Merge pull request #233 from X-lab-3D/update_zenodo_db

Update zenodo link. Hotfix cmd_pandora commands and defsault database…
X-lab-3D · Feb 27, 2023 · 3a653e6 · 3a653e6
2 parents 3fe9967 + 181750f
commit 3a653e6
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Showing 3 changed files with 5 additions and 5 deletions.
diff --git a/PANDORA/Database/Database.py b/PANDORA/Database/Database.py
@@ -356,14 +356,14 @@ def create_db_folders(db_path=None):
         else:
             print(f'WARNING: folder {D} already exists!')
 
-def fetch_database(db_out_path, db_url='https://sandbox.zenodo.org/record/1129456/files/default.tar.gz?download=1'):
+def fetch_database(db_out_path, db_url='https://sandbox.zenodo.org/record/1163695/files/default.tar.gz?download=1'):
     """Downloads the pre-generated database from zotero.
 
     Args:
         db_out_path (str): Path to the database to be downloaded,  
             should be pointing at a "PANDORA_databases" folder.
         db_url (str, optional): URL for the zenodo database. 
-            Defaults to 'https://sandbox.zenodo.org/record/1129456/files/default.tar.gz?download=1'.
+            Defaults to 'https://sandbox.zenodo.org/record/1163695/files/default.tar.gz?download=1'.
 
     Raises:
         Exception: If the PANDORA_database.pkl file is not found in the destination folder,

diff --git a/PANDORA/__init__.py b/PANDORA/__init__.py
@@ -18,7 +18,7 @@
         data = json.load(f)
         data_folder = data['data_folder_name']
 else:
-    data_folder = '~/PANDORA_database/default'
+    data_folder = '~/PANDORA_databases/default'
 
 PANDORA_data = os.path.expanduser(data_folder)
 

diff --git a/PANDORA/cmd_pandora.py b/PANDORA/cmd_pandora.py
@@ -65,7 +65,7 @@ def cmd_run_pandora():
     )
 
     parser.add_argument(
-        '-c','--clip-Ccdomain',  type=str,
+        '-c','--clip-C-domain',
         help='If provided, ignores C-like domains and Beta-2 microglobulin and only \
                 models binding groove and peptide',
         action='store_true'
@@ -145,7 +145,7 @@ def cmd_run_wrapper():
     )
 
     parser.add_argument(
-        '-c','--clip-Ccdomain',  type=str,
+        '-c','--clip-C-domain',
         help='If provided, ignores C-like domains and Beta-2 microglobulin and only \
                 models binding groove and peptide',
         action='store_true'