synkit 1.3.2b1__tar.gz → 1.4.0__tar.gz

{synkit-1.3.2b1 → synkit-1.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: synkit
-Version: 1.3.2b1
+Version: 1.4.0
 Summary: Utility for reaction modeling using graph grammar
 Project-URL: homepage, https://github.com/TieuLongPhan/SynKit
 Project-URL: source, https://github.com/TieuLongPhan/SynKit

{synkit-1.3.2b1 → synkit-1.4.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "synkit"
-version = "1.3.2b1"
+version = "1.4.0"
 description = "Utility for reaction modeling using graph grammar"
 readme = "README.md"
 long-description = { file = "CHANGELOG.md" }

{synkit-1.3.2b1 → synkit-1.4.0}/synkit/Graph/MTG/mtg.py

@@ -34,7 +34,7 @@ from synkit.Graph.MTG.utils import (
     compute_standard_order,
 )
 from synkit.Graph.canon_graph import GraphCanonicaliser
-from synkit.IO import its_to_rsmi, rsmi_to_its
+from synkit.IO import ITSFormat, its_to_rsmi, rsmi_to_its
 
 NodeID = int
 MissingOrder = Tuple[Set[float], Set[float]]
@@ -63,6 +63,9 @@ class MTG:
     :param mappings: Optional list of precomputed mappings; computed via MCS if None.
     :param node_label_names: Keys for node-label matching.
     :param canonicaliser: Optional GraphCanonicaliser for snapshot canonicalisation.
+    :param its_format: ITS format used when ``sequences`` contains RSMI strings.
+        Defaults to ``"tuple"`` for Lewis State Graph MTGs. Pass
+        ``"typesGH"`` to build legacy MTGs from strings.
     :raises ValueError: On invalid sequence or mapping lengths.
     :raises RuntimeError: On mapping failures.
     """
@@ -76,6 +79,7 @@ class MTG:
         canonicaliser: GraphCanonicaliser | None = None,
         mcs_mol: bool = False,
         mcs: bool = False,
+        its_format: ITSFormat = "tuple",
     ) -> None:
         if len(sequences) < 2:
             raise ValueError("Need at least two snapshots.")
@@ -84,6 +88,7 @@ class MTG:
         self._canonicaliser = canonicaliser
         self.mcs_mol = mcs_mol
         self.mcs = mcs
+        self.its_format = its_format
 
         self._graphs = self._prepare_graph_sequence(sequences)
         self._k = len(self._graphs)
@@ -443,7 +448,11 @@ class MTG:
     ) -> List[nx.Graph]:
         out: List[nx.Graph] = []
         for item in seq:
-            g = rsmi_to_its(item, core=False) if isinstance(item, str) else item
+            g = (
+                rsmi_to_its(item, core=False, format=self.its_format)
+                if isinstance(item, str)
+                else item
+            )
             if self._canonicaliser:
                 g = self._canonicaliser.canonicalise_graph(g).canonical_graph
             if self._is_tuple_its(g):

{synkit-1.3.2b1 → synkit-1.4.0}/synkit/Vis/__init__.py

@@ -21,6 +21,7 @@ from .reaction_drawer import (
     find_reaction_highlights,
 )
 from .its_drawer import draw_its_from_rsmi, draw_its_graph, draw_its_only
+from .mtg_drawer import draw_mtg_graph, draw_mtg_steps
 
 __all__ = [
     "GraphVisualizer",
@@ -44,4 +45,6 @@ __all__ = [
     "draw_its_from_rsmi",
     "draw_its_graph",
     "draw_its_only",
+    "draw_mtg_graph",
+    "draw_mtg_steps",
 ]