Merge pull request ccpem#52 from alan-turing-institute/pdb_to_cif

changed default filetype to cif

Author: James Parkhurst

profet/alphafold.py

@@ -44,7 +44,7 @@ def check_structure(self, uniprot_id: str) -> bool:
         r = requests.get(url)
         return r.status_code != 404
 
-    def get_file_url(self, uniprot_id: str, filetype: str = "pdb") -> str:
+    def get_file_url(self, uniprot_id: str, filetype: str = "cif") -> str:
         """
         Get file url relative to an id from the the Alphafold entry page
 
@@ -77,7 +77,7 @@ def get_file_url(self, uniprot_id: str, filetype: str = "pdb") -> str:
         # Return the URL
         return url["href"]
 
-    def make_url(self, uniprot_id: str, filetype: str = "pdb") -> str:
+    def make_url(self, uniprot_id: str, filetype: str = "cif") -> str:
         """
         Make the URL for the protein
 
@@ -109,7 +109,7 @@ def make_url(self, uniprot_id: str, filetype: str = "pdb") -> str:
     def get_pdb(
         self,
         uniprot_id: str,
-        filetype: str = "pdb",
+        filetype: str = "cif",
     ) -> tuple:
         """
         Returns pdb/cif as strings, saves to file if requested.

profet/cache.py

@@ -35,7 +35,7 @@ def __init__(self, directory: str = None):
         # The manifest filename
         self.manifest = os.path.join(self.directory, "manifest.txt")
 
-    def path(self, uniprot_id: str, filetype: str = "pdb") -> str:
+    def path(self, uniprot_id: str, filetype: str = "cif") -> str:
         """
         Get the proposed path
 

profet/command_line.py

@@ -36,7 +36,7 @@ def get_parser(parser: ArgumentParser = None) -> ArgumentParser:
         "--filetype",
         type=str,
         dest="filetype",
-        default="pdb",
+        default="cif",
         choices=["pdb", "cif"],
         help="The file type to download",
     )

profet/pdb.py

@@ -70,7 +70,7 @@ def make_url(self, uniprot_id: str, filetype: str = "pdb") -> str:
     def get_pdb(
         self,
         uniprot_id: str,
-        filetype: str = "pdb",
+        filetype: str = "cif",
     ) -> tuple:
         """
         Returns pdb/cif as strings, saves to file if requested

profet/profet.py

@@ -54,7 +54,7 @@ def cache(self) -> PDBFileCache:
     def file_from_db(
         self,
         prot_id: str,
-        filetype: str = "pdb",
+        filetype: str = "cif",
         db: str = "pdb",
     ) -> tuple:
         """
@@ -76,7 +76,7 @@ def file_from_db(
     def get_file(
         self,
         uniprot_id: str,
-        filetype: str = "pdb",
+        filetype: str = "cif",
         filesave: bool = False,
         db: str = "pdb",
     ) -> tuple:
@@ -211,7 +211,7 @@ def remove(
         """
         # Get the PDB cache
         cache = PDBFileCache(directory=self.save_directory)
-        identifier, _, _ = self.pdb.get_pdb(uniprot_id, filetype="pdb")
+        identifier, _, _ = self.pdb.get_pdb(uniprot_id, filetype="cif")
         if uniprot_id in cache:
             filename = cache[uniprot_id]
             signal_list = self.Cleaver.signal_residuenumbers_requester(