aamutils 0.0.7__tar.gz → 0.0.9__tar.gz

{aamutils-0.0.7 → aamutils-0.0.9}/PKG-INFO

@@ -1,12 +1,11 @@
 Metadata-Version: 2.3
 Name: aamutils
-Version: 0.0.7
+Version: 0.0.9
 Summary: Collection of atom-atom-mapping utility functions.
 Project-URL: homepage, https://github.com/klausweinbauer/AAMUtils
 Project-URL: source, https://github.com/klausweinbauer/AAMUtils
 Project-URL: issues, https://github.com/klausweinbauer/AAMUtils/issues
 Author-email: Klaus Weinbauer <klaus@bioinf.uni-leipzig.de>
-License-File: LICENSE
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
@@ -35,6 +34,8 @@ pip install aamutils
 
 ## Usage
 
+### Use in command line
+
 The input is a list of partial atom-atom-maps (AAMs). Data is read line-by-line
 from a text file. Each line should contain one reaction SMILES.
 
@@ -69,6 +70,17 @@ cat testinput_extended.json
     }
 ]
 ```
+### Use in script
+  ```python
+    from aamutils.aam_expand import extend_aam_from_rsmi
+
+    rsmi = "CC[CH2:3][Cl:1].[N:2]>>CC[CH2:3][N:2].[Cl:1]"
+
+    result_smiles = extend_aam_from_rsmi(rsmi)
+
+    print(result_smiles)
+    >>> "[Cl:1][CH2:3][CH2:5][CH3:4].[NH3:2]>>[ClH:1].[NH2:2][CH2:3][CH2:5][CH3:4]"
+```
 
 ## Benchmark
 

{aamutils-0.0.7 → aamutils-0.0.9}/README.md

@@ -13,6 +13,8 @@ pip install aamutils
 
 ## Usage
 
+### Use in command line
+
 The input is a list of partial atom-atom-maps (AAMs). Data is read line-by-line
 from a text file. Each line should contain one reaction SMILES.
 
@@ -47,6 +49,17 @@ cat testinput_extended.json
     }
 ]
 ```
+### Use in script
+  ```python
+    from aamutils.aam_expand import extend_aam_from_rsmi
+
+    rsmi = "CC[CH2:3][Cl:1].[N:2]>>CC[CH2:3][N:2].[Cl:1]"
+
+    result_smiles = extend_aam_from_rsmi(rsmi)
+
+    print(result_smiles)
+    >>> "[Cl:1][CH2:3][CH2:5][CH3:4].[NH3:2]>>[ClH:1].[NH2:2][CH2:3][CH2:5][CH3:4]"
+```
 
 ## Benchmark
 

aamutils-0.0.9/aamutils/aam_expand.py

@@ -0,0 +1,58 @@
+import networkx as nx
+import rdkit.Chem.rdmolfiles as rdmolfiles
+from aamutils.algorithm.ilp import expand_partial_aam_balanced
+from aamutils.utils import smiles_to_graph, graph_to_mol, set_aam
+
+
+def extend_aam_from_graph(G: nx.Graph, H: nx.Graph) -> str:
+    """
+    Extends atom-atom mappings (AAM) from two input graphs,
+    G (reactants) and H (products),by solving the AAM problem using an
+    Integer Linear Programming (ILP) approach and generating
+    a reaction SMILES (RSMI) string.
+
+    Parameters:
+    - G (nx.Graph): Graph representing the reactants.
+    Nodes should contain necessary attributes for AAM.
+    - H (nx.Graph): Graph representing the products.
+    Nodes should contain necessary attributes for AAM.
+
+    Returns:
+    - str: A reaction SMILES string (RSMI) in the format 'reactant>>product'
+    with extended atom mappings.
+    """
+    # Solve the partial AAM problem using ILP and retrieve the mapping matrix
+    M, _, _ = expand_partial_aam_balanced(G, H)
+
+    # Apply the AAM matrix to the graphs
+    set_aam(G, H, M)
+
+    # Convert the modified graphs back to RDKit molecules
+    r_mol = graph_to_mol(G)
+    p_mol = graph_to_mol(H)
+
+    # Generate reaction SMILES string from the RDKit molecules
+    result_smiles = "{}>>{}".format(
+        rdmolfiles.MolToSmiles(
+            r_mol, canonical=True, kekuleSmiles=False, allHsExplicit=True
+        ),
+        rdmolfiles.MolToSmiles(
+            p_mol, canonical=True, kekuleSmiles=False, allHsExplicit=True
+        ),
+    )
+    return result_smiles
+
+
+def extend_aam_from_rsmi(rsmi: str) -> str:
+    """
+    Extends atom-atom mappings (AAM) from a reaction SMILES (RSMI) string,
+    and returns the resulting reaction SMILES string.
+
+    Parameters:
+    - rsmi (str): A reaction SMILES string in the format 'reactant>>product'.
+
+    Returns:
+    - str: A reaction SMILES string with extended atom mappings.
+    """
+    G, H = smiles_to_graph(rsmi)
+    return extend_aam_from_graph(G, H)

{aamutils-0.0.7 → aamutils-0.0.9}/aamutils/utils.py

@@ -17,7 +17,10 @@ def mol_to_graph(mol: Chem.rdchem.Mol) -> nx.Graph:
     g = nx.Graph()
     for atom in mol.GetAtoms():
         aam = atom.GetAtomMapNum()
-        g.add_node(atom.GetIdx(), symbol=atom.GetSymbol(), aam=aam)
+        formal_charge = atom.GetFormalCharge()  # Get the formal charge of the atom
+        g.add_node(
+            atom.GetIdx(), symbol=atom.GetSymbol(), aam=aam, formal_charge=formal_charge
+        )  # Store formal charge
     for bond in mol.GetBonds():
         bond_type = str(bond.GetBondType()).split(".")[-1]
         bond_order = 1
@@ -27,14 +30,16 @@ def mol_to_graph(mol: Chem.rdchem.Mol) -> nx.Graph:
     return g
 
 
-def smiles_to_graph(smiles: str) -> nx.Graph | tuple[nx.Graph, nx.Graph]:
+def smiles_to_graph(
+    smiles: str, sanitize: bool = True
+) -> nx.Graph | tuple[nx.Graph, nx.Graph]:
     if ">>" in smiles:
         smiles_token = smiles.split(">>")
-        g = mol_to_graph(rdmolfiles.MolFromSmiles(smiles_token[0]))
-        h = mol_to_graph(rdmolfiles.MolFromSmiles(smiles_token[1]))
+        g = mol_to_graph(rdmolfiles.MolFromSmiles(smiles_token[0], sanitize=sanitize))
+        h = mol_to_graph(rdmolfiles.MolFromSmiles(smiles_token[1], sanitize=sanitize))
         return g, h
     else:
-        return mol_to_graph(rdmolfiles.MolFromSmiles(smiles))
+        return mol_to_graph(rdmolfiles.MolFromSmiles(smiles, sanitize=sanitize))
 
 
 def graph_to_mol(
@@ -54,6 +59,8 @@ def graph_to_mol(
         idx_map[n] = idx
         if aam_key in d.keys() and d[aam_key] >= 0:
             rw_mol.GetAtomWithIdx(idx).SetAtomMapNum(d[aam_key])
+        if "formal_charge" in d:  # Set the formal charge for the atom
+            rw_mol.GetAtomWithIdx(idx).SetFormalCharge(d["formal_charge"])
     for n1, n2, d in G.edges(data=True):
         idx1 = idx_map[n1]
         idx2 = idx_map[n2]

{aamutils-0.0.7 → aamutils-0.0.9}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "aamutils"
-version = "0.0.7"
+version = "0.0.9"
 authors = [
 	{name="Klaus Weinbauer", email="klaus@bioinf.uni-leipzig.de"}
 	]

aamutils-0.0.9/test/test_aam_expand.py

@@ -0,0 +1,36 @@
+import unittest
+from aamutils.utils import smiles_to_graph
+from aamutils.aam_expand import extend_aam_from_graph, extend_aam_from_rsmi
+
+
+class TestExtendAAMFromGraph(unittest.TestCase):
+    def test_extend_aam_from_graph(self):
+        """
+        Tests the extend_aam_from_graph function to ensure it correctly extends
+        atom-atom mappings and returns the expected reaction SMILES.
+        """
+        rsmi = "CC[CH2:3][Cl:1].[N:2]>>CC[CH2:3][N:2].[Cl:1]"
+        G, H = smiles_to_graph(rsmi)
+        result_smiles = extend_aam_from_graph(G, H)
+        expected = (
+            "[Cl:1][CH2:3][CH2:5][CH3:4].[NH3:2]>>[ClH:1].[NH2:2][CH2:3][CH2:5][CH3:4]"
+        )
+        self.assertEqual(result_smiles, expected)
+
+    def test_extend_aam_from_smiles(self):
+        """
+        Tests the extend_aam_from_graph function to ensure it correctly extends
+        atom-atom mappings and returns the expected reaction SMILES.
+        """
+        rsmi = "CC[CH2:3][Cl:1].[N:2]>>CC[CH2:3][N:2].[Cl:1]"
+
+        result_smiles = extend_aam_from_rsmi(rsmi)
+        expected = (
+            "[Cl:1][CH2:3][CH2:5][CH3:4].[NH3:2]>>[ClH:1].[NH2:2][CH2:3][CH2:5][CH3:4]"
+        )
+        self.assertEqual(result_smiles, expected)
+
+
+# Run the unittest
+if __name__ == "__main__":
+    unittest.main()