aamutils 0.0.5__tar.gz → 0.0.7__tar.gz

{aamutils-0.0.5 → aamutils-0.0.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: aamutils
-Version: 0.0.5
+Version: 0.0.7
 Summary: Collection of atom-atom-mapping utility functions.
 Project-URL: homepage, https://github.com/klausweinbauer/AAMUtils
 Project-URL: source, https://github.com/klausweinbauer/AAMUtils

{aamutils-0.0.5 → aamutils-0.0.7}/aamutils/algorithm/ilp.py

@@ -99,6 +99,7 @@ def expand_partial_aam_balanced(
     beta_map: None | list[tuple[int, int, int]] = None,
     bond_key="bond",
     expected_rc: None | tuple[None | int, None | int] = None,
+    time_limit: None | int = None,
 ) -> tuple[np.ndarray, str, float]:
     """Function to extend the partial atom-atom map beta of the balanced
     reaction G \u2192 H to a full atom-atom map based on the Minimal Chemical
@@ -118,6 +119,7 @@ def expand_partial_aam_balanced(
         help to get correct AAM for reactions where the Minimal Chemical
         Distance is unsuitable, e.g. for a Diels-Alder reaction you can set
         expected_rc to (6, 6).
+    :param time_limit: (optional) Set a timeout for the solver.
 
     :returns: A 3-tuple. The first element is the mapping matrix X. The second
         element is the status string of the ILP solver (e.g. 'Optimal') and the
@@ -186,7 +188,7 @@ def expand_partial_aam_balanced(
     _edge_diff_constraint(problem, lp_X, lp_D, A_G, A_H)
     _indicator_constraint(problem, lp_D, lp_G, lp_S, k)
 
-    status = problem.solve(lp.PULP_CBC_CMD(logPath=r"solver.log"))
+    status = problem.solve(lp.PULP_CBC_CMD(logPath=r"solver.log", timeLimit=time_limit))
 
     np_X = np.zeros([m, m], dtype=np.int32)
     for (i, j), v in lp_X.items():

{aamutils-0.0.5 → aamutils-0.0.7}/aamutils/mapping.py

@@ -20,6 +20,8 @@ class Mapper:
         H = mol_to_graph(h_mol)
 
         M, status, e_diff = expand_partial_aam_balanced(G, H, expected_rc=expected_rc)
+        if status != "Optimal":
+            return None
 
         set_aam(G, H, M)
 
@@ -31,7 +33,7 @@ class Mapper:
         )
         return aam_smiles
 
-    def get_aam(self, smiles: str | list[str], expected_rc) -> str | list[str]:
+    def get_aam(self, smiles: str | list[str], expected_rc=None) -> str | list[str]:
         return_list = True
         if isinstance(smiles, str):
             smiles = [smiles]
@@ -47,7 +49,6 @@ class Mapper:
                 )
             )
         aam_smiles = []
-        print(expected_rc)
         for smiles, exp_rc in zip(smiles, expected_rc):
             aam_smiles.append(self._map_rxn(smiles, expected_rc=exp_rc))
         if not return_list:

{aamutils-0.0.5 → aamutils-0.0.7}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "aamutils"
-version = "0.0.5"
+version = "0.0.7"
 authors = [
 	{name="Klaus Weinbauer", email="klaus@bioinf.uni-leipzig.de"}
 	]

{aamutils-0.0.5 → aamutils-0.0.7}/test/test_mapping.py

@@ -14,3 +14,10 @@ def test_mapper_with_expected_rc():
     rc = get_rc(its)
     assert len(rc.nodes) == 6
     assert len(rc.edges) == 6
+
+
+def test_mapper_infeasable():
+    smiles = "C>>C"
+    mapper = Mapper()
+    aam_smiles = mapper.get_aam(smiles, expected_rc=(2, 2))
+    assert aam_smiles is None