Fixed REST API endpoints

bioexcel · May 7, 2024 · 1be1704 · 1be1704
1 parent 726fb7a
commit 1be1704
Show file tree

Hide file tree

Showing 6 changed files with 43,674 additions and 32,051 deletions.
diff --git a/biobb_io/api/common.py b/biobb_io/api/common.py
@@ -100,7 +100,7 @@ def download_ligand(ligand_code, api_id, out_log=None, global_log=None):
         url = "http://mmb.irbbarcelona.org/api/pdbMonomer/" + ligand_code.lower()
         text = requests.get(url, verify=False).content.decode('utf-8')
     elif api_id == 'pdbe':
-        url = "ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/{0}/{1}/{1}_ideal.pdb".format(ligand_code.upper()[0], ligand_code.upper())
+        url = "https://www.ebi.ac.uk/pdbe/static/files/pdbechem_v2/" + ligand_code.upper() + "_ideal.pdb"
         text = urllib.request.urlopen(url).read().decode('utf-8')
 
     fu.log("Downloading %s from: %s" % (ligand_code, url), out_log, global_log)
@@ -166,10 +166,10 @@ def download_ideal_sdf(ligand_code, api_id, out_log=None, global_log=None):
     """
 
     if api_id == 'pdb':
-        url = "https://files.rcsb.org/ligands/view/" + ligand_code.upper() + "_ideal.sdf"
+        url = "https://files.rcsb.org/ligands/download/" + ligand_code.upper() + "_ideal.sdf"
         text = requests.get(url, verify=False).content.decode('utf-8')
     elif api_id == 'pdbe':
-        url = "ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/{0}/{1}/{1}_ideal.sdf".format(ligand_code.upper()[0], ligand_code.upper())
+        url = "https://www.ebi.ac.uk/pdbe/static/files/pdbechem_v2/" + ligand_code.upper() + "_ideal.sdf"
         text = urllib.request.urlopen(url).read().decode('utf-8')
 
     fu.log("Downloading %s from: %s" % (ligand_code, url), out_log, global_log)

diff --git a/biobb_io/test/reference/api/output_binding_site.json b/biobb_io/test/reference/api/output_binding_site.json
@@ -6,12 +6,12 @@
             "ligand_residues": [
                 {
                     "author_insertion_code": null,
-                    "author_residue_number": null,
-                    "chain_id": null,
-                    "chem_comp_id": null,
-                    "entity_id": null,
-                    "residue_number": null,
-                    "struct_asym_id": null
+                    "author_residue_number": 9001,
+                    "chain_id": "A",
+                    "chem_comp_id": "1C9",
+                    "entity_id": 2,
+                    "residue_number": 1,
+                    "struct_asym_id": "B"
                 }
             ],
             "site_id": "AC1",

diff --git a/biobb_io/test/reference/api/output_ligand.pdb b/biobb_io/test/reference/api/output_ligand.pdb
@@ -1,7 +1,7 @@
 HEADER    Ideal coordinates
  for PDB-CCD IBP
 COMPND    IBP
-AUTHOR    pdbccdutils 0.8.0
+AUTHOR    pdbccdutils 0.8.4
 AUTHOR    RDKit 2023.03.3
 HETATM    1 C1   IBP A   1      -0.364  -0.176  -3.442  1.00 20.00           C  
 HETATM    2 C2   IBP A   1      -0.931  -0.349   2.970  1.00 20.00           C