Removed unused method and tests.

prointvar/pdbx.py

@@ -553,37 +553,6 @@ def add_mmcif_res_full(data):
     return table
 
 
-def get_mmcif_res_split(data):
-    """
-    Utility that adds new columns to the table.
-    Adds new columns from the 'full res' (i.e. seq_id + ins_code).
-    
-    adds: 'label_seq_id', 'auth_seq_id', and 'pdbx_PDB_ins_code'
-    
-    :param data: pandas DataFrame object
-    :return: returns a modified pandas DataFrame
-    """
-
-    table = data
-    seq_ids = []
-    ins_codes = []
-    for i in table.index:
-        values = string_split(table.loc[i, "label_seq_id_full"])
-        if len(values) == 1:
-            values.append('?')
-        elif len(values) == 2 and values[0] == '-':
-            values = ["".join(values), '?']
-        elif len(values) == 3 and values[0] == '-':
-            values = ["".join(values[0] + values[1]), values[2]]
-        seq_ids.append(values[0])
-        ins_codes.append(values[1])
-    table["label_seq_id"] = seq_ids
-    table["auth_seq_id"] = seq_ids
-    table["pdbx_PDB_ins_code"] = ins_codes
-
-    return table
-
-
 def fix_pdb_ins_code(data):
     """
     Utility that fixes the 'pdbx_PDB_ins_code' column to match is expected

tests/test_pdbx.py

@@ -23,7 +23,7 @@
                             write_mmcif_from_table, get_mmcif_selected_from_table,
                             get_contact_indexes_from_table, add_mmcif_contacts,
                             add_mmcif_res_full, parse_pdb_atoms_from_file,
-                            get_mmcif_res_split, get_atom_line, write_pdb_from_table,
+                            get_atom_line, write_pdb_from_table,
                             add_mmcif_atom_altloc, residues_aggregation,
                             remove_multiple_altlocs, add_mmcif_new_pro_ids,
                             remove_partial_residues, get_coordinates, get_sequence,
@@ -65,7 +65,6 @@ def setUp(self):
         self.parser_categories = parse_mmcif_categories_from_file
         self.add_contacts = add_mmcif_contacts
         self.add_res_full = add_mmcif_res_full
-        self.get_mmcif_res_split = get_mmcif_res_split
         self.write_pdb_from_table = write_pdb_from_table
         self.get_atom_line = get_atom_line
         self.add_mmcif_atom_altloc = add_mmcif_atom_altloc
@@ -106,7 +105,6 @@ def tearDown(self):
         self.parser_categories = None
         self.add_contacts = None
         self.add_res_full = None
-        self.get_mmcif_res_split = None
         self.write_pdb_from_table = None
         self.get_atom_line = None
         self.add_mmcif_atom_altloc = None
@@ -476,36 +474,6 @@ def test_read_pdb(self):
         else:
             raise IOError("%s" % self.inputpdb)
 
-    def test_get_res_split(self):
-        if os.path.isfile(self.inputpdb):
-            data = self.parser_pdb(self.inputpdb)
-            data = self.get_mmcif_res_split(data)
-            self.assertIn('label_seq_id_full', [k for k in data])
-            self.assertIn('label_seq_id', [k for k in data])
-            self.assertIn('auth_seq_id', [k for k in data])
-            self.assertIn('pdbx_PDB_ins_code', [k for k in data])
-            self.assertEqual('118', data.loc[0, 'label_seq_id_full'])
-            self.assertEqual('118', data.loc[0, 'label_seq_id'])
-            self.assertEqual('118', data.loc[0, 'auth_seq_id'])
-            self.assertEqual('?', data.loc[0, 'pdbx_PDB_ins_code'])
-            self.assertEqual('.', data.loc[0, 'label_alt_id'])
-        else:
-            raise IOError("%s" % self.inputpdb)
-
-    def test_get_res_split_various(self):
-        data = pd.DataFrame([{'label_seq_id_full': '1'}])
-        data = self.get_mmcif_res_split(data)
-        self.assertEqual('1', data.loc[0, 'label_seq_id'])
-        self.assertEqual('?', data.loc[0, 'pdbx_PDB_ins_code'])
-        data = pd.DataFrame([{'label_seq_id_full': '-10'}])
-        data = self.get_mmcif_res_split(data)
-        self.assertEqual('-10', data.loc[0, 'label_seq_id'])
-        self.assertEqual('?', data.loc[0, 'pdbx_PDB_ins_code'])
-        data = pd.DataFrame([{'label_seq_id_full': '-100A'}])
-        data = self.get_mmcif_res_split(data)
-        self.assertEqual('-100', data.loc[0, 'label_seq_id'])
-        self.assertEqual('A', data.loc[0, 'pdbx_PDB_ins_code'])
-
     def test_parse_pdb_altloc(self):
         if os.path.isfile(self.inputpdb2):
             data = self.parser_pdb(self.inputpdb2, remove_altloc=False)
@@ -660,6 +628,7 @@ def test_get_real_residue_ranges(self):
         self.assertEqual(ends, ('136', '452'))
         self.assertEqual(end_inscodes, ('?', '?'))
 
+
 if __name__ == '__main__':
     logging.basicConfig(stream=sys.stderr)
     logging.getLogger("prointvar").setLevel(logging.DEBUG)