dcatoolkit 0.2.0__tar.gz → 0.2.1__tar.gz

{dcatoolkit-0.2.0/src/dcatoolkit.egg-info → dcatoolkit-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: dcatoolkit
-Version: 0.2.0
+Version: 0.2.1
 Summary: Collection of useful modules and representations for managing DCA output data.
 Author-email: Raheel Syed Ahmed <raheelsyedahmed@gmail.com>
 Maintainer-email: Raheel Syed Ahmed <raheelsyedahmed@gmail.com>

{dcatoolkit-0.2.0 → dcatoolkit-0.2.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "dcatoolkit"
-version = "0.2.0"
+version = "0.2.1"
 description = "Collection of useful modules and representations for managing DCA output data."
 keywords = ["dca", "toolkit", "DI", "coevolution"]
 

{dcatoolkit-0.2.0 → dcatoolkit-0.2.1}/src/dcatoolkit/__init__.py

@@ -1,5 +1,5 @@
 
-__version__ = "0.1.9"
+__version__ = "0.2.1"
 from .representation import Pairs, DirectInformationData, StructureInformation, ResidueAlignment, MMCIFInformation, PDBInformation
 from .analytics import MSATools
 

{dcatoolkit-0.2.0 → dcatoolkit-0.2.1}/src/dcatoolkit/representation.py

@@ -624,7 +624,7 @@ class StructureInformation:
     """
     @overload
     @staticmethod
-    def fetch_pdb(pdb_id: str, struc_format: Literal["mmcif"]="mmcif", model_num: int=1) -> 'MMCIFInformation':
+    def fetch_pdb(pdb_id: str, struc_format: Literal["mmcif"], model_num: int=1) -> 'MMCIFInformation':
         ...
 
     @overload
@@ -1159,6 +1159,8 @@ class PDBInformation(StructureInformation):
         if chain1 in self.unique_chains and chain2 in self.unique_chains:
             shift1 = non_hetero_structure[non_hetero_structure.chain_id == chain1][0].res_id - 1
             shift2 = non_hetero_structure[non_hetero_structure.chain_id == chain2][0].res_id - 1
+            shift1 *= -1
+            shift2 *= -1
             return shift1, shift2
         else:
             return shift1, shift2
@@ -1195,8 +1197,8 @@ class PDBInformation(StructureInformation):
             ind = np.unravel_index(np.argmin(dist_matrix), dist_matrix.shape)
             # Use the indices to access the atom in the atom array and get the correct atom name.
             # Generate the auth ids of the residues in the pairs ndarray
-            orig_res_id1 = row['residue1'] - shift1
-            orig_res_id2 = row['residue2'] - shift2
+            orig_res_id1 = row['residue1'] + shift1
+            orig_res_id2 = row['residue2'] + shift2
             min_dist_pairs_atoms.append((orig_res_id1, orig_res_id2, row['residue1'], row['residue2'], chain1_res1_structure[ind[0]].atom_name, chain2_res2_structure[ind[1]].atom_name))
         min_dist_pairs_atoms_arr = np.array(min_dist_pairs_atoms, dtype={'names': ['residue1','residue2','auth_residue1','auth_residue2','atom_name1','atom_name2'], 'formats': [int,int,int,int,'<U10','<U10']})
         return min_dist_pairs_atoms_arr    
@@ -1235,7 +1237,7 @@ class PDBInformation(StructureInformation):
             if not(chain1==chain2 and res1 >= res2):
                 if not auth_contacts:
                     shift1, shift2 = self.get_shift_values(chain1, chain2)
-                    contacts_set.add((res1 - shift1, res2 - shift2))
+                    contacts_set.add((res1 + shift1, res2 + shift2))
                 else:
                     contacts_set.add((res1, res2))
         return contacts_set

{dcatoolkit-0.2.0 → dcatoolkit-0.2.1/src/dcatoolkit.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: dcatoolkit
-Version: 0.2.0
+Version: 0.2.1
 Summary: Collection of useful modules and representations for managing DCA output data.
 Author-email: Raheel Syed Ahmed <raheelsyedahmed@gmail.com>
 Maintainer-email: Raheel Syed Ahmed <raheelsyedahmed@gmail.com>

{dcatoolkit-0.2.0 → dcatoolkit-0.2.1}/tests/test_contacts.py

@@ -59,9 +59,9 @@ def check_contacts(test_CA: bool, threshold: float):
         
         cif_file_contacts = read_contacts(corresponding_file)
         chain1, auth_chain1, chain2, auth_chain2 = pdb_id_chain_map[pdb_id]
-        fetch_cif_contacts = {(int(x[0]), int(x[1])) for x in MMCIFInformation.fetch_pdb(pdb_id).get_contacts(test_CA, threshold, chain1, chain2, auth_contacts=True)}
+        fetch_cif_contacts = {(int(x[0]), int(x[1])) for x in MMCIFInformation.fetch_pdb(pdb_id, 'mmcif').get_contacts(test_CA, threshold, chain1, chain2, auth_contacts=True)}
         read_cif_contacts = {(int(x[0]), int(x[1])) for x in MMCIFInformation.read_mmCIF_file(str(cif_file)).get_contacts(test_CA, threshold, chain1, chain2, auth_contacts=True)}
-        fetch_authchain_cif_contacts = {(int(x[0]), int(x[1])) for x in MMCIFInformation.fetch_pdb(pdb_id).get_contacts(test_CA, threshold, auth_chain1, auth_chain2, auth_contacts=True, auth_chain_id_supplied=True)}
+        fetch_authchain_cif_contacts = {(int(x[0]), int(x[1])) for x in MMCIFInformation.fetch_pdb(pdb_id, 'mmcif').get_contacts(test_CA, threshold, auth_chain1, auth_chain2, auth_contacts=True, auth_chain_id_supplied=True)}
         read_authchain_cif_contacts = {(int(x[0]), int(x[1])) for x in MMCIFInformation.read_mmCIF_file(str(cif_file)).get_contacts(test_CA, threshold, auth_chain1, auth_chain2, auth_contacts=True, auth_chain_id_supplied=True)}
         fetch_pdb_contacts = {(int(x[0]), int(x[1])) for x in PDBInformation.fetch_pdb(pdb_id, struc_format="pdb").get_contacts(test_CA, threshold, auth_chain1, auth_chain2, auth_contacts=True)}
         read_pdb_contacts = {(int(x[0]), int(x[1])) for x in PDBInformation.read_pdb_file(f"tests/pdb_info/{pdb_id.lower()}.pdb").get_contacts(test_CA, threshold, auth_chain1, auth_chain2, auth_contacts=True)}