helmkit 0.5.1__tar.gz

helmkit-0.5.1/.gitignore

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+# Python-generated files
+__pycache__/
+*.py[oc]
+build/
+dist/
+wheels/
+*.egg-info
+
+# Virtual environments
+.venv

helmkit-0.5.1/.python-version

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+3.12

helmkit-0.5.1/LICENSE

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+MIT License
+
+Copyright (c) 2025 adaliaramon
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

helmkit-0.5.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: helmkit
+Version: 0.5.1
+Summary: Parse HELM strings into RDKit molecules
+License-File: LICENSE
+Requires-Python: >=3.11
+Requires-Dist: rdkit>=2025.3.3
+Description-Content-Type: text/markdown
+
+# helmkit
+
+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}$$$$"
+molecule = Molecule(helm_string)
+
+# Access the RDKit molecule object
+rdkit_mol = molecule.mol
+```
+
+## Installation
+
+To install `helmkit`, you can use either [`uv`](https://github.com/astral-sh/uv) or `pip`.
+
+### With [`uv`](https://github.com/astral-sh/uv)
+
+```bash
+uv pip install helmkit
+```
+
+or if you have added it as a dependency to your `pyproject.toml`:
+
+```bash
+uv add helmkit
+```
+
+### Without `uv`
+
+```bash
+pip install helmkit
+```
+
+## Quick Example
+
+```python
+from helmkit import Molecule
+from rdkit.Chem import AllChem, Draw
+
+# Create a simple tripeptide (Ala-Arg-Gly)
+molecule = Molecule("PEPTIDE1{A.R.G}$$$$")
+
+# Generate 2D coordinates for visualization
+AllChem.Compute2DCoords(molecule.mol)
+
+# Save the image
+img = Draw.MolToImage(molecule.mol)
+img.save("tripeptide.png")
+```
+
+## Understanding HELM Notation
+
+HELM (Hierarchical Editing Language for Macromolecules) is a notation for representing complex biomolecules. A basic HELM string has the following format:
+
+```
+PEPTIDE1{A.R.G}|PEPTIDE2{S.G.C}$PEPTIDE1,PEPTIDE2,1:R1-3:R3$$$V2.0
+```
+
+Where:
+- `PEPTIDE1{A.R.G}` defines the first chain (a peptide with amino acids A, R, G)
+- `PEPTIDE2{S.G.C}` defines the second chain
+- `PEPTIDE1,PEPTIDE2,1:R1-3:R3` defines a connection between the chains (R1 of residue 1 in PEPTIDE1 connects to R3 of residue 3 in PEPTIDE2)
+- `$` characters separate different sections of the HELM string
+
+## Using Custom Monomer Data
+
+By default, helmkit uses the monomer data in `helmkit/data/monomers.sdf`. To use a custom SDF file:
+
+```python
+from helmkit import Molecule, load_monomer_library
+
+# Load your custom monomer data
+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}$$$$", monomer_df=custom_monomers)
+```
+
+## SDF File Structure Requirements
+
+The SDF file containing monomer data must have the following properties for each molecule:
+
+### Required Properties:
+- `symbol`: A unique identifier for the monomer (e.g., "A" for alanine)
+- `m_RgroupIdx`: Comma-separated list of R-group atom indices (e.g., "1,2,None,None")
+
+### Optional Properties:
+- `m_Rgroups`: Comma-separated list of R-group types (e.g., "H,OH,None,None")
+- `m_type`: Monomer type (e.g., "aa" for amino acid)
+- `m_subtype`: Monomer subtype
+- `m_abbr`: Monomer abbreviation
+
+### Example SDF Entry:
+
+```
+Your molecule atom data here...
+...
+
+> <symbol>
+A
+
+> <m_Rgroups>
+H,OH,None,None
+
+> <m_RgroupIdx>
+1,2,None,None
+
+> <m_type>
+aa
+
+> <m_subtype>
+natural
+
+> <m_abbr>
+Ala
+
+$$$$
+```
+
+## Parallel Processing of Peptides
+
+For workflows involving a large number of peptides, `helmkit` provides a function to process them in parallel, significantly improving performance.
+
+```python
+from helmkit import load_monomer_library
+from helmkit import load_peptides_in_parallel
+
+# Load your custom monomer data (optional)
+custom_sdf_path = "/path/to/your/custom_monomers.sdf"
+monomer_db = load_monomer_library(custom_sdf_path)
+
+# A list of HELM strings
+helm_strings = ["PEPTIDE1{A.R.G}$$$$", "PEPTIDE1{S.G.T}$$$$"]
+
+# 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-0.5.1/README.md

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+# helmkit
+
+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}$$$$"
+molecule = Molecule(helm_string)
+
+# Access the RDKit molecule object
+rdkit_mol = molecule.mol
+```
+
+## Installation
+
+To install `helmkit`, you can use either [`uv`](https://github.com/astral-sh/uv) or `pip`.
+
+### With [`uv`](https://github.com/astral-sh/uv)
+
+```bash
+uv pip install helmkit
+```
+
+or if you have added it as a dependency to your `pyproject.toml`:
+
+```bash
+uv add helmkit
+```
+
+### Without `uv`
+
+```bash
+pip install helmkit
+```
+
+## Quick Example
+
+```python
+from helmkit import Molecule
+from rdkit.Chem import AllChem, Draw
+
+# Create a simple tripeptide (Ala-Arg-Gly)
+molecule = Molecule("PEPTIDE1{A.R.G}$$$$")
+
+# Generate 2D coordinates for visualization
+AllChem.Compute2DCoords(molecule.mol)
+
+# Save the image
+img = Draw.MolToImage(molecule.mol)
+img.save("tripeptide.png")
+```
+
+## Understanding HELM Notation
+
+HELM (Hierarchical Editing Language for Macromolecules) is a notation for representing complex biomolecules. A basic HELM string has the following format:
+
+```
+PEPTIDE1{A.R.G}|PEPTIDE2{S.G.C}$PEPTIDE1,PEPTIDE2,1:R1-3:R3$$$V2.0
+```
+
+Where:
+- `PEPTIDE1{A.R.G}` defines the first chain (a peptide with amino acids A, R, G)
+- `PEPTIDE2{S.G.C}` defines the second chain
+- `PEPTIDE1,PEPTIDE2,1:R1-3:R3` defines a connection between the chains (R1 of residue 1 in PEPTIDE1 connects to R3 of residue 3 in PEPTIDE2)
+- `$` characters separate different sections of the HELM string
+
+## Using Custom Monomer Data
+
+By default, helmkit uses the monomer data in `helmkit/data/monomers.sdf`. To use a custom SDF file:
+
+```python
+from helmkit import Molecule, load_monomer_library
+
+# Load your custom monomer data
+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}$$$$", monomer_df=custom_monomers)
+```
+
+## SDF File Structure Requirements
+
+The SDF file containing monomer data must have the following properties for each molecule:
+
+### Required Properties:
+- `symbol`: A unique identifier for the monomer (e.g., "A" for alanine)
+- `m_RgroupIdx`: Comma-separated list of R-group atom indices (e.g., "1,2,None,None")
+
+### Optional Properties:
+- `m_Rgroups`: Comma-separated list of R-group types (e.g., "H,OH,None,None")
+- `m_type`: Monomer type (e.g., "aa" for amino acid)
+- `m_subtype`: Monomer subtype
+- `m_abbr`: Monomer abbreviation
+
+### Example SDF Entry:
+
+```
+Your molecule atom data here...
+...
+
+> <symbol>
+A
+
+> <m_Rgroups>
+H,OH,None,None
+
+> <m_RgroupIdx>
+1,2,None,None
+
+> <m_type>
+aa
+
+> <m_subtype>
+natural
+
+> <m_abbr>
+Ala
+
+$$$$
+```
+
+## Parallel Processing of Peptides
+
+For workflows involving a large number of peptides, `helmkit` provides a function to process them in parallel, significantly improving performance.
+
+```python
+from helmkit import load_monomer_library
+from helmkit import load_peptides_in_parallel
+
+# Load your custom monomer data (optional)
+custom_sdf_path = "/path/to/your/custom_monomers.sdf"
+monomer_db = load_monomer_library(custom_sdf_path)
+
+# A list of HELM strings
+helm_strings = ["PEPTIDE1{A.R.G}$$$$", "PEPTIDE1{S.G.T}$$$$"]
+
+# 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-0.5.1/pyproject.toml

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+[project]
+name = "helmkit"
+version = "0.5.1"
+description = "Parse HELM strings into RDKit molecules"
+readme = "README.md"
+requires-python = ">=3.11"
+dependencies = [
+    "rdkit>=2025.3.3",
+]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[dependency-groups]
+dev = [
+    "dead>=2.1.0",
+    "polars>=1.31.0",
+    "pre-commit>=4.2.0",
+    "pypept",
+    "pytest>=8.4.1",
+    "pyupgrade>=3.20.0",
+    "reorder-python-imports>=3.15.0",
+    "tqdm>=4.67.1",
+]
+
+[tool.uv.sources]
+pypept = { git = "https://github.com/Boehringer-Ingelheim/pyPept.git" }
+
+[tool.hatch.build]
+exclude = [
+    ".github",
+    ".gitignore",
+    ".pre-commit-config.yaml",
+    "benchmarks",
+    "dev",
+    "tests",
+]

helmkit-0.5.1/src/helmkit/__init__.py

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+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",
+]