biobb-io 5.0.1__tar.gz → 5.1.0__tar.gz

{biobb_io-5.0.1 → biobb_io-5.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biobb_io
-Version: 5.0.1
+Version: 5.1.0
 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 +17,14 @@ 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==5.1.0
 
 [![](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:5.1.0--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 +62,7 @@ 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
+v5.1.0 2025.1
 
 ### Installation
 Using PIP:
@@ -71,7 +71,7 @@ Using PIP:
 
 * Installation:
 
-        pip install "biobb_io==5.0.1"
+        pip install "biobb_io==5.1.0"
 
 * Usage: [Python API documentation](https://biobb-io.readthedocs.io/en/latest/modules.html)
 
@@ -79,7 +79,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_io==5.0.1"
+        conda install -c bioconda "biobb_io==5.1.0"
 
 
 * 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 +88,12 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_io:5.0.1--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_io:5.1.0--pyhdfd78af_0
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_io:5.0.1--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_io:5.1.0--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 +105,7 @@ 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:5.1.0--pyhdfd78af_0
 
 
 * Usage:
@@ -118,10 +118,10 @@ 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-5.1.0}/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:5.1.0--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
+v5.1.0 2025.1
 
 ### Installation
 Using PIP:
@@ -50,7 +50,7 @@ Using PIP:
 
 * Installation:
 
-        pip install "biobb_io==5.0.1"
+        pip install "biobb_io==5.1.0"
 
 * 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==5.1.0"
 
 
 * 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:5.1.0--pyhdfd78af_0
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_io:5.0.1--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_io:5.1.0--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:5.1.0--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-5.1.0}/biobb_io/__init__.py

@@ -2,4 +2,4 @@ from . import api
 
 name = "biobb_io"
 __all__ = ["api"]
-__version__ = "5.0.1"
+__version__ = "5.1.0"

{biobb_io-5.0.1 → biobb_io-5.1.0}/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-5.1.0}/biobb_io/api/alphafold.py

@@ -118,6 +118,8 @@ def alphafold(output_pdb_path: str, properties: Optional[dict] = None, **kwargs)
         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."""

{biobb_io-5.0.1 → biobb_io-5.1.0}/biobb_io/api/api_binding_site.py

@@ -130,6 +130,8 @@ def api_binding_site(
         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."""

{biobb_io-5.0.1 → biobb_io-5.1.0}/biobb_io/api/canonical_fasta.py

@@ -120,6 +120,8 @@ def canonical_fasta(
         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."""

{biobb_io-5.0.1 → biobb_io-5.1.0}/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 +85,42 @@ 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_mmcif(pdb_code, api_id, out_log=None, global_log=None):
     """
     Returns:
@@ -112,9 +149,7 @@ 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 +208,12 @@ 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 +261,13 @@ 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 +306,11 @@ 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 +422,7 @@ 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-5.1.0}/biobb_io/api/ideal_sdf.py

@@ -118,6 +118,8 @@ def ideal_sdf(output_sdf_path: str, properties: Optional[dict] = None, **kwargs)
         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."""

{biobb_io-5.0.1 → biobb_io-5.1.0}/biobb_io/api/ligand.py

@@ -27,7 +27,7 @@ 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 +38,7 @@ 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 +64,7 @@ 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
 
@@ -118,6 +118,8 @@ def ligand(output_pdb_path: str, properties: Optional[dict] = None, **kwargs) ->
         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."""

biobb_io-5.1.0/biobb_io/api/mddb.py

@@ -0,0 +1,196 @@
+#!/usr/bin/env python
+
+"""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
+
+from biobb_io.api.common import (
+    check_mandatory_property,
+    check_output_path,
+    download_mddb_top,
+    write_pdb,
+    download_mddb_trj,
+    write_bin
+)
+
+
+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.
+            * **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.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)
+
+        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(
+        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)
+
+
+if __name__ == "__main__":
+    main()

{biobb_io-5.0.1 → biobb_io-5.1.0}/biobb_io/api/memprotmd_sim.py

@@ -113,6 +113,8 @@ def memprotmd_sim(
         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."""

{biobb_io-5.0.1 → biobb_io-5.1.0}/biobb_io/api/memprotmd_sim_list.py

@@ -102,6 +102,8 @@ def memprotmd_sim_list(
         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."""

{biobb_io-5.0.1 → biobb_io-5.1.0}/biobb_io/api/memprotmd_sim_search.py

@@ -113,6 +113,8 @@ def memprotmd_sim_search(
         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."""

{biobb_io-5.0.1 → biobb_io-5.1.0}/biobb_io/api/mmcif.py

@@ -118,6 +118,8 @@ def mmcif(output_mmcif_path: str, properties: Optional[dict] = None, **kwargs) -
         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."""

{biobb_io-5.0.1 → biobb_io-5.1.0}/biobb_io/api/pdb.py

@@ -123,6 +123,8 @@ def pdb(output_pdb_path: str, properties: Optional[dict] = None, **kwargs) -> in
         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."""

{biobb_io-5.0.1 → biobb_io-5.1.0}/biobb_io/api/pdb_cluster_zip.py

@@ -132,7 +132,10 @@ 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([
+            # self.stage_io_dict.get("unique_dir", ""),
+            unique_dir
+        ])
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -150,6 +153,8 @@ def pdb_cluster_zip(
         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."""

{biobb_io-5.0.1 → biobb_io-5.1.0}/biobb_io/api/pdb_variants.py

@@ -131,14 +131,10 @@ class PdbVariants(BiobbObject):
             for k in mapdic.keys():
                 for fragment in mapdic[k]:
                     if (
-                        int(fragment["unp_start"])
-                        <= int(uni_mut["resnum"])
-                        <= int(fragment["unp_end"])
+                        int(fragment["unp_start"]) <= int(uni_mut["resnum"]) <= int(fragment["unp_end"])
                     ):
                         resnum = (
-                            int(uni_mut["resnum"])
-                            + int(fragment["pdb_start"])
-                            - int(fragment["unp_start"])
+                            int(uni_mut["resnum"]) + int(fragment["pdb_start"]) - int(fragment["unp_start"])
                         )
                         mutations.append(
                             k[-1] + "." + uni_mut["wt"] + str(resnum) + uni_mut["mt"]
@@ -179,6 +175,8 @@ def pdb_variants(
         **kwargs,
     ).launch()
 
+    pdb_variants.__doc__ = PdbVariants.__doc__
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""

{biobb_io-5.0.1 → biobb_io-5.1.0}/biobb_io/api/structure_info.py

@@ -118,6 +118,8 @@ def structure_info(
         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."""

{biobb_io-5.0.1 → biobb_io-5.1.0}/biobb_io.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
-Name: biobb_io
-Version: 5.0.1
+Name: biobb-io
+Version: 5.1.0
 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 +17,14 @@ 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==5.1.0
 
 [![](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:5.1.0--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 +62,7 @@ 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
+v5.1.0 2025.1
 
 ### Installation
 Using PIP:
@@ -71,7 +71,7 @@ Using PIP:
 
 * Installation:
 
-        pip install "biobb_io==5.0.1"
+        pip install "biobb_io==5.1.0"
 
 * Usage: [Python API documentation](https://biobb-io.readthedocs.io/en/latest/modules.html)
 
@@ -79,7 +79,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_io==5.0.1"
+        conda install -c bioconda "biobb_io==5.1.0"
 
 
 * 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 +88,12 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_io:5.0.1--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_io:5.1.0--pyhdfd78af_0
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_io:5.0.1--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_io:5.1.0--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 +105,7 @@ 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:5.1.0--pyhdfd78af_0
 
 
 * Usage:
@@ -118,10 +118,10 @@ 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-5.1.0}/biobb_io.egg-info/SOURCES.txt

@@ -16,6 +16,7 @@ biobb_io/api/canonical_fasta.py
 biobb_io/api/common.py
 biobb_io/api/ideal_sdf.py
 biobb_io/api/ligand.py
+biobb_io/api/mddb.py
 biobb_io/api/memprotmd_sim.py
 biobb_io/api/memprotmd_sim_list.py
 biobb_io/api/memprotmd_sim_search.py

{biobb_io-5.0.1 → biobb_io-5.1.0}/biobb_io.egg-info/entry_points.txt

@@ -4,6 +4,7 @@ api_binding_site = biobb_io.api.api_binding_site:main
 canonical_fasta = biobb_io.api.canonical_fasta:main
 ideal_sdf = biobb_io.api.ideal_sdf:main
 ligand = biobb_io.api.ligand:main
+mddb = biobb_io.api.mddb:main
 memprotmd_sim = biobb_io.api.memprotmd_sim:main
 memprotmd_sim_list = biobb_io.api.memprotmd_sim_list:main
 memprotmd_sim_search = biobb_io.api.memprotmd_sim_search:main

biobb_io-5.1.0/biobb_io.egg-info/requires.txt

@@ -0,0 +1 @@
+biobb_common==5.1.0

{biobb_io-5.0.1 → biobb_io-5.1.0}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setuptools.setup(
     name="biobb_io",
-    version="5.0.1",
+    version="5.1.0",
     author="Biobb developers",
     author_email="pau.andrio@bsc.es",
     description="Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks.",
@@ -19,7 +19,7 @@ setuptools.setup(
     },
     packages=setuptools.find_packages(exclude=["docs", "test"]),
     package_data={"biobb_io": ["py.typed"]},
-    install_requires=["biobb_common==5.0.0"],
+    install_requires=["biobb_common==5.1.0"],
     python_requires=">=3.9",
     entry_points={
         "console_scripts": [
@@ -28,6 +28,7 @@ setuptools.setup(
             "canonical_fasta = biobb_io.api.canonical_fasta:main",
             "ideal_sdf = biobb_io.api.ideal_sdf:main",
             "ligand = biobb_io.api.ligand:main",
+            "mddb = biobb_io.api.mddb:main",
             "memprotmd_sim_list = biobb_io.api.memprotmd_sim_list:main",
             "memprotmd_sim_search = biobb_io.api.memprotmd_sim_search:main",
             "memprotmd_sim = biobb_io.api.memprotmd_sim:main",

biobb_io-5.0.1/biobb_io.egg-info/requires.txt

@@ -1 +0,0 @@
-biobb_common==5.0.0