Optionally retrieve entity ids for released pdbs

requirements.txt

@@ -1,8 +1,14 @@
-tqdm==4.31.1
+tqdm
+#==4.31.1
 lxml
 requests>=2.20.0
 psutil>=5.6.6
-subprocess32==3.5.4
-wget==3.2
+subprocess32
+#==3.5.4
+#
+wget
+#==3.2
 biopython>=1.78
-pysolr==3.10.0b2
+pysolr
+#==3.10.0b2
+setuptools

setup.py

@@ -6,7 +6,7 @@
 
 setup(
     name="spyprot",
-    version='0.8.8',
+    version='0.9.0',
     author="INTERDISCIPLINARY LABORATORY of BIOLOGICAL SYSTEMS MODELLING, University of Warsaw, Warsaw, Poland",
     author_email="[email protected], [email protected]",
     description="This package provides a set of tools for accessing protein databases and manipulating PDB/CIF files.",

spyprot/fetchChainInfo.py

@@ -826,16 +826,17 @@ class ReleasedPDBs(PDBeSolrSearch):
 
           Return empty list if None found
           example:
-          a = ReleasedProteins("2020-10-10", "2020-11-10").get()
+          a = ReleasedPDBs("2020-10-10", "2020-11-10").get()
 
           Parameters
           ==========
           from_date: datetime or string in format YYYY-MM-DD
           to_date: datetime or string in format YYYY-MM-DD
-          uniq_chains: if True return a list of tuples containing (PDBCode, Chain), else return just PDBCodes.
+          uniq_chains: (default: True) if True return a list of tuples containing (PDBCode, Chain), else return just PDBCodes.
+          with_entity_id: (default: False) if True add entity_id to the returned tuple (PDBCode, EntityId, Chain) - to work must be combined with "uniq_chains" set to True
        '''
 
-    def __init__(self, from_date, to_date='', uniq_chains=True, only_prot=True, only_rna=False):
+    def __init__(self, from_date, to_date='', uniq_chains=True, only_prot=True, only_rna=False, with_entity_id=False):
         super().__init__()
         if type(from_date) is datetime.date:
             from_date = from_date.strftime("%Y-%m-%d")
@@ -860,8 +861,12 @@ def __init__(self, from_date, to_date='', uniq_chains=True, only_prot=True, only
         for i in range(len(documents)):
             pid = documents[i]['pdb_id']
             chain_id = documents[i]['chain_id']
+            entity_id = documents[i]['entity_id']
             if uniq_chains:
-                self.results.append((pid, sorted(chain_id)[0]))
+                if with_entity_id:
+                    self.results.append((pid, entity_id, sorted(chain_id)[0]))
+                else:
+                    self.results.append((pid, sorted(chain_id)[0]))
             else:
                 if pid not in self.results:
                     self.results.append(pid)