helmkit 0.3.2__tar.gz → 0.3.3__tar.gz

{helmkit-0.3.2 → helmkit-0.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: helmkit
-Version: 0.3.2
+Version: 0.3.3
 Summary: Parse HELM strings into RDKit molecules
 License-File: LICENSE
 Requires-Python: >=3.11

{helmkit-0.3.2 → helmkit-0.3.3}/benchmarks/README.md

@@ -37,13 +37,13 @@ and average parsing time:
 |-------------------------------------|---------------:|-------------------------:|--------------------:|
 | `pyPept`                            |         676.65 |                  0.14400 |                6.94 |
 | `helmkit` (DB reload every peptide) |         252.67 |                  0.05383 |               18.58 |
-| `helmkit`                           |           2.83 |                  0.00060 |             1658.68 |
-| `helmkit` (parallel loading)        |           1.42 |                  0.00030 |             3305.63 |
+| `helmkit`                           |           2.07 |                  0.00044 |             2267.63 |
+| `helmkit` (parallel loading)        |           1.40 |                  0.00030 |             3352.86 |
 
-`helmkit` outperforms `pyPept` by approximately 239× when loading the monomer library
+`helmkit` outperforms `pyPept` by approximately 327x when loading the monomer library
 once per session. When forced to reload the library for every peptide, `helmkit` is
 still about 3× faster. If we use parallelized loading in `helmkit`, we achieve an
-additional 2.5× speedup, resulting in a total speedup of approximately 477× over
+additional 1.5× speedup, resulting in a total speedup of approximately 477× over
 `pyPept`.
 
 ## Environment

{helmkit-0.3.2 → helmkit-0.3.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "helmkit"
-version = "0.3.2"
+version = "0.3.3"
 description = "Parse HELM strings into RDKit molecules"
 readme = "README.md"
 requires-python = ">=3.11"

{helmkit-0.3.2 → helmkit-0.3.3}/src/helmkit/molecule.py

@@ -2,7 +2,6 @@ import multiprocessing
 import re
 import warnings
 from functools import lru_cache
-from functools import reduce
 from importlib.resources import files
 from typing import Dict
 from typing import List
@@ -409,9 +408,10 @@ class Molecule:
             self.mol = Chem.RWMol()
             return
 
-        mols = (monomer["m_romol"] for monomer in self.monomers)
-        combined = reduce(Chem.CombineMols, mols)
-        self.mol = Chem.RWMol(combined)
+        combined = Chem.RWMol(self.monomers[0]["m_romol"])
+        for monomer in self.monomers[1:]:
+            combined.InsertMol(monomer["m_romol"])
+        self.mol = combined
 
     def _add_bonds(self) -> None:
         """Add bonds between monomers based on bond list."""

{helmkit-0.3.2 → helmkit-0.3.3}/uv.lock

@@ -140,7 +140,7 @@ wheels = [
 
 [[package]]
 name = "helmkit"
-version = "0.3.2"
+version = "0.3.3"
 source = { editable = "." }
 dependencies = [
     { name = "rdkit" },