biobb-io 5.0.1__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__ = "5.0.1"
+__version__ = "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/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/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/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/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/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()

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
 
@@ -27,7 +24,7 @@ class Ligand(BiobbObject):
         output_pdb_path (str): Path to the output PDB ligand file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_ligand.pdb>`_. 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 <https://www.ebi.ac.uk/pdbe/pdbe-rest-api>`_), mmb (`MMB PDB mirror API <http://mmb.irbbarcelona.org/api/>`_).
+            * **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 <https://www.ebi.ac.uk/pdbe/pdbe-rest-api>`_), mmb (`MMB PDB mirror API <http://mmb.irbbarcelona.org/api/>`_).
             * **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.
@@ -38,7 +35,7 @@ class Ligand(BiobbObject):
             from biobb_io.api.ligand import ligand
             prop = {
                 'ligand_code': 'CPB',
-                'api_id': 'mmb'
+                'api_id': 'pdbe'
             }
             ligand(output_pdb_path='/path/to/newLigand.pdb',
                     properties=prop)
@@ -64,7 +61,7 @@ class Ligand(BiobbObject):
         self.io_dict = {"out": {"output_pdb_path": output_pdb_path}}
 
         # Properties specific for BB
-        self.api_id = properties.get("api_id", "mmb")
+        self.api_id = properties.get("api_id", "pdbe")
         self.ligand_code = properties.get("ligand_code", None)
         self.properties = properties
 
@@ -113,41 +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()
-
-
-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

@@ -0,0 +1,175 @@
+#!/usr/bin/env python
+
+"""Module containing the MDDB class and the command line interface."""
+
+from typing import Optional
+from biobb_common.generic.biobb_object import BiobbObject
+from biobb_common.tools.file_utils import launchlogger
+
+from biobb_io.api.common import (
+    check_mandatory_property,
+    check_output_path,
+    download_mddb_top,
+    write_pdb,
+    download_mddb_trj,
+    write_bin,
+    download_mddb_file
+)
+
+
+class MDDB(BiobbObject):
+    """
+    | biobb_io MDDB
+    | This class is a wrapper for downloading a trajectory / topology pair from the MDDB Database.
+    | Wrapper for the `MDDB Database <https://mmb.mddbr.eu/>`_ for downloading a trajectory and its corresponding topology.
+
+    Args:
+        output_top_path (str): Path to the output toplogy file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_mddb.pdb>`_. Accepted formats: pdb (edam:format_1476).
+        output_trj_path (str): Path to the output trajectory file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_mddb.xtc>`_. Accepted formats: mdcrd (edam:format_3878), trr (edam:format_3910), xtc (edam:format_3875).
+        properties (dic - Python dictionary object containing the tool parameters, not input/output files):
+            * **project_id** (*str*) - (None) Project accession or identifier.
+            * **node_id** (*str*) - ("mmb") MDDB node identifier.
+            * **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.
+
+    Examples:
+        This is a use example of how to use the building block from Python::
+
+            from biobb_io.api.mddb import mddb
+            prop = {
+                'project_id': 'A0001',
+                'trj_format': 'xtc'
+            }
+            mddb(output_top_path='/path/to/newTopology.pdb',
+                 output_trj_path='/path/to/newTrajectory.pdb',
+                 properties=prop)
+
+    Info:
+        * wrapped_software:
+            * name: MDDB Database
+            * license: Apache-2.0
+        * ontology:
+            * name: EDAM
+            * schema: http://edamontology.org/EDAM.owl
+
+    """
+
+    def __init__(self, output_top_path, output_trj_path, properties=None, **kwargs) -> None:
+        properties = properties or {}
+
+        # Call parent class constructor
+        super().__init__(properties)
+        self.locals_var_dict = locals().copy()
+
+        # Input/Output files
+        self.io_dict = {"out": {"output_top_path": output_top_path, "output_trj_path": output_trj_path}}
+
+        # Properties specific for BB
+        self.project_id = properties.get("project_id", None)
+        self.node_id = properties.get("node_id", "mmb")
+        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
+        self.check_properties(properties)
+        self.check_arguments()
+
+    def check_data_params(self, out_log, err_log):
+        """Checks all the input/output paths and parameters"""
+        self.output_top_path = check_output_path(
+            self.io_dict["out"]["output_top_path"],
+            "output_top_path",
+            False,
+            out_log,
+            self.__class__.__name__,
+        )
+        self.output_trj_path = check_output_path(
+            self.io_dict["out"]["output_trj_path"],
+            "output_trj_path",
+            False,
+            out_log,
+            self.__class__.__name__,
+        )
+
+    @launchlogger
+    def launch(self) -> int:
+        """Execute the :class:`MDDB <api.mddb.MDDB>` api.mddb.MDDB object."""
+
+        # check input/output paths and parameters
+        self.check_data_params(self.out_log, self.err_log)
+
+        # Setup Biobb
+        if self.check_restart():
+            return 0
+
+        check_mandatory_property(
+            self.project_id, "project_id", self.out_log, self.__class__.__name__
+        )
+
+        self.project_id = self.project_id.strip().upper()
+
+        # Downloading topology file
+        top_string = download_mddb_top(
+            self.project_id,
+            self.node_id,
+            self.selection,
+            self.out_log,
+            self.global_log,
+            self.__class__.__name__
+        )
+        write_pdb(top_string, self.output_top_path, None, self.out_log, self.global_log)
+
+        # Downloading trajectory file
+        trj_string = download_mddb_trj(
+            self.project_id,
+            self.node_id,
+            self.trj_format,
+            self.frames,
+            self.selection,
+            self.out_log,
+            self.global_log,
+            self.__class__.__name__,
+        )
+        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
+
+
+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()
+
+
+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()