Update features and fix bug (#13)

* update

* test mod compatible

* add graph visualizer

* fix lint

* add copy right for FGUtils

* prepare release

* add partial map expansion

* add testcase for partial expansion ver1

* update new features

* prepare release

.gitignore

@@ -6,3 +6,5 @@
 *.json
 test_mod.py
 test_format.py
+*dev_zone
+test_format.py

Test/SynAAM/test_aam_validator.py

@@ -0,0 +1,97 @@
+import unittest
+from synutility.SynAAM.aam_validator import AAMValidator
+
+
+class TestAMMValidator(unittest.TestCase):
+
+    def setUp(self):
+        self.true_pair = (
+            (
+                "[CH:8]=1[S:9][CH:10]=[C:6]([C:5]#[C:4][CH2:3][N:2]([C:11]2=[CH:12]"
+                + "[CH:13]=[CH:14][CH:15]=[CH:16]2)[CH3:1])[CH:7]=1.[OH2:17]>>[C:5]([N:2]"
+                + "([CH3:1])[C:11]1=[CH:12][CH:13]=[CH:14][CH:15]=[CH:16]1)([C:6]2="
+                + "[CH:10][S:9][CH:8]=[CH:7]2)=[CH:4][CH:3]=[O:17]"
+            ),
+            (
+                "[OH2:17].[cH:12]1[cH:13][cH:14][cH:15][cH:16][c:11]1[N:2]([CH3:1])"
+                + "[CH2:3][C:4]#[C:5][c:6]1[cH:10][s:9][cH:8][cH:7]1>>[cH:12]1[cH:13]"
+                + "[cH:14][cH:15][cH:16][c:11]1[N:2]([CH3:1])[C:5](=[CH:4][CH:3]=[O:17])"
+                + "[c:6]1[cH:10][s:9][cH:8][cH:7]1"
+            ),
+        )
+        self.false_pair = (
+            (
+                "[CH:8]=1[S:9][CH:10]=[C:6]([C:5]#[C:4][CH2:3][N:2]([C:11]2=[CH:12]"
+                + "[CH:13]=[CH:14][CH:15]=[CH:16]2)[CH3:1])[CH:7]=1.[OH2:17]>>[C:5]"
+                + "([N:2]([CH3:1])[C:11]1=[CH:12][CH:13]=[CH:14][CH:15]=[CH:16]1)"
+                + "([C:6]2=[CH:10][S:9][CH:8]=[CH:7]2)=[CH:4][CH:3]=[O:17]"
+            ),
+            (
+                "[CH3:1][N:2]([CH2:3][C:4]#[C:5][c:7]1[cH:8][cH:9][s:10][cH:11]1)"
+                + "[c:12]1[cH:13][cH:14][cH:15][cH:16][cH:17]1.[OH2:6]>>[CH3:1][N:2]"
+                + "([C:3](=[CH:4][CH:5]=[O:6])[c:7]1[cH:8][cH:9][s:10][cH:11]1)"
+                + "[c:12]1[cH:13][cH:14][cH:15][cH:16][cH:17]1"
+            ),
+        )
+        self.tautomer = (
+            "[CH3:1][C:2](=[O:3])[OH:4].[CH3:5][CH2:6][OH:7]>>[CH3:1][C:2](=[O:3])"
+            + "[O:7][CH2:6][CH3:5].[OH2:4]",
+            "[CH3:1][C:2](=[O:3])[OH:4].[CH3:5][CH2:6][OH:7]>>"
+            + "[CH3:1][C:2](=[O:4])[O:7][CH2:6][CH3:5].[OH2:3]",
+        )
+
+        self.data_dict_1 = {"ref": self.true_pair[0], "map": self.true_pair[1]}
+        self.data_dict_2 = {"ref": self.false_pair[0], "map": self.false_pair[1]}
+        self.data_dict_3 = {"ref": self.tautomer[0], "map": self.tautomer[1]}
+        self.data = [self.data_dict_1, self.data_dict_2, self.data_dict_3]
+
+    def test_smiles_check(self):
+
+        self.assertTrue(
+            AAMValidator.smiles_check(
+                *self.true_pair, check_method="RC", ignore_aromaticity=False
+            )
+        )
+        self.assertFalse(
+            AAMValidator.smiles_check(
+                *self.false_pair, check_method="RC", ignore_aromaticity=False
+            )
+        )
+
+    def test_smiles_check_tautomer(self):
+        self.assertFalse(
+            AAMValidator.smiles_check(
+                self.tautomer[0],
+                self.tautomer[1],
+                check_method="RC",
+                ignore_aromaticity=False,
+            )
+        )
+
+        self.assertTrue(
+            AAMValidator.smiles_check_tautomer(
+                self.tautomer[0],
+                self.tautomer[1],
+                check_method="RC",
+                ignore_aromaticity=True,
+            )
+        )
+
+    def test_validate_smiles_dataframe(self):
+
+        results = AAMValidator.validate_smiles(
+            data=self.data,
+            ground_truth_col="ref",
+            mapped_cols=["map"],
+            check_method="RC",
+            ignore_aromaticity=False,
+            n_jobs=2,
+            verbose=0,
+            ignore_tautomers=False,
+        )
+        self.assertEqual(results[0]["accuracy"], 66.67)
+        self.assertEqual(results[0]["success_rate"], 100)
+
+
+if __name__ == "__main__":
+    unittest.main()

Test/SynAAM/test_inference.py

@@ -0,0 +1,25 @@
+import unittest
+from synutility.SynIO.Format.chemical_conversion import smart_to_gml
+from synutility.SynAAM.inference import aam_infer
+
+
+class TestAAMInference(unittest.TestCase):
+
+    def setUp(self):
+
+        self.rsmi = "BrCc1ccc(Br)cc1.COCCO>>Br.COCCOCc1ccc(Br)cc1"
+        self.gml = smart_to_gml("[Br:1][CH3:2].[OH:3][H:4]>>[Br:1][H:4].[CH3:2][OH:3]")
+        self.expect = (
+            "[Br:1][CH2:2][C:3]1=[CH:4][CH:6]=[C:7]([Br:8])[CH:9]"
+            + "=[CH:5]1.[CH3:10][O:11][CH2:12][CH2:13][O:14][H:15]>>"
+            + "[Br:1][H:15].[CH2:2]([C:3]1=[CH:4][CH:6]=[C:7]([Br:8])"
+            + "[CH:9]=[CH:5]1)[O:14][CH2:13][CH2:12][O:11][CH3:10]"
+        )
+
+    def test_aam_infer(self):
+        result = aam_infer(self.rsmi, self.gml)
+        self.assertEqual(result[0], self.expect)
+
+
+if __name__ == "__main__":
+    unittest.main()

Test/SynIO/Format/test_its_construction.py → Test/SynAAM/test_its_construction.py

@@ -1,6 +1,6 @@
 import unittest
 import networkx as nx
-from synutility.SynIO.Format.its_construction import ITSConstruction
+from synutility.SynAAM.its_construction import ITSConstruction
 
 
 class TestITSConstruction(unittest.TestCase):

Test/SynAAM/test_normalize_aam.py

@@ -21,7 +21,7 @@ def test_fix_rsmi(self):
         for both reactants and products."""
         input_rsmi = "[C:0]>>[C:1]"
         expected_rsmi = "[C:1]>>[C:2]"
-        self.assertEqual(self.normalizer.fix_rsmi(input_rsmi), expected_rsmi)
+        self.assertEqual(self.normalizer.fix_aam_rsmi(input_rsmi), expected_rsmi)
 
     def test_extract_subgraph(self):
         """Test extraction of a subgraph based on specified indices."""

Test/SynAAM/test_partial_expand.py

@@ -1,4 +1,8 @@
 import unittest
+from synutility.SynAAM.aam_validator import AAMValidator
+from synutility.SynAAM.its_construction import ITSConstruction
+from synutility.SynIO.Format.chemical_conversion import rsmi_to_graph
+
 from synutility.SynAAM.partial_expand import PartialExpand
 
 
@@ -16,7 +20,7 @@ def test_expand(self):
         # Perform the expansion
         output_rsmi = PartialExpand.expand(input_rsmi)
         # Assert the result matches the expected output
-        self.assertEqual(output_rsmi, expected_rsmi)
+        self.assertTrue(AAMValidator.smiles_check(output_rsmi, expected_rsmi, "ITS"))
 
     def test_expand_2(self):
         input_rsmi = "CC[CH2:3][Cl:1].[NH2:2][H:4]>>CC[CH2:3][NH2:2].[Cl:1][H:4]"
@@ -25,7 +29,22 @@ def test_expand_2(self):
             "[CH3:1][CH2:2][CH2:3][Cl:4].[NH2:5][H:6]"
             + ">>[CH3:1][CH2:2][CH2:3][NH2:5].[Cl:4][H:6]"
         )
-        self.assertEqual(output_rsmi, expected_rsmi)
+        self.assertTrue(AAMValidator.smiles_check(output_rsmi, expected_rsmi, "ITS"))
+
+    def test_graph_expand(self):
+        input_rsmi = "BrCc1ccc(Br)cc1.COCCO>>Br.COCCOCc1ccc(Br)cc1"
+        expect = (
+            "[Br:1][CH2:2][C:3]1=[CH:4][CH:6]=[C:7]([Br:8])[CH:9]=[CH:5]1."
+            + "[CH3:10][O:11][CH2:12][CH2:13][O:14][H:15]>>[Br:1][H:15]"
+            + ".[CH2:2]([C:3]1=[CH:4][CH:6]=[C:7]([Br:8])[CH:9]=[CH:5]1)"
+            + "[O:14][CH2:13][CH2:12][O:11][CH3:10]"
+        )
+        r, p = rsmi_to_graph(
+            "[Br:1][CH3:2].[OH:3][H:4]>>[Br:1][H:4].[CH3:2][OH:3]", sanitize=False
+        )
+        its = ITSConstruction().ITSGraph(r, p)
+        output = PartialExpand.graph_expand(its, input_rsmi)
+        self.assertTrue(AAMValidator.smiles_check(output, expect))
 
 
 if __name__ == "__main__":

Test/SynGraph/Transform/test_multi_step.py

@@ -0,0 +1,55 @@
+import unittest
+from synutility.SynIO.Format.chemical_conversion import smart_to_gml
+from synutility.SynGraph.Transform.multi_step import (
+    perform_multi_step_reaction,
+    remove_reagent_from_smiles,
+    calculate_max_depth,
+    find_all_paths,
+)
+
+
+class TestMultiStep(unittest.TestCase):
+    def setUp(self) -> None:
+        smarts = [
+            "[CH2:4]([CH:5]=[O:6])[H:7]>>[CH2:4]=[CH:5][O:6][H:7]",
+            (
+                "[CH2:2]=[O:3].[CH2:4]=[CH:5][O:6][H:7]>>[CH2:2]([O:3][H:7])[CH2:4]"
+                + "[CH:5]=[O:6]"
+            ),
+            "[CH2:4]([CH:5]=[O:6])[H:8]>>[CH2:4]=[CH:5][O:6][H:8]",
+            (
+                "[CH2:2]([OH:3])[CH:4]=[CH:5][O:6][H:8]>>[CH2:2]=[CH:4][CH:5]=[O:6]"
+                + ".[OH:3][H:8]"
+            ),
+        ]
+        self.gml = [smart_to_gml(value) for value in smarts]
+        self.order = [0, 1, 0, -1]
+        self.rsmi = "CC=O.CC=O.CCC=O>>CC=O.CC=C(C)C=O.O"
+
+    def test_remove_reagent_from_smiles(self):
+        rsmi = remove_reagent_from_smiles(self.rsmi)
+        self.assertEqual(rsmi, "CC=O.CCC=O>>CC=C(C)C=O.O")
+
+    def test_perform_multi_step_reaction(self):
+        results, _ = perform_multi_step_reaction(self.gml, self.order, self.rsmi)
+        self.assertEqual(len(results), 4)
+
+    def test_calculate_max_depth(self):
+        _, reaction_tree = perform_multi_step_reaction(self.gml, self.order, self.rsmi)
+        max_depth = calculate_max_depth(reaction_tree)
+        self.assertEqual(max_depth, 4)
+
+    def test_find_all_paths(self):
+        results, reaction_tree = perform_multi_step_reaction(
+            self.gml, self.order, self.rsmi
+        )
+        target_products = sorted(self.rsmi.split(">>")[1].split("."))
+        max_depth = len(results)
+        all_paths = find_all_paths(reaction_tree, target_products, self.rsmi, max_depth)
+        self.assertEqual(len(all_paths), 1)
+        real_path = all_paths[0][1:]  # remove the original reaction
+        self.assertEqual(len(real_path), 4)
+
+
+if __name__ == "__main__":
+    unittest.main()

Test/SynIO/Format/test_chemcal_conversion.py

@@ -0,0 +1,94 @@
+import unittest
+import networkx as nx
+
+from synutility.SynChem.Reaction.standardize import Standardize
+from synutility.SynIO.Format.chemical_conversion import (
+    smiles_to_graph,
+    rsmi_to_graph,
+    graph_to_rsmi,
+    smart_to_gml,
+    gml_to_smart,
+)
+
+from synutility.SynGraph.Morphism.misc import rule_isomorphism
+
+
+class TestChemicalConversions(unittest.TestCase):
+
+    def setUp(self) -> None:
+        self.rsmi = "[CH2:1]([H:4])[CH2:2][OH:3]>>[CH2:1]=[CH2:2].[H:4][OH:3]"
+        self.gml = (
+            "rule [\n"
+            '   ruleID "rule"\n'
+            "   left [\n"
+            '      edge [ source 1 target 4 label "-" ]\n'
+            '      edge [ source 1 target 2 label "-" ]\n'
+            '      edge [ source 2 target 3 label "-" ]\n'
+            "   ]\n"
+            "   context [\n"
+            '      node [ id 1 label "C" ]\n'
+            '      node [ id 4 label "H" ]\n'
+            '      node [ id 2 label "C" ]\n'
+            '      node [ id 3 label "O" ]\n'
+            "   ]\n"
+            "   right [\n"
+            '      edge [ source 1 target 2 label "=" ]\n'
+            '      edge [ source 4 target 3 label "-" ]\n'
+            "   ]\n"
+            "]"
+        )
+
+        self.std = Standardize()
+
+    def test_smiles_to_graph_valid(self):
+        # Test converting a valid SMILES to a graph
+        result = smiles_to_graph("[CH3:1][CH2:2][OH:3]", False, True, True)
+        self.assertIsInstance(result, nx.Graph)
+        self.assertEqual(result.number_of_nodes(), 3)
+
+    def test_smiles_to_graph_invalid(self):
+        # Test converting an invalid SMILES string to a graph
+        result = smiles_to_graph("invalid_smiles", True, False, False)
+        self.assertIsNone(result)
+
+    def test_rsmi_to_graph_valid(self):
+        # Test converting valid reaction SMILES to graphs for reactants and products
+        reactants_graph, products_graph = rsmi_to_graph(self.rsmi, sanitize=True)
+        self.assertIsInstance(reactants_graph, nx.Graph)
+        self.assertEqual(reactants_graph.number_of_nodes(), 3)
+        self.assertIsInstance(products_graph, nx.Graph)
+        self.assertEqual(products_graph.number_of_nodes(), 3)
+
+        reactants_graph, products_graph = rsmi_to_graph(self.rsmi, sanitize=False)
+        self.assertIsInstance(reactants_graph, nx.Graph)
+        self.assertEqual(reactants_graph.number_of_nodes(), 4)
+        self.assertIsInstance(products_graph, nx.Graph)
+        self.assertEqual(products_graph.number_of_nodes(), 4)
+
+    def test_rsmi_to_graph_invalid(self):
+        # Test handling of invalid RSMI format
+        result = rsmi_to_graph("invalid_format")
+        self.assertEqual((None, None), result)
+
+    def test_graph_to_rsmi(self):
+        r, p = rsmi_to_graph(self.rsmi, sanitize=False)
+        rsmi = graph_to_rsmi(r, p)
+        self.assertIsInstance(rsmi, str)
+        self.assertEqual(self.std.fit(rsmi, False), self.std.fit(self.rsmi, False))
+
+    def test_smart_to_gml(self):
+        result = smart_to_gml(self.rsmi, core=False, sanitize=False, reindex=False)
+        self.assertIsInstance(result, str)
+        self.assertEqual(result, self.gml)
+
+        result = smart_to_gml(self.rsmi, core=False, sanitize=False, reindex=True)
+        self.assertTrue(rule_isomorphism(result, self.gml))
+
+    def test_gml_to_smart(self):
+        smarts, _ = gml_to_smart(self.gml)
+        self.assertIsInstance(smarts, str)
+        self.assertEqual(self.std.fit(smarts, False), self.std.fit(self.rsmi, False))
+
+
+if __name__ == "__main__":
+    unittest.main()

lint.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
 flake8 . --count --max-complexity=13 --max-line-length=120 \
-	--per-file-ignores="__init__.py:F401, chemical_reaction_visualizer.py:E501, test_reagent.py:E501" \
+	--per-file-ignores="__init__.py:F401, chemical_reaction_visualizer.py:E501, test_reagent.py:E501, inference.py:F401" \
 	--exclude venv,core_engine.py,rule_apply.py \
 	--statistics

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "synutility"
-version = "0.0.11"
+version = "0.0.12"
 authors = [
     {name="Tieu Long Phan", email="tieu@bioinf.uni-leipzig.de"}
 ]