Remove potential circular import

Author: Old-Shatterhand

glyles/glycans/factory/factory_o.py

@@ -4,7 +4,7 @@
 from rdkit.Chem.rdchem import BondType
 
 from glyles.glycans.utils import Config, Enantiomer, Lactole, Tree, find_longest_c_chain
-from glyles.utils import smiles2mol
+from glyles.glycans.utils import smiles2mol
 
 
 class OpenFactory:

glyles/glycans/mono/monomer.py

@@ -8,7 +8,7 @@
 from glyles.glycans.mono.reactor import SMILESReaktor
 from glyles.glycans.utils import Config, find_isomorphism_nx
 from glyles.iupac.IUPACLexer import IUPACLexer
-from glyles.utils import smiles2mol
+from glyles.glycans.utils import smiles2mol
 
 
 def shift(d, offset):

glyles/glycans/poly/glycan.py

@@ -19,7 +19,7 @@
 from glyles.glycans.utils import ParseError
 from glyles.gwb.GWBLexer import GWBLexer
 from glyles.iupac.IUPACLexer import IUPACLexer
-from glyles.utils import smiles2mol
+from glyles.glycans.utils import smiles2mol
 
 if not hasattr(IUPACLexer, "MOD"):
     IUPACLexer.MOD = IUPACLexer.QMARK + 1

glyles/glycans/poly/merger.py

@@ -6,7 +6,7 @@
 import numpy as np
 
 from glyles.glycans.utils import sanitize_smiles
-from glyles.utils import smiles2mol
+from glyles.glycans.utils import smiles2mol
 
 
 def masked2nx(smiles: str, mask: list[int]) -> nx.Graph:

glyles/glycans/utils.py

@@ -1,17 +1,14 @@
 import re
-from collections import deque
 from enum import Enum
+from collections import deque
+from itertools import permutations
 
-import networkx as nx
 import numpy as np
+import networkx as nx
 from networkx.algorithms import isomorphism
-
-from itertools import permutations
-
+from rdkit import Chem
 from rdkit.Chem.rdchem import ChiralType
 
-from glyles.utils import smiles2mol
-
 
 class Verbosity(Enum):
     """
@@ -95,6 +92,11 @@ class ParseError(ValueError):
 }
 
 
+def smiles2mol(smiles: str):
+    smiles = re.sub("\[CH[0-9]\]", "C", smiles)
+    return Chem.MolFromSmiles(smiles)
+
+
 def sanitize_smiles(smiles, mask=None):
     """
     Sanitize the smiles string by removing unnecessary brackets.

tests/test_utils.py

@@ -4,7 +4,7 @@
 from rdkit.Chem import MolFromSmiles
 from rdkit.Chem.rdchem import ChiralType
 
-from glyles.glycans.utils import find_isomorphism_nx as iso
+from glyles.glycans.utils import find_isomorphism_nx
 
 CHIRALITY = [ChiralType.CHI_TETRAHEDRAL_CW, ChiralType.CHI_TETRAHEDRAL_CCW]
 
@@ -41,7 +41,7 @@ def compare_smiles(computed, solution):
 ])
 def test_isomorphism(data):
     smiles1, smiles2, size, name = data
-    mapping = iso(smiles1, smiles2, name)
+    mapping = find_isomorphism_nx(smiles1, smiles2, name)
 
     assert len(mapping) == size
     check_map(smiles1, smiles2, mapping)