helmkit 0.2.0__tar.gz → 0.3.1__tar.gz

helmkit-0.3.1/.github/workflows/main.yml

@@ -0,0 +1,22 @@
+name: Run tests
+
+on:
+  push:
+    paths:
+      - '**/*.py'
+  pull_request:
+    paths:
+      - '**/*.py'
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v6
+      - name: Install dependencies
+        run: uv sync -U
+      - name: Test with pytest
+        run: uv run pytest

{helmkit-0.2.0 → helmkit-0.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: helmkit
-Version: 0.2.0
+Version: 0.3.1
 Summary: Parse HELM strings into RDKit molecules
 License-File: LICENSE
 Requires-Python: >=3.11
@@ -11,19 +11,53 @@ Description-Content-Type: text/markdown
 
 A Python library for converting HELM (Hierarchical Editing Language for Macromolecules) notation to RDKit molecules.
 
+## Table of Contents
+
+- [Basic Usage](#basic-usage)
+- [Installation](#installation)
+- [Quick Example](#quick-example)
+- [Understanding HELM Notation](#understanding-helm-notation)
+- [Using Custom Monomer Data](#using-custom-monomer-data)
+- [SDF File Structure Requirements](#sdf-file-structure-requirements)
+- [Parallel Processing of Peptides](#parallel-processing-of-peptides)
+- [Development Setup](#development-setup)
+- [Running Tests](#running-tests)
+
 ## Basic Usage
 
 ```python
 from helmkit import Molecule
 
 # Create a molecule from a HELM string
-helm_string = "PEPTIDE1{A.R.G}$$$"
+helm_string = "PEPTIDE1{A.R.G}$$$$"
 molecule = Molecule(helm_string)
 
 # Access the RDKit molecule object
 rdkit_mol = molecule.mol
 ```
 
+## Installation
+
+To install `helmkit`, you can use either [`uv`](https://github.com/astral-sh/uv) or `pip`.
+
+### With [`uv`](https://github.com/astral-sh/uv)
+
+```bash
+uv pip install helmkit
+```
+
+or if you have added it as a dependency to your `pyproject.toml`:
+
+```bash
+uv add helmkit
+```
+
+### Without `uv`
+
+```bash
+pip install helmkit
+```
+
 ## Quick Example
 
 ```python
@@ -31,7 +65,7 @@ from helmkit import Molecule
 from rdkit.Chem import AllChem, Draw
 
 # Create a simple tripeptide (Ala-Arg-Gly)
-molecule = Molecule("PEPTIDE1{A.R.G}$$$")
+molecule = Molecule("PEPTIDE1{A.R.G}$$$$")
 
 # Generate 2D coordinates for visualization
 AllChem.Compute2DCoords(molecule.mol)
@@ -67,7 +101,7 @@ custom_sdf_path = "/path/to/your/custom_monomers.sdf"
 custom_monomers = load_monomer_library(custom_sdf_path)
 
 # Create molecule with custom monomer data
-molecule = Molecule("PEPTIDE1{A.R.G}$$$", monomer_df=custom_monomers)
+molecule = Molecule("PEPTIDE1{A.R.G}$$$$", monomer_df=custom_monomers)
 ```
 
 ## SDF File Structure Requirements
@@ -110,3 +144,39 @@ Ala
 
 $$$$
 ```
+
+## Parallel Processing of Peptides
+
+For workflows involving a large number of peptides, `helmkit` provides a function to process them in parallel, significantly improving performance.
+
+```python
+from helmkit import load_monomer_library
+from helmkit import load_peptides_in_parallel
+
+# Load your custom monomer data (optional)
+custom_sdf_path = "/path/to/your/custom_monomers.sdf"
+monomer_db = load_monomer_library(custom_sdf_path)
+
+# A list of HELM strings
+helm_strings = ["PEPTIDE1{A.R.G}$$$$", "PEPTIDE1{S.G.T}$$$$"]
+
+# Process peptides in parallel
+molecules = load_peptides_in_parallel(helm_strings, monomer_db)
+```
+
+## Development Setup
+
+To set up a development environment, first clone the repository.
+Then, from the root of the repository, use `uv` to sync the environment:
+
+```bash
+uv sync -U
+```
+
+## Running Tests
+
+To run the test suite, execute `pytest` from the root of the repository:
+
+```bash
+pytest
+```

{helmkit-0.2.0 → helmkit-0.3.1}/README.md

@@ -2,19 +2,53 @@
 
 A Python library for converting HELM (Hierarchical Editing Language for Macromolecules) notation to RDKit molecules.
 
+## Table of Contents
+
+- [Basic Usage](#basic-usage)
+- [Installation](#installation)
+- [Quick Example](#quick-example)
+- [Understanding HELM Notation](#understanding-helm-notation)
+- [Using Custom Monomer Data](#using-custom-monomer-data)
+- [SDF File Structure Requirements](#sdf-file-structure-requirements)
+- [Parallel Processing of Peptides](#parallel-processing-of-peptides)
+- [Development Setup](#development-setup)
+- [Running Tests](#running-tests)
+
 ## Basic Usage
 
 ```python
 from helmkit import Molecule
 
 # Create a molecule from a HELM string
-helm_string = "PEPTIDE1{A.R.G}$$$"
+helm_string = "PEPTIDE1{A.R.G}$$$$"
 molecule = Molecule(helm_string)
 
 # Access the RDKit molecule object
 rdkit_mol = molecule.mol
 ```
 
+## Installation
+
+To install `helmkit`, you can use either [`uv`](https://github.com/astral-sh/uv) or `pip`.
+
+### With [`uv`](https://github.com/astral-sh/uv)
+
+```bash
+uv pip install helmkit
+```
+
+or if you have added it as a dependency to your `pyproject.toml`:
+
+```bash
+uv add helmkit
+```
+
+### Without `uv`
+
+```bash
+pip install helmkit
+```
+
 ## Quick Example
 
 ```python
@@ -22,7 +56,7 @@ from helmkit import Molecule
 from rdkit.Chem import AllChem, Draw
 
 # Create a simple tripeptide (Ala-Arg-Gly)
-molecule = Molecule("PEPTIDE1{A.R.G}$$$")
+molecule = Molecule("PEPTIDE1{A.R.G}$$$$")
 
 # Generate 2D coordinates for visualization
 AllChem.Compute2DCoords(molecule.mol)
@@ -58,7 +92,7 @@ custom_sdf_path = "/path/to/your/custom_monomers.sdf"
 custom_monomers = load_monomer_library(custom_sdf_path)
 
 # Create molecule with custom monomer data
-molecule = Molecule("PEPTIDE1{A.R.G}$$$", monomer_df=custom_monomers)
+molecule = Molecule("PEPTIDE1{A.R.G}$$$$", monomer_df=custom_monomers)
 ```
 
 ## SDF File Structure Requirements
@@ -101,3 +135,39 @@ Ala
 
 $$$$
 ```
+
+## Parallel Processing of Peptides
+
+For workflows involving a large number of peptides, `helmkit` provides a function to process them in parallel, significantly improving performance.
+
+```python
+from helmkit import load_monomer_library
+from helmkit import load_peptides_in_parallel
+
+# Load your custom monomer data (optional)
+custom_sdf_path = "/path/to/your/custom_monomers.sdf"
+monomer_db = load_monomer_library(custom_sdf_path)
+
+# A list of HELM strings
+helm_strings = ["PEPTIDE1{A.R.G}$$$$", "PEPTIDE1{S.G.T}$$$$"]
+
+# Process peptides in parallel
+molecules = load_peptides_in_parallel(helm_strings, monomer_db)
+```
+
+## Development Setup
+
+To set up a development environment, first clone the repository.
+Then, from the root of the repository, use `uv` to sync the environment:
+
+```bash
+uv sync -U
+```
+
+## Running Tests
+
+To run the test suite, execute `pytest` from the root of the repository:
+
+```bash
+pytest
+```

{helmkit-0.2.0 → helmkit-0.3.1}/benchmarks/README.md

@@ -33,15 +33,18 @@ that `pyPept` cannot handle were excluded (monomers with names containing whites
 hyphens or parenthesis), resulting in a total of 4694 peptides. We measured the total
 and average parsing time:
 
-| Tool                                | Total Time (s) | Avg Time per Peptide (s) |
-|-------------------------------------|----------------|--------------------------|
-| `pyPept`                            | 676.65         | 0.144                    |
-| `helmkit`                           | 3.60           | 0.00077                  |
-| `helmkit` (DB reload every peptide) | 261.81         | 0.056                    |
+| Tool                                | Total Time (s) | Avg Time per Peptide (s) | Peptides per Second |
+|-------------------------------------|---------------:|-------------------------:|--------------------:|
+| `pyPept`                            |         676.65 |                  0.14400 |                6.94 |
+| `helmkit` (DB reload every peptide) |         261.81 |                  0.05600 |               17.93 |
+| `helmkit`                           |           3.60 |                  0.00077 |             1303.89 |
+| `helmkit` (parallel loading)        |           1.42 |                  0.00030 |             3305.63 |
 
 `helmkit` outperforms `pyPept` by approximately 188× when loading the monomer library
 once per session. When forced to reload the library for every peptide (needs disabling
-memoization in the source code), `helmkit` is still about 3× faster.
+memoization in the source code), `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 `pyPept`.
 
 ## Environment
 
@@ -52,4 +55,4 @@ versions:
 - `polars 1.31.0` (CSV parsing and dataframe processing)
 - `rdkit 2025.3.3` (target output format and structure processing)
 - `pypept 1.0.0` (commit `ade9f5840691ad1f8fa22d13939a665c25175d5a`)
-- `helmkit 0.1.0` (local development version)
+- `helmkit 0.3.0` (local development version)

{helmkit-0.2.0 → helmkit-0.3.1}/benchmarks/helmkit-benchmark.py

@@ -14,12 +14,12 @@ def main():
     # (as these do not work with pyPept)
     regex = r"\[[^\]]*[\(\s-][^\]]*\]"
     df = df.filter(pl.col("HELM").str.contains(regex).not_())
+    helms = df["HELM"].to_list()
 
     monomer_db = load_monomer_library(data_dir / "monomers.sdf")
 
     start = time.perf_counter()
-    for row in df.iter_rows(named=True):
-        helm = row["HELM"]
+    for helm in helms:
         Molecule(helm, monomer_db)
     end = time.perf_counter()
     print(f"Processed {df.height} peptides in {end - start:.2f} seconds")

helmkit-0.3.1/benchmarks/helmkit-parallel-benchmark.py

@@ -0,0 +1,29 @@
+import time
+from pathlib import Path
+
+import polars as pl
+from helmkit import load_monomer_library
+from helmkit import load_peptides_in_parallel
+
+
+def main():
+    data_dir = Path(__file__).parent / "data"
+    df = pl.read_csv(data_dir / "peptides.csv")
+
+    # Remove peptides with monomers containing parentheses, spaces or hyphens
+    # (as these do not work with pyPept)
+    regex = r"\[[^\]]*[\(\s-][^\]]*\]"
+    df = df.filter(pl.col("HELM").str.contains(regex).not_())
+    helms = df["HELM"].to_list()
+
+    monomer_db = load_monomer_library(data_dir / "monomers.sdf")
+
+    start = time.perf_counter()
+    load_peptides_in_parallel(helms, monomer_db)
+    end = time.perf_counter()
+    print(f"Processed {df.height} peptides in {end - start:.2f} seconds")
+    print(f"Average time per peptide: {(end - start) / df.height:.6f} seconds")
+
+
+if __name__ == "__main__":
+    main()

{helmkit-0.2.0 → helmkit-0.3.1}/benchmarks/helmkit-with-reload-benchmark.py

@@ -14,10 +14,10 @@ def main():
     # (as these do not work with pyPept)
     regex = r"\[[^\]]*[\(\s-][^\]]*\]"
     df = df.filter(pl.col("HELM").str.contains(regex).not_())
+    helms = df["HELM"].to_list()
 
     start = time.perf_counter()
-    for row in df.iter_rows(named=True):
-        helm = row["HELM"]
+    for helm in helms:
         monomer_db = load_monomer_library(data_dir / "monomers.sdf")
         Molecule(helm, monomer_db)
     end = time.perf_counter()

{helmkit-0.2.0 → helmkit-0.3.1}/benchmarks/pypept-benchmark.py

@@ -15,13 +15,13 @@ def main():
     # (as these do not work with pyPept)
     regex = r"\[[^\]]*[\(\s-][^\]]*\]"
     df = df.filter(pl.col("HELM").str.contains(regex).not_())
+    helms = df["HELM"].to_list()
 
     monomer_lib_dir = str(data_dir.relative_to(Path.cwd()))
     monomer_lib = "monomers.sdf"
 
     start = time.perf_counter()
-    for row in df.iter_rows(named=True):
-        helm = row["HELM"]
+    for helm in helms:
         converter = Converter(helm=helm)
         sequence = Sequence(converter.get_biln(), monomer_lib_dir, monomer_lib)
         Molecule(sequence)

{helmkit-0.2.0 → helmkit-0.3.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "helmkit"
-version = "0.2.0"
+version = "0.3.1"
 description = "Parse HELM strings into RDKit molecules"
 readme = "README.md"
 requires-python = ">=3.11"
@@ -16,6 +16,7 @@ build-backend = "hatchling.build"
 dev = [
     "polars>=1.31.0",
     "pypept",
+    "pytest>=8.4.1",
     "pyupgrade>=3.20.0",
     "reorder-python-imports>=3.15.0",
     "tqdm>=4.67.1",

helmkit-0.3.1/src/helmkit/__init__.py

@@ -0,0 +1,11 @@
+from .molecule import load_monomer_library
+from .molecule import load_peptides_in_parallel
+from .molecule import Molecule
+from .molecule import SequenceConstants
+
+__all__ = [
+    "load_monomer_library",
+    "load_peptides_in_parallel",
+    "Molecule",
+    "SequenceConstants",
+]

{helmkit-0.2.0 → helmkit-0.3.1}/src/helmkit/molecule.py

@@ -1,4 +1,5 @@
 import copy
+import multiprocessing
 import re
 import warnings
 from functools import lru_cache
@@ -68,8 +69,14 @@ def infer_attachment_points(molecule: Chem.Mol, rgroup_indices: List[int]) -> Li
 
 
 @lru_cache
-def load_monomer_library(library_path: str) -> Dict:
+def load_monomer_library(library_path: Optional[str] = None) -> Dict:
     """Load and prepare monomer data from SDF file."""
+    if library_path is None:
+        library_path = str(
+            files(SequenceConstants.def_path).joinpath(
+                SequenceConstants.def_lib_filename
+            )
+        )
     monomers_dict = {}
     supplier = Chem.SDMolSupplier(library_path)
 
@@ -111,10 +118,7 @@ class Molecule:
         self.chain_offset = {}
 
         if monomer_df is None:
-            default_monomer_df_filepath = files(SequenceConstants.def_path).joinpath(
-                SequenceConstants.def_lib_filename
-            )
-            self.monomer_df = load_monomer_library(str(default_monomer_df_filepath))
+            self.monomer_df = load_monomer_library()
         else:
             self.monomer_df = monomer_df
 
@@ -456,3 +460,15 @@ class Molecule:
         """Clean up the molecule by removing dummy atoms and sanitizing."""
         self.mol = Chem.DeleteSubstructs(self.mol, Chem.MolFromSmarts("[#0]"))
         Chem.SanitizeMol(self.mol)
+
+
+def _load_peptide(helm: str, monomer_df: Optional[Dict] = None) -> Molecule:
+    return Molecule(helm, monomer_df)
+
+
+def load_peptides_in_parallel(
+    helms: List[str], monomer_df: Optional[Dict] = None
+) -> List[Molecule]:
+    args = [(helm, monomer_df) for helm in helms]
+    with multiprocessing.Pool() as pool:
+        return pool.starmap(_load_peptide, args)

helmkit-0.3.1/tests/backup

@@ -0,0 +1,66 @@
+import pytest
+from pathlib import Path
+from rdkit import Chem
+from helmkit.molecule import (
+    Molecule,
+    load_monomer_library,
+    load_peptides_in_parallel,
+)
+
+
+@pytest.fixture(scope="module")
+def monomer_library():
+    """Fixture to load the monomer library for testing."""
+    path = Path(__file__).parent / "data" / "monomers.sdf"
+    return load_monomer_library(path)
+
+
+def test_load_monomer_library(monomer_library):
+    """Test loading the monomer library."""
+    assert "A" in monomer_library
+    assert "G" in monomer_library
+    assert "T" in monomer_library
+    assert monomer_library["A"]["m_type"] == "aa"
+    assert monomer_library["A"]["m_romol"].GetNumAtoms() > 0
+
+
+def test_simple_peptide(monomer_library):
+    """Test creating a simple peptide from a HELM string."""
+    helm = "PEPTIDE1{A.G.T}$$$$"
+    mol = Molecule(helm, monomer_df=monomer_library)
+    assert isinstance(mol.mol, Chem.Mol)
+    # Number of atoms will vary based on monomer definitions, but it should be > 0
+    assert mol.mol.GetNumAtoms() > 0
+
+
+def test_peptide_with_connection(monomer_library):
+    """Test a peptide with a connection."""
+    helm = "PEPTIDE1{A.G.G}$PEPTIDE1,PEPTIDE1,1:R3-3:R1$$$"
+    mol = Molecule(helm, monomer_df=monomer_library)
+    assert isinstance(mol.mol, Chem.Mol)
+    assert mol.mol.GetNumAtoms() > 0
+
+
+def test_invalid_monomer(monomer_library):
+    """Test HELM string with an invalid monomer."""
+    helm = "PEPTIDE1{X.Y.Z}$$$$"
+    with pytest.raises(ValueError, match="Monomer X not found in monomer library"):
+        Molecule(helm, monomer_df=monomer_library)
+
+
+def test_invalid_helm_string(monomer_library):
+    """Test an invalid HELM string."""
+    helm = "PEPTIDE1{A.G.T}"
+    mol = Molecule(helm, monomer_df=monomer_library)
+    assert len(mol.monomers) == 3
+
+
+def test_load_peptides_in_parallel(monomer_library):
+    """Test loading peptides in parallel."""
+    helms = ["PEPTIDE1{A.G.T}$$$$", "PEPTIDE1{G.A}$$$$"]
+    molecules = load_peptides_in_parallel(helms, monomer_df=monomer_library)
+    assert len(molecules) == 2
+    assert isinstance(molecules[0].mol, Chem.Mol)
+    assert isinstance(molecules[1].mol, Chem.Mol)
+    assert molecules[0].mol.GetNumAtoms() > 0
+    assert molecules[1].mol.GetNumAtoms() > 0

helmkit-0.3.1/tests/test_cycpeptmpdb.py

@@ -0,0 +1,29 @@
+from pathlib import Path
+
+import polars as pl
+from helmkit import load_monomer_library
+from helmkit import Molecule
+from rdkit import Chem
+from tqdm import tqdm
+
+
+def test():
+    data_dir = Path(__file__).parent / "data"
+    df = pl.read_csv(data_dir / "peptides.csv")
+    monomer_db = load_monomer_library(data_dir / "monomers.sdf")
+    for row in tqdm(df.iter_rows(named=True), total=df.height):
+        helm = row["HELM"]
+        smiles = row["SMILES"]
+        try:
+            m = Molecule(helm, monomer_db)
+        except:
+            print(row)
+            raise
+        inchi1 = Chem.MolToInchi(m.mol)
+        other = Chem.MolFromSmiles(smiles)
+        inchi2 = Chem.MolToInchi(other)
+        assert inchi1 == inchi2
+
+
+if __name__ == "__main__":
+    test()

helmkit-0.3.1/tests/test_parallel_load.py

@@ -0,0 +1,28 @@
+from pathlib import Path
+
+import polars as pl
+from helmkit import load_monomer_library
+from helmkit import load_peptides_in_parallel
+from rdkit import Chem
+from tqdm import tqdm
+
+
+def test():
+    data_dir = Path(__file__).parent / "data"
+    df = pl.read_csv(data_dir / "peptides.csv")
+    monomer_db = load_monomer_library(str(data_dir / "monomers.sdf"))
+    helms = df["HELM"].to_list()
+
+    molecules_parallel = load_peptides_in_parallel(helms, monomer_db)
+    for m, row in tqdm(
+        zip(molecules_parallel, df.iter_rows(named=True)), total=df.height
+    ):
+        smiles = row["SMILES"]
+        inchi1 = Chem.MolToInchi(m.mol)
+        other = Chem.MolFromSmiles(smiles)
+        inchi2 = Chem.MolToInchi(other)
+        assert inchi1 == inchi2
+
+
+if __name__ == "__main__":
+    test()

helmkit-0.2.0/tests/random_peptides.py → helmkit-0.3.1/tests/test_random_peptides.py

@@ -5,7 +5,7 @@ from rdkit import Chem
 from tqdm import tqdm
 
 
-def main():
+def test():
     random.seed(0)
     aminoacids = "ACDEFGHIKLMNPQRSTVWY"
     for _ in tqdm(range(1000)):
@@ -15,9 +15,8 @@ def main():
         molecule = Molecule(helm)
         inchi1 = Chem.MolToInchi(molecule.mol)
         inchi2 = Chem.MolToInchi(Chem.MolFromSequence(peptide))
-        if inchi1 != inchi2:
-            raise ValueError(f"{inchi1} != {inchi2}")
+        assert inchi1 == inchi2
 
 
 if __name__ == "__main__":
-    main()
+    test()

{helmkit-0.2.0 → helmkit-0.3.1}/uv.lock

@@ -113,7 +113,7 @@ wheels = [
 
 [[package]]
 name = "helmkit"
-version = "0.1.0"
+version = "0.3.0"
 source = { editable = "." }
 dependencies = [
     { name = "rdkit" },
@@ -123,6 +123,7 @@ dependencies = [
 dev = [
     { name = "polars" },
     { name = "pypept" },
+    { name = "pytest" },
     { name = "pyupgrade" },
     { name = "reorder-python-imports" },
     { name = "tqdm" },
@@ -135,6 +136,7 @@ requires-dist = [{ name = "rdkit", specifier = ">=2025.3.3" }]
 dev = [
     { name = "polars", specifier = ">=1.31.0" },
     { name = "pypept", git = "https://github.com/Boehringer-Ingelheim/pyPept.git" },
+    { name = "pytest", specifier = ">=8.4.1" },
     { name = "pyupgrade", specifier = ">=3.20.0" },
     { name = "reorder-python-imports", specifier = ">=3.15.0" },
     { name = "tqdm", specifier = ">=4.67.1" },
@@ -177,6 +179,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/d7/91/c1b597004248bd7ce6c9593465308a1a5f0467c4ec4056aa51a6c017a669/igraph-0.11.9-pp311-pypy311_pp73-win_amd64.whl", hash = "sha256:f35694100691bf8ef0c370615d87bcf1d6c0f15e356269c6357f8f78a9f1acea", size = 2926242, upload-time = "2025-06-11T09:27:18.553Z" },
 ]
 
+[[package]]
+name = "iniconfig"
+version = "2.1.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/f2/97/ebf4da567aa6827c909642694d71c9fcf53e5b504f2d96afea02718862f3/iniconfig-2.1.0.tar.gz", hash = "sha256:3abbd2e30b36733fee78f9c7f7308f2d0050e88f0087fd25c2645f63c773e1c7", size = 4793, upload-time = "2025-03-19T20:09:59.721Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/2c/e1/e6716421ea10d38022b952c159d5161ca1193197fb744506875fbb87ea7b/iniconfig-2.1.0-py3-none-any.whl", hash = "sha256:9deba5723312380e77435581c6bf4935c94cbfab9b1ed33ef8d238ea168eb760", size = 6050, upload-time = "2025-03-19T20:10:01.071Z" },
+]
+
 [[package]]
 name = "numpy"
 version = "2.3.1"
@@ -235,6 +246,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/48/6b/1c6b515a83d5564b1698a61efa245727c8feecf308f4091f565988519d20/numpy-2.3.1-pp311-pypy311_pp73-win_amd64.whl", hash = "sha256:e610832418a2bc09d974cc9fecebfa51e9532d6190223bc5ef6a7402ebf3b5cb", size = 12927246, upload-time = "2025-06-21T12:27:38.618Z" },
 ]
 
+[[package]]
+name = "packaging"
+version = "25.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/a1/d4/1fc4078c65507b51b96ca8f8c3ba19e6a61c8253c72794544580a7b6c24d/packaging-25.0.tar.gz", hash = "sha256:d443872c98d677bf60f6a1f2f8c1cb748e8fe762d2bf9d3148b5599295b0fc4f", size = 165727, upload-time = "2025-04-19T11:48:59.673Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/20/12/38679034af332785aac8774540895e234f4d07f7545804097de4b666afd8/packaging-25.0-py3-none-any.whl", hash = "sha256:29572ef2b1f17581046b3a2227d5c611fb25ec70ca1ba8554b24b0e69331a484", size = 66469, upload-time = "2025-04-19T11:48:57.875Z" },
+]
+
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 name = "pandas"
 version = "2.3.1"
@@ -360,6 +380,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/34/e7/ae39f538fd6844e982063c3a5e4598b8ced43b9633baa3a85ef33af8c05c/pillow-11.3.0-pp311-pypy311_pp73-win_amd64.whl", hash = "sha256:c84d689db21a1c397d001aa08241044aa2069e7587b398c8cc63020390b1c1b8", size = 6984598, upload-time = "2025-07-01T09:16:27.732Z" },
 ]
 
+[[package]]
+name = "pluggy"
+version = "1.6.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/f9/e2/3e91f31a7d2b083fe6ef3fa267035b518369d9511ffab804f839851d2779/pluggy-1.6.0.tar.gz", hash = "sha256:7dcc130b76258d33b90f61b658791dede3486c3e6bfb003ee5c9bfb396dd22f3", size = 69412, upload-time = "2025-05-15T12:30:07.975Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/54/20/4d324d65cc6d9205fabedc306948156824eb9f0ee1633355a8f7ec5c66bf/pluggy-1.6.0-py3-none-any.whl", hash = "sha256:e920276dd6813095e9377c0bc5566d94c932c33b27a3e3945d8389c374dd4746", size = 20538, upload-time = "2025-05-15T12:30:06.134Z" },
+]
+
 [[package]]
 name = "polars"
 version = "1.31.0"
@@ -374,6 +403,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/40/4b/0673a68ac4d6527fac951970e929c3b4440c654f994f0c957bd5556deb38/polars-1.31.0-cp39-abi3-win_arm64.whl", hash = "sha256:62ef23bb9d10dca4c2b945979f9a50812ac4ace4ed9e158a6b5d32a7322e6f75", size = 31469078, upload-time = "2025-06-18T11:59:59.242Z" },
 ]
 
+[[package]]
+name = "pygments"
+version = "2.19.2"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/b0/77/a5b8c569bf593b0140bde72ea885a803b82086995367bf2037de0159d924/pygments-2.19.2.tar.gz", hash = "sha256:636cb2477cec7f8952536970bc533bc43743542f70392ae026374600add5b887", size = 4968631, upload-time = "2025-06-21T13:39:12.283Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/c7/21/705964c7812476f378728bdf590ca4b771ec72385c533964653c68e86bdc/pygments-2.19.2-py3-none-any.whl", hash = "sha256:86540386c03d588bb81d44bc3928634ff26449851e99741617ecb9037ee5ec0b", size = 1225217, upload-time = "2025-06-21T13:39:07.939Z" },
+]
+
 [[package]]
 name = "pypept"
 version = "1.0.0"
@@ -387,6 +425,22 @@ dependencies = [
     { name = "requests" },
 ]
 
+[[package]]
+name = "pytest"
+version = "8.4.1"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "colorama", marker = "sys_platform == 'win32'" },
+    { name = "iniconfig" },
+    { name = "packaging" },
+    { name = "pluggy" },
+    { name = "pygments" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/08/ba/45911d754e8eba3d5a841a5ce61a65a685ff1798421ac054f85aa8747dfb/pytest-8.4.1.tar.gz", hash = "sha256:7c67fd69174877359ed9371ec3af8a3d2b04741818c51e5e99cc1742251fa93c", size = 1517714, upload-time = "2025-06-18T05:48:06.109Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/29/16/c8a903f4c4dffe7a12843191437d7cd8e32751d5de349d45d3fe69544e87/pytest-8.4.1-py3-none-any.whl", hash = "sha256:539c70ba6fcead8e78eebbf1115e8b589e7565830d7d006a8723f19ac8a0afb7", size = 365474, upload-time = "2025-06-18T05:48:03.955Z" },
+]
+
 [[package]]
 name = "python-dateutil"
 version = "2.9.0.post0"

helmkit-0.2.0/src/helmkit/__init__.py

@@ -1,5 +0,0 @@
-from .molecule import load_monomer_library
-from .molecule import Molecule
-from .molecule import SequenceConstants
-
-__all__ = ["Molecule", "load_monomer_library", "SequenceConstants"]

helmkit-0.2.0/tests/cycpeptmpdb.py

@@ -1,43 +0,0 @@
-from pathlib import Path
-
-import polars as pl
-from helmkit import load_monomer_library
-from helmkit import Molecule
-from rdkit import Chem
-from rdkit.Chem import AllChem
-from rdkit.Chem import Draw
-from tqdm import tqdm
-
-
-def main():
-    data_dir = Path(__file__).parent / "data"
-    df = pl.read_csv(data_dir / "peptides.csv")
-    monomer_db = load_monomer_library(data_dir / "monomers.sdf")
-    for row in tqdm(df.iter_rows(named=True), total=df.height):
-        helm = row["HELM"]
-        smiles = row["SMILES"]
-        try:
-            m = Molecule(helm, monomer_db)
-        except:
-            print(row)
-            raise
-        inchi1 = Chem.MolToInchi(m.mol)
-        other = Chem.MolFromSmiles(smiles)
-        inchi2 = Chem.MolToInchi(other)
-        if inchi1 != inchi2:
-            mistmatches_dir = Path(__file__).parent / "mismatches"
-            mistmatches_dir.mkdir(exist_ok=True)
-            AllChem.Compute2DCoords(m.mol, clearConfs=True)
-            Chem.AssignAtomChiralTagsFromStructure(m.mol)
-            AllChem.Compute2DCoords(other, clearConfs=True)
-            Chem.AssignAtomChiralTagsFromStructure(other)
-            # Draw the two molecules to an image
-            img = Draw.MolsToGridImage(
-                [m.mol, other], molsPerRow=2, subImgSize=(800, 800)
-            )
-            img.save(mistmatches_dir / f"{row['ID']}.png")
-            raise ValueError(f"{inchi1} != {inchi2} for row {row}")
-
-
-if __name__ == "__main__":
-    main()