of a simulation experiment used by GROMACS), xtc (Portable binary format for trajectories produced by GROMACS package).
             * **frames** (*str*) - (None) Specify a frame range for the returned trajectory. Ranges are defined by dashes, and multiple ranges can be defined separated by commas. It can also be defined as the start:end:step format (ie: '10:20:2').
             * **selection** (*str*) - (None) Specify a NGL-formatted selection for the returned trajectory. See here for the kind of selection that can be used: http://nglviewer.org/ngl/api/manual/usage/selection-language.html.
+            * **extra_files** (*list*) - (None) List of extra files to download. It should be a tuple with the name of the file and the path to be saved.
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
             * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
@@ -47,8 +46,8 @@ class MDDB(BiobbObject):
                 'trj_format': 'xtc'
             }
             mddb(output_top_path='/path/to/newTopology.pdb',
-                output_trj_path='/path/to/newTrajectory.pdb',
-                properties=prop)
+                 output_trj_path='/path/to/newTrajectory.pdb',
+                 properties=prop)
 
     Info:
         * wrapped_software:
@@ -76,6 +75,7 @@ class MDDB(BiobbObject):
         self.trj_format = properties.get("trj_format", "xtc")
         self.frames = properties.get("frames", "")
         self.selection = properties.get("selection", "*")
+        self.extra_files = properties.get("extra_files", [])
         self.properties = properties
 
         # Check the properties
@@ -140,6 +140,20 @@ class MDDB(BiobbObject):
         )
         write_bin(trj_string, self.output_trj_path, self.out_log, self.global_log)
 
+        for (extra_file, extra_path) in self.extra_files:
+            try:
+                file_string = download_mddb_file(
+                    self.project_id,
+                    self.node_id,
+                    extra_file,
+                    self.out_log,
+                    self.global_log,
+                    self.__class__.__name__,
+                )
+                write_bin(file_string, extra_path, self.out_log, self.global_log)
+            except Exception:
+                pass
+
         self.check_arguments(output_files_created=True, raise_exception=False)
 
         return 0
@@ -148,49 +162,14 @@ class MDDB(BiobbObject):
 def mddb(output_top_path: str, output_trj_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`MDDB <api.mddb.MDDB>` class and
     execute the :meth:`launch() <api.mddb.MDDB.launch>` method."""
+    return MDDB(**dict(locals())).launch()
 
-    return MDDB(
-        output_top_path=output_top_path, output_trj_path=output_trj_path, properties=properties, **kwargs
-    ).launch()
-
-    mddb.__doc__ = MDDB.__doc__
-
-
-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 trajectory / topology pair from the MDDB Database.",
-        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_top_path",
-        required=True,
-        help="Path to the output toplogy file. Accepted formats: pdb.",
-    )
-    required_args.add_argument(
-        "-t",
-        "--output_trj_path",
-        required=True,
-        help="Path to the output trajectory file. Accepted formats: mdcrd, trr, xtc.",
-    )
-
-    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
-    mddb(output_top_path=args.output_top_path, output_trj_path=args.output_trj_path, properties=properties)
 
+mddb.__doc__ = MDDB.__doc__
+main = MDDB.get_main(
+    mddb,
+    "This class is a wrapper for downloading a trajectory / topology pair from the MDDB Database.",
+)
 
 if __name__ == "__main__":
     main()

biobb_io/api/memprotmd_sim.py

@@ -2,10 +2,7 @@
 
 """Module containing the MemProtMDSim 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
 
@@ -108,43 +105,11 @@ def memprotmd_sim(
 ) -> int:
     """Execute the :class:`MemProtMDSim <api.memprotmd_sim.MemProtMDSim>` class and
     execute the :meth:`launch() <api.memprotmd_sim.MemProtMDSim.launch>` method."""
+    return MemProtMDSim(**dict(locals())).launch()
 
-    return MemProtMDSim(
-        output_simulation=output_simulation, properties=properties, **kwargs
-    ).launch()
-
-    memprotmd_sim.__doc__ = MemProtMDSim.__doc__
-
-
-def main():
-    """Command line execution of this building block. Please check the command line documentation."""
-    parser = argparse.ArgumentParser(
-        description="Wrapper for the MemProtMD DB REST API (http://memprotmd.bioch.ox.ac.uk/) to download a simulation.",
-        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_simulation",
-        required=True,
-        help="Path to the output simulation in a ZIP file. Accepted formats: zip.",
-    )
-
-    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
-    memprotmd_sim(output_simulation=args.output_simulation, properties=properties)
 
+memprotmd_sim.__doc__ = MemProtMDSim.__doc__
+main = MemProtMDSim.get_main(memprotmd_sim, "Wrapper for the MemProtMD DB REST API (http://memprotmd.bioch.ox.ac.uk/) to download a simulation.")
 
 if __name__ == "__main__":
     main()

biobb_io/api/memprotmd_sim_list.py

@@ -2,13 +2,9 @@
 
 """Module containing the MemProtMDSimList 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
-
 from biobb_io.api.common import check_output_path, get_memprotmd_sim_list, write_json
 
 
@@ -97,45 +93,11 @@ def memprotmd_sim_list(
 ) -> int:
     """Execute the :class:`MemProtMDSimList <api.memprotmd_sim_list.MemProtMDSimList>` class and
     execute the :meth:`launch() <api.memprotmd_sim_list.MemProtMDSimList.launch>` method."""
+    return MemProtMDSimList(**dict(locals())).launch()
 
-    return MemProtMDSimList(
-        output_simulations=output_simulations, properties=properties, **kwargs
-    ).launch()
-
-    memprotmd_sim_list.__doc__ = MemProtMDSimList.__doc__
-
-
-def main():
-    """Command line execution of this building block. Please check the command line documentation."""
-    parser = argparse.ArgumentParser(
-        description="Wrapper for the MemProtMD DB REST API (http://memprotmd.bioch.ox.ac.uk/) to get all available membrane-protein systems (simulations).",
-        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_simulations",
-        required=True,
-        help="Path to the output JSON file. 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
-    memprotmd_sim_list(
-        output_simulations=args.output_simulations, properties=properties
-    )
 
+memprotmd_sim_list.__doc__ = MemProtMDSimList.__doc__
+main = MemProtMDSimList.get_main(memprotmd_sim_list, "Wrapper for the MemProtMD DB REST API (http://memprotmd.bioch.ox.ac.uk/) to get all available membrane-protein systems (simulations).")
 
 if __name__ == "__main__":
     main()

biobb_io/api/memprotmd_sim_search.py

@@ -2,10 +2,7 @@
 
 """Module containing the MemProtMDSimSearch 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
 
@@ -108,45 +105,11 @@ def memprotmd_sim_search(
 ) -> int:
     """Execute the :class:`MemProtMDSimSearch <api.memprotmd_sim_search.MemProtMDSimSearch>` class and
     execute the :meth:`launch() <api.memprotmd_sim_search.MemProtMDSimSearch.launch>` method."""
+    return MemProtMDSimSearch(**dict(locals())).launch()
 
-    return MemProtMDSimSearch(
-        output_simulations=output_simulations, properties=properties, **kwargs
-    ).launch()
-
-    memprotmd_sim_search.__doc__ = MemProtMDSimSearch.__doc__
-
-
-def main():
-    """Command line execution of this building block. Please check the command line documentation."""
-    parser = argparse.ArgumentParser(
-        description="Wrapper for the MemProtMD DB REST API (http://memprotmd.bioch.ox.ac.uk/) to perform advanced searches.",
-        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_simulations",
-        required=True,
-        help="Path to the output JSON file. 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
-    memprotmd_sim_search(
-        output_simulations=args.output_simulations, properties=properties
-    )
 
+memprotmd_sim_search.__doc__ = MemProtMDSimSearch.__doc__
+main = MemProtMDSimSearch.get_main(memprotmd_sim_search, "Wrapper for the MemProtMD DB REST API (http://memprotmd.bioch.ox.ac.uk/) to perform advanced searches.")
 
 if __name__ == "__main__":
     main()

biobb_io/api/mmcif.py

@@ -2,10 +2,7 @@
 
 """Module containing the Mmcif 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
 
@@ -113,43 +110,11 @@ class Mmcif(BiobbObject):
 def mmcif(output_mmcif_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`Mmcif <api.mmcif.Mmcif>` class and
     execute the :meth:`launch() <api.mmcif.Mmcif.launch>` method."""
+    return Mmcif(**dict(locals())).launch()
 
-    return Mmcif(
-        output_mmcif_path=output_mmcif_path, properties=properties, **kwargs
-    ).launch()
-
-    mmcif.__doc__ = Mmcif.__doc__
-
-
-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 MMCIF 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_mmcif_path",
-        required=True,
-        help="Path to the output MMCIF file. Accepted formats: cif, mmcif.",
-    )
-
-    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
-    mmcif(output_mmcif_path=args.output_mmcif_path, properties=properties)
 
+mmcif.__doc__ = Mmcif.__doc__
+main = Mmcif.get_main(mmcif, "This class is a wrapper for downloading a MMCIF structure from the Protein Data Bank.")
 
 if __name__ == "__main__":
     main()

biobb_io/api/pdb.py

@@ -2,10 +2,7 @@
 
 """Module containing the Pdb 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
 
@@ -118,43 +115,11 @@ class Pdb(BiobbObject):
 def pdb(output_pdb_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`Pdb <api.pdb.Pdb>` class and
     execute the :meth:`launch() <api.pdb.Pdb.launch>` method."""
+    return Pdb(**dict(locals())).launch()
 
-    return Pdb(
-        output_pdb_path=output_pdb_path, properties=properties, **kwargs
-    ).launch()
-
-    pdb.__doc__ = Pdb.__doc__
-
-
-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
-    pdb(output_pdb_path=args.output_pdb_path, properties=properties)
 
+pdb.__doc__ = Pdb.__doc__
+main = Pdb.get_main(pdb, "This class is a wrapper for downloading a PDB structure from the Protein Data Bank.")
 
 if __name__ == "__main__":
     main()

biobb_io/api/pdb_cluster_zip.py

@@ -2,11 +2,8 @@
 
 """PdbClusterZip Module"""
 
-import argparse
 import os
 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
@@ -132,10 +129,7 @@ class PdbClusterZip(BiobbObject):
         fu.log("Zipping the pdb files to: %s" % self.output_pdb_zip_path)
         fu.zip_list(self.output_pdb_zip_path, file_list, out_log=self.out_log)
 
-        self.tmp_files.extend([
-            # self.stage_io_dict.get("unique_dir", ""),
-            unique_dir
-        ])
+        self.tmp_files.extend([unique_dir])
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -148,43 +142,11 @@ def pdb_cluster_zip(
 ) -> int:
     """Execute the :class:`PdbClusterZip <api.pdb_cluster_zip.PdbClusterZip>` class and
     execute the :meth:`launch() <api.pdb_cluster_zip.PdbClusterZip.launch>` method."""
+    return PdbClusterZip(**dict(locals())).launch()
 
-    return PdbClusterZip(
-        output_pdb_zip_path=output_pdb_zip_path, properties=properties, **kwargs
-    ).launch()
-
-    pdb_cluster_zip.__doc__ = PdbClusterZip.__doc__
-
-
-def main():
-    """Command line execution of this building block. Please check the command line documentation."""
-    parser = argparse.ArgumentParser(
-        description="Wrapper for the Protein Data Bank in Europe (https://www.ebi.ac.uk/pdbe/), the Protein Data Bank (https://www.rcsb.org/) and the MMB PDB mirror (http://mmb.irbbarcelona.org/api/) for downloading a PDB cluster.",
-        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_zip_path",
-        required=True,
-        help="Path to the ZIP or PDB file containing the output PDB files. Accepted formats: pdb, zip.",
-    )
-
-    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
-    pdb_cluster_zip(output_pdb_zip_path=args.output_pdb_zip_path, properties=properties)
 
+pdb_cluster_zip.__doc__ = PdbClusterZip.__doc__
+main = PdbClusterZip.get_main(pdb_cluster_zip, "Wrapper for the Protein Data Bank in Europe (https://www.ebi.ac.uk/pdbe/), the Protein Data Bank (https://www.rcsb.org/) and the MMB PDB mirror (http://mmb.irbbarcelona.org/api/) for downloading a PDB cluster.")
 
 if __name__ == "__main__":
     main()

biobb_io/api/pdb_variants.py

@@ -2,12 +2,9 @@
 
 """PdbVariants Module"""
 
-import argparse
 import re
-from typing import Optional
-
 import requests
-from biobb_common.configuration import settings
+from typing import Optional
 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
@@ -168,47 +165,11 @@ def pdb_variants(
 ) -> int:
     """Execute the :class:`PdbVariants <api.pdb_variants.PdbVariants>` class and
     execute the :meth:`launch() <api.pdb_variants.PdbVariants.launch>` method."""
+    return PdbVariants(**dict(locals())).launch()
 
-    return PdbVariants(
-        output_mutations_list_txt=output_mutations_list_txt,
-        properties=properties,
-        **kwargs,
-    ).launch()
-
-    pdb_variants.__doc__ = PdbVariants.__doc__
-
-
-def main():
-    """Command line execution of this building block. Please check the command line documentation."""
-    parser = argparse.ArgumentParser(
-        description="Wrapper for the UNIPROT (http://www.uniprot.org/) mirror of the MMB group REST API (http://mmb.irbbarcelona.org/api/) for creating a list of all the variants mapped to a PDB code from the corresponding UNIPROT entries.",
-        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_mutations_list_txt",
-        required=True,
-        help="Path to the TXT file containing an ASCII comma separated values of the mutations. Accepted formats: txt.",
-    )
-
-    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
-    pdb_variants(
-        output_mutations_list_txt=args.output_mutations_list_txt, properties=properties
-    )
 
+pdb_variants.__doc__ = PdbVariants.__doc__
+main = PdbVariants.get_main(pdb_variants, "Wrapper for the UNIPROT (http://www.uniprot.org/) mirror of the MMB group REST API (http://mmb.irbbarcelona.org/api/) for creating a list of all the variants mapped to a PDB code from the corresponding UNIPROT entries.")
 
 if __name__ == "__main__":
     main()

biobb_io/api/structure_info.py

@@ -2,10 +2,7 @@
 
 """Module containing the StructureInfo 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
 
@@ -113,43 +110,11 @@ def structure_info(
 ) -> int:
     """Execute the :class:`StructureInfo <api.structure_info.StructureInfo>` class and
     execute the :meth:`launch() <api.structure_info.StructureInfo.launch>` method."""
+    return StructureInfo(**dict(locals())).launch()
 
-    return StructureInfo(
-        output_json_path=output_json_path, properties=properties, **kwargs
-    ).launch()
-
-    structure_info.__doc__ = StructureInfo.__doc__
-
-
-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 getting all the available information of a 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_json_path",
-        required=True,
-        help="Path to the output JSON file with all the structure information. 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
-    structure_info(output_json_path=args.output_json_path, properties=properties)
 
+structure_info.__doc__ = StructureInfo.__doc__
+main = StructureInfo.get_main(structure_info, "This class is a wrapper for getting all the available information of a structure from the Protein Data Bank.")
 
 if __name__ == "__main__":
     main()

{biobb_io-5.1.0.dist-info → biobb_io-5.1.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
-Name: biobb-io
-Version: 5.1.0
+Metadata-Version: 2.4
+Name: biobb_io
+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 ==5.1.0
+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:5.1.0--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
-v5.1.0 2025.1
+v5.1.1 2025.1
 
 ### Installation
 Using PIP:
@@ -71,7 +83,7 @@ Using PIP:
 
 * Installation:
 
-        pip install "biobb_io==5.1.0"
+        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==5.1.0"
+        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:5.1.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_io:5.1.1--pyhdfd78af_0
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_io:5.1.0--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:5.1.0--pyhdfd78af_0
+        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:5.1.1--pyhdfd78af_0
 
 
 * Usage:

biobb_io-5.1.1.dist-info/RECORD

@@ -0,0 +1,25 @@
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+biobb_io/test/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+biobb_io-5.1.1.dist-info/licenses/LICENSE,sha256=z8d0m5b2O9McPEK1xHG_dWgUBT6EfBDz6wA0F7xSPTA,11358
+biobb_io-5.1.1.dist-info/METADATA,sha256=LTPhHWFk9SzHSC-AxEUmkmrGU8wdoAvhSlTRHJfFxxc,7049
+biobb_io-5.1.1.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+biobb_io-5.1.1.dist-info/entry_points.txt,sha256=dDYvVClLKe_Aa3HaMm-7WuS2d16FKGxlnKl816Cf5T4,644
+biobb_io-5.1.1.dist-info/top_level.txt,sha256=1VPldlX2AnFaqODGFJK10WN8AOQuulpX88bLSaQdoS8,9
+biobb_io-5.1.1.dist-info/RECORD,,

{biobb_io-5.1.0.dist-info → biobb_io-5.1.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.2)
+Generator: setuptools (78.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

biobb_io-5.1.0.dist-info/RECORD

@@ -1,25 +0,0 @@
-biobb_io/__init__.py,sha256=y_NxlBZAIu68iadiLxWmXIu6Oxx3QnJ7mqtfnVoR1o0,77
-biobb_io/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biobb_io/api/__init__.py,sha256=s4K59-8EX7yX2qBtB8717ynIEjQ0lVNTp0BDSoc_raM,558
-biobb_io/api/alphafold.py,sha256=VitY1VGJcxo_WysO6r7qMxtMGAkNpr-EO3SqyNp76n8,5445
-biobb_io/api/api_binding_site.py,sha256=E28InSCJ6cSeZRu4UDWr3ee1yQhPlKqUlG8eklMt9_o,5939
-biobb_io/api/canonical_fasta.py,sha256=vc2-s8eBOo-QtJ1V9Io1eKQtmuJ17mH_6sPYIA1HIPk,5839
-biobb_io/api/common.py,sha256=gD4Pl76uI2htDzxiOHGNdsZdO-CtU8G6BQ4d_RPIeSo,15059
-biobb_io/api/ideal_sdf.py,sha256=9snXVskC63Ro13UhOwwCkAv89dyjkZ0AtHYy9VOAqvM,5641
-biobb_io/api/ligand.py,sha256=1bBHRbtRFpr3eNjjXjmmdOPe18UOqdx_FxQ4wyY9zuM,5694
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-biobb_io-5.1.0.dist-info/LICENSE,sha256=z8d0m5b2O9McPEK1xHG_dWgUBT6EfBDz6wA0F7xSPTA,11358
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