helmkit 0.5.1__tar.gz → 0.5.3__tar.gz

{helmkit-0.5.1 → helmkit-0.5.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: helmkit
-Version: 0.5.1
+Version: 0.5.3
 Summary: Parse HELM strings into RDKit molecules
 License-File: LICENSE
 Requires-Python: >=3.11

{helmkit-0.5.1 → helmkit-0.5.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "helmkit"
-version = "0.5.1"
+version = "0.5.3"
 description = "Parse HELM strings into RDKit molecules"
 readme = "README.md"
 requires-python = ">=3.11"

{helmkit-0.5.1 → helmkit-0.5.3}/src/helmkit/data/monomers.sdf

@@ -32960,8 +32960,8 @@ MolEngine07221613482D
   4  5  1  0  0  0  0
   5  1  1  0  0  0  0
   2  6  1  6  0  0  0
-  1  7  1  1  0  0  0
-  4  8  1  1  0  0  0
+  1  7  1  0  0  0  0
+  4  8  1  0  0  0  0
   7  9  1  0  0  0  0
   9 10  1  0  0  0  0
   6 11  1  0  0  0  0
@@ -37330,8 +37330,8 @@ MolEngine07221613482D
   4  5  1  0  0  0  0
   5  1  1  0  0  0  0
   2  6  1  6  0  0  0
-  1  7  1  1  0  0  0
-  4  8  1  1  0  0  0
+  1  7  1  0  0  0  0
+  4  8  1  0  0  0  0
   7  9  1  0  0  0  0
   9 10  1  0  0  0  0
   6 11  1  0  0  0  0
@@ -37960,8 +37960,8 @@ MolEngine07221613482D
   4  5  1  0  0  0  0
   5  1  1  0  0  0  0
   2  6  1  6  0  0  0
-  1  7  1  1  0  0  0
-  4  8  1  1  0  0  0
+  1  7  1  0  0  0  0
+  4  8  1  0  0  0  0
   7  9  1  0  0  0  0
   9 10  1  0  0  0  0
   6 11  1  0  0  0  0

{helmkit-0.5.1 → helmkit-0.5.3}/src/helmkit/molecule.py

@@ -1,3 +1,4 @@
+import bisect
 import multiprocessing
 import re
 import warnings
@@ -739,11 +740,24 @@ class Molecule:
         matches = self.mol.GetSubstructMatches(pattern)
         atoms_to_delete = sorted({idx for match in matches for idx in match})
         self.mol = Chem.DeleteSubstructs(self.mol, pattern)
+
+        def correction(offset: int, idx: int) -> int:
+            return bisect.bisect_left(atoms_to_delete, idx) - bisect.bisect_left(
+                atoms_to_delete, offset
+            )
+
+        for i, (m1, a1, m2, a2) in enumerate(self.bondlist):
+            offset1 = self.offset[m1]
+            offset2 = self.offset[m2]
+            self.bondlist[i][1] -= correction(offset1, offset1 + a1)
+            self.bondlist[i][3] -= correction(offset2, offset2 + a2)
+
         self.offset = [
-            offset - sum(d <= offset for d in atoms_to_delete) for offset in self.offset
+            offset - sum(d < offset for d in atoms_to_delete) for offset in self.offset
         ]
 
-    def get_broken_bond_idx(self) -> List[int]:
+    @property
+    def bond_indices(self) -> List[int]:
         return [
             self.mol.GetBondBetweenAtoms(
                 self.offset[monomer1_idx] + atom1_idx,
@@ -752,6 +766,13 @@ class Molecule:
             for monomer1_idx, atom1_idx, monomer2_idx, atom2_idx in self.bondlist
         ]
 
+    @property
+    def monomer_indices(self) -> List[int]:
+        return [
+            bisect.bisect_right(self.offset, i) - 1
+            for i in range(self.mol.GetNumAtoms())
+        ]
+
 
 def _init_pool(monomer_df: MonomerLibrary):
     global _monomer_df

{helmkit-0.5.1 → helmkit-0.5.3}/uv.lock

@@ -196,7 +196,7 @@ wheels = [
 
 [[package]]
 name = "helmkit"
-version = "0.5.1"
+version = "0.5.3"
 source = { editable = "." }
 dependencies = [
     { name = "rdkit" },