biobb-io 5.1.1__py3-none-any.whl → 5.2.1__py3-none-any.whl

biobb_io/__init__.py

@@ -2,4 +2,4 @@ from . import api
 
 name = "biobb_io"
 __all__ = ["api"]
-__version__ = "5.1.1"
+__version__ = "5.2.1"

biobb_io/api/api_binding_site.py

@@ -95,7 +95,7 @@ class ApiBindingSite(BiobbObject):
         )
 
         self.pdb_code = self.pdb_code.strip().lower()
-        url = "https://www.ebi.ac.uk/pdbe/api/pdb/entry/binding_sites/%s"
+        url = "https://www.ebi.ac.uk/pdbe/api/v2/pdb/entry/binding_sites/%s/1"
 
         # get JSON object
         json_string = download_binding_site(
@@ -104,7 +104,7 @@ class ApiBindingSite(BiobbObject):
 
         # get number of binding sites
         fu.log(
-            "%d binding sites found" % (len(json.loads(json_string)[self.pdb_code])),
+            "%d binding sites found" % (len(json.loads(json_string)[self.pdb_code]['data'])),
             self.out_log,
             self.global_log,
         )

biobb_io/api/canonical_fasta.py

@@ -18,13 +18,13 @@ class CanonicalFasta(BiobbObject):
     """
     | biobb_io CanonicalFasta
     | This class is a wrapper for downloading a FASTA structure from the Protein Data Bank.
-    | Wrapper for the `Protein Data Bank <https://www.rcsb.org/>`_ and the `MMB PDB mirror <http://mmb.irbbarcelona.org/api/>`_ for downloading a single FASTA structure.
+    | Wrapper for the `Protein Data Bank <https://www.rcsb.org/>`_ and the `MMB PDB mirror <https://mdb-login.bsc.es/api/>`_ for downloading a single FASTA structure.
 
     Args:
         output_fasta_path (str): Path to the canonical FASTA file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/canonical_fasta.fasta>`_. Accepted formats: fasta (edam:format_1929).
         properties (dic - Python dictionary object containing the tool parameters, not input/output files):
             * **pdb_code** (*str*) - (None) RSCB PDB code.
-            * **api_id** (*str*) - ("pdbe") Identifier of the PDB REST API from which the PDB structure will be downloaded. Values: pdbe (`PDB in Europe REST API <https://www.ebi.ac.uk/pdbe/pdbe-rest-api>`_), pdb (`RCSB PDB REST API <https://data.rcsb.org/>`_), 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>`_), pdb (`RCSB PDB REST API <https://data.rcsb.org/>`_), mmb (`MMB PDB mirror API <https://mdb-login.bsc.es/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.

biobb_io/api/common.py

@@ -57,7 +57,7 @@ def download_pdb(pdb_code, api_id, out_log=None, global_log=None):
     """
 
     if api_id == "mmb":
-        url = "https://mmb.irbbarcelona.org/api/pdb/" + pdb_code + "/coords/?"
+        url = "https://mdb-login.bsc.es/api/pdb/" + pdb_code + "/coords/?"
     elif api_id == "pdb":
         url = "https://files.rcsb.org/download/" + pdb_code + ".pdb"
     elif api_id == "pdbe":
@@ -73,7 +73,7 @@ def download_af(uniprot_code, out_log=None, global_log=None, classname=None):
         String: Content of the pdb file.
     """
 
-    url = "https://alphafold.ebi.ac.uk/files/AF-" + uniprot_code + "-F1-model_v3.pdb"
+    url = "https://alphafold.ebi.ac.uk/files/AF-" + uniprot_code + "-F1-model_v6.pdb"
 
     fu.log("Downloading %s from: %s" % (uniprot_code, url), out_log, global_log)
 
@@ -146,7 +146,7 @@ def download_mmcif(pdb_code, api_id, out_log=None, global_log=None):
     """
 
     if api_id == "mmb":
-        url = "http://mmb.irbbarcelona.org/api/pdb/" + pdb_code + ".cif"
+        url = "https://mdb-login.bsc.es/api/pdb/" + pdb_code + ".cif"
     elif api_id == "pdb":
         url = "https://files.rcsb.org/download/" + pdb_code + ".cif"
     elif api_id == "pdbe":
@@ -163,11 +163,12 @@ def download_ligand(ligand_code, api_id, out_log=None, global_log=None):
     """
 
     if api_id == "mmb":
-        url = "http://mmb.irbbarcelona.org/api/pdbMonomer/" + ligand_code.lower()
+        url = "https://mdb-login.bsc.es/api/pdbMonomer/" + ligand_code.lower()
         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"
+            "https://files.rcsb.org/ligands/view/" + ligand_code.upper() + ".cif"
         )
         text = urllib.request.urlopen(url).read().decode("utf-8")
 
@@ -186,11 +187,11 @@ def download_fasta(pdb_code, api_id, out_log=None, global_log=None):
     """
 
     if api_id == "mmb":
-        url = "http://mmb.irbbarcelona.org/api/pdb/" + pdb_code + ".fasta"
+        url = "https://mdb-login.bsc.es/api/pdb/" + pdb_code + ".fasta"
     elif api_id == "pdb":
         url = "https://www.rcsb.org/fasta/entry/" + pdb_code
     elif api_id == "pdbe":
-        url = "https://www.ebi.ac.uk/pdbe/entry/pdb/" + pdb_code + "/fasta"
+        url = "https://www.ebi.ac.uk/pdbe/api/v2/pdb/entry/" + pdb_code + "/fasta"
 
     fu.log("Downloading %s from: %s" % (pdb_code, url), out_log, global_log)
     return requests.get(url, verify=True).content.decode("utf-8")
@@ -198,7 +199,7 @@ def download_fasta(pdb_code, api_id, out_log=None, global_log=None):
 
 def download_binding_site(
     pdb_code,
-    url="https://www.ebi.ac.uk/pdbe/api/pdb/entry/binding_sites/%s",
+    url="https://www.ebi.ac.uk/pdbe/api/v2/pdb/entry/binding_sites/%s/1",
     out_log=None,
     global_log=None,
 ):
@@ -231,7 +232,7 @@ def download_ideal_sdf(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.sdf"
+            "https://files.wwpdb.org/pub/pdb/refdata/chem_comp/" + ligand_code.upper()[-1] + "/" + ligand_code.upper() + "/" + ligand_code.upper() + "_ideal.sdf"
         )
         text = urllib.request.urlopen(url).read().decode("utf-8")
 
@@ -242,7 +243,7 @@ def download_ideal_sdf(ligand_code, api_id, out_log=None, global_log=None):
 
 def download_str_info(
     pdb_code,
-    url="http://mmb.irbbarcelona.org/api/pdb/%s.json",
+    url="https://mdb-login.bsc.es/api/pdb/%s.json",
     out_log=None,
     global_log=None,
 ):
@@ -312,7 +313,7 @@ def get_cluster_pdb_codes(pdb_code, cluster, out_log=None, global_log=None):
     Returns:
         String list: The list of pdb_codes of the selected cluster.
     """
-    url = "http://mmb.irbbarcelona.org/api/pdb/"
+    url = "https://mdb-login.bsc.es/api/pdb/"
     pdb_codes = set()
 
     url = url + pdb_code.lower() + "/clusters/cl-" + str(cluster) + ".json"
@@ -356,7 +357,7 @@ def get_uniprot(pdb_code, url, out_log=None, global_log=None):
 
 
 def get_variants(
-    uniprot_id, url="http://mmb.irbbarcelona.org/api", out_log=None, global_log=None
+    uniprot_id, url="https://mdb-login.bsc.es/api", out_log=None, global_log=None
 ):
     """Returns the variants of the `uniprot_id` code.
 

biobb_io/api/ligand.py

@@ -18,13 +18,13 @@ class Ligand(BiobbObject):
     """
     | biobb_io Ligand
     | This class is a wrapper for downloading a PDB ligand from the Protein Data Bank.
-    | 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.
+    | Wrapper for the `Protein Data Bank in Europe <https://www.ebi.ac.uk/pdbe/>`_ and the `MMB PDB mirror <https://mdb-login.bsc.es/api/>`_ for downloading a single PDB ligand.
 
     Args:
         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*) - ("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/>`_).
+            * **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 <https://mdb-login.bsc.es/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.
@@ -114,7 +114,7 @@ def ligand(output_pdb_path: str, properties: Optional[dict] = None, **kwargs) ->
 
 
 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.")
+main = Ligand.get_main(ligand, "Wrapper for the Protein Data Bank in Europe (https://www.ebi.ac.uk/pdbe/) and the MMB PDB mirror (https://mdb-login.bsc.es/api/) for downloading a single PDB ligand.")
 
 if __name__ == "__main__":
     main()

biobb_io/api/mddb.py

@@ -169,6 +169,7 @@ mddb.__doc__ = MDDB.__doc__
 main = MDDB.get_main(
     mddb,
     "This class is a wrapper for downloading a trajectory / topology pair from the MDDB Database.",
+    custom_flags={"output_top_path": "-o", "output_trj_path": "-t"}
 )
 
 if __name__ == "__main__":

biobb_io/api/memprotmd_sim_list.py

@@ -15,7 +15,7 @@ class MemProtMDSimList(BiobbObject):
     | Wrapper for the `MemProtMD DB REST API <http://memprotmd.bioch.ox.ac.uk/>`_ to get all available membrane-protein systems (simulations).
 
     Args:
-        output_simulations (str): Path to the output JSON file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_sim_list.json>`_. Accepted formats: json (edam:format_3464).
+        output_simulations (str): Path to the output JSON file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_sim_list_schema_validator.json>`_. Accepted formats: json (edam:format_3464).
         properties (dic - Python dictionary object containing the tool parameters, not input/output files):
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.

biobb_io/api/memprotmd_sim_search.py

@@ -16,7 +16,7 @@ class MemProtMDSimSearch(BiobbObject):
     | Wrapper for the `MemProtMD DB REST API <http://memprotmd.bioch.ox.ac.uk/>`_ to perform advanced searches.
 
     Args:
-        output_simulations (str): Path to the output JSON file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_sim_search.json>`_. Accepted formats: json (edam:format_3464).
+        output_simulations (str): Path to the output JSON file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_sim_search_schema_validator.json>`_. Accepted formats: json (edam:format_3464).
         properties (dic - Python dictionary object containing the tool parameters, not input/output files):
             * **collection_name** (*str*) - ("refs") Name of the collection to query.
             * **keyword** (*str*) - (None) String to search for in the database metadata. Examples are families like gpcr or porin. Values: porin, outer membrane protein, membrane protein, gpcr (7-transmembrane domain receptors transducing extracellular signals into cells), ion channels, rhodopsin (The most famous GPCRs), abc, mip (Major Intrinsic Protein (MIP)/FNT superfamily: specific for the transport of water and small neutral solutes), ligand-gated (Ligand-dependent signal conversion from chemical signals to electric signals), ammonia (Regulating transepithelial ammonia secretion), mapeg (Eicosanoid and Glutathione metabolism proteins), transmembrane (Heme biosynthesis), protein, kinase (Tyrosine-protein kinases: regulate central nervous system; gene transcription and cell differentiation), glycoprotein (Expression of TCR complex), immunoglobulin (Recognition; binding and adhesion process of cells), integrin (Bridges for cell-cell and cell-extracellular matrix interaction), bnip3 (BNip3 protein family: protect cell from apoptosis), bcl-2 (Regulating cell-death; either induce apoptotic or inhibit apoptosis), atpase (ATPase regulators; P-P-bond hydrolysis-driven transporter), cytochrome (Terminal oxidase enzyme in electron transfer chain), nadp (Transmembrane proteins with NAD(P)-binding Rossmann-fold domains: monoamine oxidase; deaminates norepinephrine; epinephrine; serotonin and dopamine), a4 (Amyloid beta A4 protein; involved in alzheimer's diseases), lysosome (Lysosome-associated membrane glycoprotein: specific to lysosomes; CD107), necrosis (Tumor necrosis factor recepto: binding with TNF and NGF; interacting with a variety of signal molecules; highly associated with apoptosis), oxidoreductase (DHODH; biosynthesis of orotate), ceramidase (Neutral/alkaline ceramidase: converting sphingolipid to sphingosine), dehydrogenase (Aldehyde dehydrogenase:ALDH; Oxidation of aldehydes), mitochondrial, plastid.

biobb_io/api/mmcif.py

@@ -18,13 +18,13 @@ class Mmcif(BiobbObject):
     """
     | biobb_io Mmcif
     | This class is a wrapper for downloading a MMCIF structure from the Protein Data Bank.
-    | 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 single MMCIF structure.
+    | 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 <https://mdb-login.bsc.es/api/>`_ for downloading a single MMCIF structure.
 
     Args:
         output_mmcif_path (str): Path to the output MMCIF file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/ref_output.mmcif>`_. Accepted formats: cif (edam:format_1477), mmcif (edam:format_1477).
         properties (dic - Python dictionary object containing the tool parameters, not input/output files):
             * **pdb_code** (*str*) - (None) RSCB PDB code.
-            * **api_id** (*str*) - ("pdbe") Identifier of the PDB REST API from which the MMCIF structure will be downloaded. Values: pdbe (`PDB in Europe REST API <https://www.ebi.ac.uk/pdbe/pdbe-rest-api>`_), pdb (`RCSB PDB REST API <https://data.rcsb.org/>`_), mmb (`MMB PDB mirror API <http://mmb.irbbarcelona.org/api/>`_).
+            * **api_id** (*str*) - ("pdbe") Identifier of the PDB REST API from which the MMCIF structure will be downloaded. Values: pdbe (`PDB in Europe REST API <https://www.ebi.ac.uk/pdbe/pdbe-rest-api>`_), pdb (`RCSB PDB REST API <https://data.rcsb.org/>`_), mmb (`MMB PDB mirror API <https://mdb-login.bsc.es/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.

biobb_io/api/pdb.py

@@ -18,14 +18,14 @@ class Pdb(BiobbObject):
     """
     | biobb_io Pdb
     | This class is a wrapper for downloading a PDB structure from the Protein Data Bank.
-    | 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 single PDB structure.
+    | 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 <https://mdb-login.bsc.es/api/>`_ for downloading a single PDB structure.
 
     Args:
         output_pdb_path (str): Path to the output PDB file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_pdb.pdb>`_. Accepted formats: pdb (edam:format_1476).
         properties (dic - Python dictionary object containing the tool parameters, not input/output files):
             * **pdb_code** (*str*) - (None) RSCB PDB code.
             * **filter** (*str*) - (["ATOM", "MODEL", "ENDMDL"]) Array of groups to be kept. If value is None or False no filter will be applied. All the possible values are defined in the `official PDB specification <http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html)>`_.
-            * **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>`_), pdb (`RCSB PDB REST API <https://data.rcsb.org/>`_), 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>`_), pdb (`RCSB PDB REST API <https://data.rcsb.org/>`_), mmb (`MMB PDB mirror API <https://mdb-login.bsc.es/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.

biobb_io/api/pdb_cluster_zip.py

@@ -21,7 +21,7 @@ class PdbClusterZip(BiobbObject):
     """
     | biobb_io PdbClusterZip
     | This class is a wrapper for downloading a PDB cluster from the Protein Data Bank.
-    | 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.
+    | 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 <https://mdb-login.bsc.es/api/>`_ for downloading a PDB cluster.
 
     Args:
         output_pdb_zip_path (str): Path to the ZIP file containing the output PDB files. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_pdb_cluster.zip>`_. Accepted formats: zip (edam:format_3987).
@@ -29,7 +29,7 @@ class PdbClusterZip(BiobbObject):
             * **pdb_code** (*str*) - (None) RSCB PDB code.
             * **filter** (*str*) - (["ATOM", "MODEL", "ENDMDL"]) Array of groups to be kept. If value is None or False no filter will be applied. All the possible values are defined in the official PDB specification (http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html)
             * **cluster** (*int*) - (90) Sequence Similarity Cutoff. Values: 50 (structures having less than 50% sequence identity to each other), 70 (structures having less than 70% sequence identity to each other), 90 (structures having less than 90% sequence identity to each other), 95 (structures having less than 95% sequence identity to each other).
-            * **api_id** (*str*) - ("pdbe") Identifier of the PDB REST API from which the PDB structure will be downloaded. Values: pdbe (`PDB in Europe REST API <https://www.ebi.ac.uk/pdbe/pdbe-rest-api>`_), pdb (`RCSB PDB REST API <https://data.rcsb.org/>`_), 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>`_), pdb (`RCSB PDB REST API <https://data.rcsb.org/>`_), mmb (`MMB PDB mirror API <https://mdb-login.bsc.es/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.
@@ -129,7 +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([unique_dir])
+        self.tmp_files.append(unique_dir)
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -146,7 +146,7 @@ def pdb_cluster_zip(
 
 
 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.")
+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 (https://mdb-login.bsc.es/api/) for downloading a PDB cluster.")
 
 if __name__ == "__main__":
     main()

biobb_io/api/pdb_variants.py

@@ -21,7 +21,7 @@ class PdbVariants(BiobbObject):
     """
     | biobb_io PdbVariants
     | This class creates a text file containing a list of all the variants mapped to a PDB code from the corresponding UNIPROT entries.
-    | Wrapper for the `UNIPROT <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.
+    | Wrapper for the `UNIPROT <http://www.uniprot.org/>`_ mirror of the `MMB group REST API <https://mdb-login.bsc.es/api/>`_ for creating a list of all the variants mapped to a PDB code from the corresponding UNIPROT entries.
 
     Args:
         output_mutations_list_txt (str): Path to the TXT file containing an ASCII comma separated values of the mutations. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_pdb_variants.txt>`_. Accepted formats: txt (edam:format_2330).
@@ -96,7 +96,7 @@ class PdbVariants(BiobbObject):
 
         self.pdb_code = self.pdb_code.strip().lower()
 
-        url = "http://mmb.irbbarcelona.org/api"
+        url = "https://mdb-login.bsc.es/api"
         uniprot_id = get_uniprot(self.pdb_code, url, self.out_log, self.global_log)
         url_mapPDBRes = (
             url + "/uniprot/" + uniprot_id + "/mapPDBRes?pdbId=" + self.pdb_code
@@ -169,7 +169,7 @@ def pdb_variants(
 
 
 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.")
+main = PdbVariants.get_main(pdb_variants, "Wrapper for the UNIPROT (http://www.uniprot.org/) mirror of the MMB group REST API (https://mdb-login.bsc.es/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

@@ -18,7 +18,7 @@ class StructureInfo(BiobbObject):
     """
     | biobb_io StructureInfo
     | This class is a wrapper for getting all the available information of a structure from the Protein Data Bank.
-    | Wrapper for the `MMB PDB mirror <http://mmb.irbbarcelona.org/api/>`_ for getting all the available information of a structure from the Protein Data Bank.
+    | Wrapper for the `MMB PDB mirror <https://mdb-login.bsc.es/api/>`_ for getting all the available information of a structure from the Protein Data Bank.
 
     Args:
         output_json_path (str): Path to the output JSON file with all the structure information. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/ref_str_info.json>`_. Accepted formats: json (edam:format_3464).
@@ -92,7 +92,7 @@ class StructureInfo(BiobbObject):
         )
 
         self.pdb_code = self.pdb_code.strip().lower()
-        url = "http://mmb.irbbarcelona.org/api/pdb/%s.json"
+        url = "https://mdb-login.bsc.es/api/pdb/%s.json"
 
         # Downloading PDB file
         json_string = download_str_info(

{biobb_io-5.1.1.dist-info → biobb_io-5.2.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.4
-Name: biobb_io
-Version: 5.1.1
+Metadata-Version: 2.1
+Name: biobb-io
+Version: 5.2.1
 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
@@ -9,34 +9,22 @@ Project-URL: Documentation, http://biobb-io.readthedocs.io/en/latest/
 Project-URL: Bioexcel, https://bioexcel.eu/
 Keywords: Bioinformatics Workflows BioExcel Compatibility
 Classifier: Development Status :: 5 - Production/Stable
-Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: POSIX
 Classifier: Operating System :: Unix
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-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
+Requires-Dist: biobb-common ==5.2.0
 
 [![](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:5.1.1--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:5.2.1--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/)
@@ -74,7 +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
-v5.1.1 2025.1
+v5.2.1 2025.2
 
 ### Installation
 Using PIP:
@@ -83,7 +71,7 @@ Using PIP:
 
 * Installation:
 
-        pip install "biobb_io==5.1.1"
+        pip install "biobb_io==5.2.1"
 
 * Usage: [Python API documentation](https://biobb-io.readthedocs.io/en/latest/modules.html)
 
@@ -91,7 +79,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_io==5.1.1"
+        conda install -c bioconda "biobb_io==5.2.1"
 
 
 * 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)
@@ -100,12 +88,12 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_io:5.1.1--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_io:5.2.1--pyhdfd78af_0
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_io:5.1.1--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_io:5.2.1--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).
@@ -117,7 +105,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:5.1.1--pyhdfd78af_0
+        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:5.2.1--pyhdfd78af_0
 
 
 * Usage:
@@ -132,8 +120,8 @@ The command list and specification can be found at the [Command Line documentati
 ### 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 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) 2015-2025 [Barcelona Supercomputing Center](https://www.bsc.es/)
-* (c) 2015-2025 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
+* (c) 2015-2026 [Barcelona Supercomputing Center](https://www.bsc.es/)
+* (c) 2015-2026 [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-5.2.1.dist-info/RECORD

@@ -0,0 +1,25 @@
+biobb_io/__init__.py,sha256=0UYKlC_5BLNwipIP_D-5dKDohnUNRVUh2aNNf1O3lRI,77
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+biobb_io/api/__init__.py,sha256=s4K59-8EX7yX2qBtB8717ynIEjQ0lVNTp0BDSoc_raM,558
+biobb_io/api/alphafold.py,sha256=EsUHtbypku6rNtMaDrnKf3KLoanuOOB0LOZOnenmoP0,4371
+biobb_io/api/api_binding_site.py,sha256=MoLqQc_oEa0EM3CBmBEcaUsdovEXSl08DByU1gx9fG4,4832
+biobb_io/api/canonical_fasta.py,sha256=VRcvi4eYe8UfrdMxneED0bUR6oIIBxL7Z8vKWhQynxk,4747
+biobb_io/api/common.py,sha256=Ru8rhtPTumdql56vDG9BXzqvp6YEyRR6CKV83IcVt6M,15898
+biobb_io/api/ideal_sdf.py,sha256=BKpFIPcZ8vV6ayQXCmP3Kt_rcQf3ltQCRTtcCqGHriE,4566
+biobb_io/api/ligand.py,sha256=N3roz0nbBdSW3RWmEdh6s1-NEZXgrgaThUWytdrX6Vs,4601
+biobb_io/api/mddb.py,sha256=RWw1MgTTUpvdV-k7ZGNxBr4_wMXf29kGMZKdDj9UTYA,7135
+biobb_io/api/memprotmd_sim.py,sha256=UKgc4UJPukjmBwelVcKbFqGqQhA9BOtfrlJiHf_aW5Q,4120
+biobb_io/api/memprotmd_sim_list.py,sha256=aF4bXr--GZ8byK3ydtvrIL1OesvPLeTERAHsZ5r6AeE,4076
+biobb_io/api/memprotmd_sim_search.py,sha256=VkbHE_qVoQov3iJQFaOy43ZSahCqOHy-7F2s9idcXxE,6436
+biobb_io/api/mmcif.py,sha256=6rHPSj4IcF0nCO2qSNph2ueFj0qWjIMx8ctY9wF5oV0,4622
+biobb_io/api/pdb.py,sha256=gJI5rrf0OeSayPoa2A-4E0dmmi4RpQ1uO3nDYxzji5k,4969
+biobb_io/api/pdb_cluster_zip.py,sha256=FWNnWaq2VnapKWY2eyEo_4oa0rKQ_uXiwI6D_zTnwhg,6622
+biobb_io/api/pdb_variants.py,sha256=Hi7Iv95Yr4vdPF_5jCcesEzD-yGDkh3Kz2VKP9xySH8,6698
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+biobb_io/test/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+biobb_io-5.2.1.dist-info/LICENSE,sha256=z8d0m5b2O9McPEK1xHG_dWgUBT6EfBDz6wA0F7xSPTA,11358
+biobb_io-5.2.1.dist-info/METADATA,sha256=areSXPTzUEO4pwQTu-AOiJBWZEBoL0pfrXmECedHuB0,6794
+biobb_io-5.2.1.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
+biobb_io-5.2.1.dist-info/entry_points.txt,sha256=dDYvVClLKe_Aa3HaMm-7WuS2d16FKGxlnKl816Cf5T4,644
+biobb_io-5.2.1.dist-info/top_level.txt,sha256=1VPldlX2AnFaqODGFJK10WN8AOQuulpX88bLSaQdoS8,9
+biobb_io-5.2.1.dist-info/RECORD,,

{biobb_io-5.1.1.dist-info → biobb_io-5.2.1.dist-info}/WHEEL

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

biobb_io-5.1.1.dist-info/RECORD

@@ -1,25 +0,0 @@
-biobb_io/__init__.py,sha256=yuyKuMxXekhEdVhlQAADYrFWmGfm2YyXpYKUdIDHuvc,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=EsUHtbypku6rNtMaDrnKf3KLoanuOOB0LOZOnenmoP0,4371
-biobb_io/api/api_binding_site.py,sha256=2n2iPJozRKBZ7N_6nEibt8bx58Tp2TTzKpH5g6L5_7c,4819
-biobb_io/api/canonical_fasta.py,sha256=ohuVq410Vk_OvnMVYxReb9QUuce3Ki3FFhV_DJhKZW8,4753
-biobb_io/api/common.py,sha256=KY3ayHCaGBe9zTLDdDc_wK13xXeIaEHTegeWPR2t02M,15766
-biobb_io/api/ideal_sdf.py,sha256=BKpFIPcZ8vV6ayQXCmP3Kt_rcQf3ltQCRTtcCqGHriE,4566
-biobb_io/api/ligand.py,sha256=pMd5wvYqYNlVYT5MatrX346whVfwYY58B2RR_FqEwhE,4610
-biobb_io/api/mddb.py,sha256=J5qgudIQEeE9-UXwjFPQAiFkc7aHXVMMG7Z_j2Dj3yI,7067
-biobb_io/api/memprotmd_sim.py,sha256=UKgc4UJPukjmBwelVcKbFqGqQhA9BOtfrlJiHf_aW5Q,4120
-biobb_io/api/memprotmd_sim_list.py,sha256=WOg4YqWfMvIAgz_19oZ-8asKJnFv8MmRfz0t5ZQhUZo,4059
-biobb_io/api/memprotmd_sim_search.py,sha256=vWfBxNYCmGwGyzTpHnmnuwQ39ZXWO8T0MhdjGjGgZr4,6419
-biobb_io/api/mmcif.py,sha256=M8Tlto6d2hLTUwZGo6zIUGO5bzN6ZwMqYoiMMu1b-rM,4628
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-biobb_io/api/pdb_cluster_zip.py,sha256=9s_HXWep7X3h-kNq1cYbadXgDmsAlG8_Sat0q0snyDA,6633
-biobb_io/api/pdb_variants.py,sha256=BGIbsHl64IANiq2R39dycIxBRGPjm3u1oGpTyeWQ2nA,6707
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-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
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-biobb_io-5.1.1.dist-info/top_level.txt,sha256=1VPldlX2AnFaqODGFJK10WN8AOQuulpX88bLSaQdoS8,9
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