cavefiller 0.2.0__tar.gz

cavefiller-0.2.0/LICENSE

@@ -0,0 +1,201 @@
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cavefiller-0.2.0/PKG-INFO

@@ -0,0 +1,225 @@
+Metadata-Version: 2.4
+Name: cavefiller
+Version: 0.2.0
+Summary: A tool to find and fill protein cavities with water molecules using KVFinder and Packmol
+Author: CaveFiller Contributors
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: typer>=0.9.0
+Requires-Dist: pykvfinder>=0.6.0
+Requires-Dist: rdkit>=2022.9.1
+Requires-Dist: numpy>=1.20.0
+Requires-Dist: biopython>=1.79
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: black>=22.0.0; extra == "dev"
+Requires-Dist: ruff>=0.1.0; extra == "dev"
+Dynamic: license-file
+
+# CaveFiller
+
+A Python tool to find and fill protein cavities with water molecules using KVFinder, Monte Carlo sampling, and RDKit-based explicit water generation.
+
+## Features
+
+-  **Cavity Detection**: Uses pyKVFinder to detect cavities in protein structures
+-  **Interactive Selection**: Select specific cavities to fill with user-defined water counts
+-  **Monte Carlo Sampling**: Places water molecules using Monte Carlo sampling with clash detection
+-  **Explicit Waters**: Builds full H-O-H waters with RDKit (including hydrogens)
+-  **CLI Interface**: Easy-to-use command-line interface built with Typer
+
+## Installation
+
+### Prerequisites
+
+1. **Python**: Python 3.8 or higher
+
+### Install CaveFiller
+
+```bash
+# Clone the repository
+git clone https://github.com/Desperadus/CaveFiller.git
+cd CaveFiller
+
+# Install the package
+pip install -e .
+```
+
+## Usage
+
+### Basic Usage
+
+```bash
+cavefiller protein.pdb
+```
+
+This will:
+1. Detect cavities in `protein.pdb`
+2. Display a list of found cavities with their volumes and areas
+3. Prompt you to select which cavities to fill
+4. Prompt you for the number of water molecules per cavity
+5. Place waters using Monte Carlo sampling with clash detection
+6. Build explicit RDKit H-O-H waters and export a combined PDB
+7. Save the output to `./output/protein_filled.pdb`
+
+### Command-line Options
+
+```bash
+cavefiller [PROTEIN_FILE] [OPTIONS]
+```
+
+**Arguments:**
+- `PROTEIN_FILE`: Path to the protein PDB file (required)
+
+**Options:**
+- `--output-dir PATH`: Directory to save output files (default: `./output`)
+- `--probe-in FLOAT`: Probe In radius for cavity detection in Ångströms (default: 1.4)
+- `--probe-out FLOAT`: Probe Out radius for cavity detection in Ångströms (default: 4.0)
+- `--volume-cutoff FLOAT`: Minimum cavity volume to consider in Ų (default: 5.0)
+- `--auto-select`: Automatically select all cavities without user interaction
+- `--cavity-ids TEXT`: Comma-separated list of cavity IDs to fill (e.g., '1,2,3')
+- `--waters-per-cavity TEXT`: Comma-separated list of water counts (e.g., '10,15,20'), must match cavity-ids order
+- `--optimize-mmff94 / --no-optimize-mmff94`: Enable/disable MMFF94 with protein fixed (default: enabled)
+- `--mmff-max-iterations INTEGER`: Max MMFF94 iterations (default: 300)
+
+Recommended usage:
+- Prefer interactive/manual cavity and water-count selection over `--auto-select`. Auto-selection often overfills cavities with too many waters.
+- Keep `--optimize-mmff94` enabled (recommended) to refine water placement after Monte Carlo sampling.
+
+### Examples
+
+**Interactive cavity and water selection:**
+```bash
+cavefiller protein.pdb --output-dir results
+```
+
+**Auto-select all cavities with default water counts (not generally recommended):**
+```bash
+cavefiller protein.pdb --auto-select
+```
+
+**Fill specific cavities with specific water counts:**
+```bash
+cavefiller protein.pdb --cavity-ids "1,3,5" --waters-per-cavity "10,15,20"
+```
+
+**Custom cavity detection parameters:**
+```bash
+cavefiller protein.pdb --probe-in 1.2 --probe-out 5.0 --volume-cutoff 10.0
+```
+
+## Workflow
+
+1. **Cavity Detection**: The tool uses pyKVFinder to detect cavities in the input protein structure
+2. **Cavity Analysis**: Displays information about detected cavities (ID, volume, surface area)
+3. **Cavity Selection**: 
+   - Interactive mode: User selects cavities and specifies water counts
+   - Auto mode: All cavities are selected with automatic water count estimation
+   - Command-line mode: Specific cavities and water counts are pre-selected
+4. **Water Placement**: 
+   - Monte Carlo sampling places waters randomly in cavity
+   - Clash detection validates each position against protein atoms and other waters
+   - Uses Van der Waals radii for distance calculations
+5. **RDKit Water Construction**:
+   - Explicit H-O-H waters are generated with ideal geometry
+   - Waters include hydrogens and proper HOH residue records in the output PDB
+
+## Algorithm Details
+
+### Monte Carlo Sampling
+- Samples around cavity grid points with small local jitter
+- Validates position stays near cavity voxels (< 0.7 Å from a grid point)
+- Checks for clashes with protein atoms (minimum distance based on VDW radii)
+- Checks for clashes with other waters (minimum 2.7 Å separation)
+- Attempts up to 500 placements per water molecule
+
+### Clash Detection
+- Uses Van der Waals radii for different atom types (H, C, N, O, S, P)
+- Minimum water-protein distance: 2.35 Å
+- Minimum water-water distance: 2.7 Å
+- Tolerance of 0.5 Å for VDW overlap
+
+### RDKit Water Geometry
+- Creates proper H-O-H geometry for each water
+- Writes explicit HOH residues (O, H1, H2) into output PDB
+
+## Output
+
+The tool generates the following files in the output directory:
+
+- `protein_filled.pdb`: Protein structure with explicit water molecules in selected cavities
+
+## Dependencies
+
+- **typer**: CLI framework
+- **pyKVFinder**: Cavity detection
+- **rdkit**: Molecular manipulation and explicit water generation
+- **numpy**: Numerical operations
+- **biopython**: PDB file handling
+
+## Development
+
+### Running Tests
+
+```bash
+pip install -e ".[dev]"
+pytest
+```
+
+### Code Formatting
+
+```bash
+black cavefiller/
+ruff check cavefiller/
+```
+
+### Automated CI/CD and PyPI Publishing
+
+This repository includes GitHub Actions workflow at `.github/workflows/ci-cd.yml` that:
+- Runs `pytest` on every push to `main`
+- Runs `pytest` on every pull request targeting `main`
+- Builds package distributions after tests pass
+- Publishes to PyPI only when you push a version tag like `v0.1.1`
+
+#### One-time setup for automatic PyPI publishing
+
+1. Create a PyPI account at https://pypi.org and create your project once (or publish once manually so the name exists).
+2. In PyPI, open your project settings and add a **Trusted Publisher**:
+   - Owner: your GitHub username/org
+   - Repository: `Desperadus/CaveFiller`
+   - Workflow name: `CI/CD`
+   - Environment: leave empty (unless you choose to use one)
+3. In GitHub, ensure Actions are enabled for the repository.
+
+No PyPI API token secret is needed when using Trusted Publishing.
+
+#### Releasing a new version
+
+1. Bump version in both:
+   - `pyproject.toml` (`project.version`)
+   - `cavefiller/__init__.py` (`__version__`)
+2. Commit and push to `main`.
+3. Create and push a matching tag:
+
+```bash
+git tag v0.1.1
+git push origin v0.1.1
+```
+
+The workflow validates that the tag matches `pyproject.toml` (for example, tag `v0.1.1` must match version `0.1.1`) before publishing.
+
+## License
+
+See LICENSE file for details.
+
+## Citation
+
+If you use CaveFiller in your research, please cite:
+
+- pyKVFinder: Guerra et al. (2020) BMC Bioinformatics
+- RDKit: RDKit: Open-source cheminformatics; http://www.rdkit.org
+
+## Contributing
+
+Contributions are welcome! Please feel free to submit a Pull Request.

cavefiller-0.2.0/README.md

@@ -0,0 +1,206 @@
+# CaveFiller
+
+A Python tool to find and fill protein cavities with water molecules using KVFinder, Monte Carlo sampling, and RDKit-based explicit water generation.
+
+## Features
+
+-  **Cavity Detection**: Uses pyKVFinder to detect cavities in protein structures
+-  **Interactive Selection**: Select specific cavities to fill with user-defined water counts
+-  **Monte Carlo Sampling**: Places water molecules using Monte Carlo sampling with clash detection
+-  **Explicit Waters**: Builds full H-O-H waters with RDKit (including hydrogens)
+-  **CLI Interface**: Easy-to-use command-line interface built with Typer
+
+## Installation
+
+### Prerequisites
+
+1. **Python**: Python 3.8 or higher
+
+### Install CaveFiller
+
+```bash
+# Clone the repository
+git clone https://github.com/Desperadus/CaveFiller.git
+cd CaveFiller
+
+# Install the package
+pip install -e .
+```
+
+## Usage
+
+### Basic Usage
+
+```bash
+cavefiller protein.pdb
+```
+
+This will:
+1. Detect cavities in `protein.pdb`
+2. Display a list of found cavities with their volumes and areas
+3. Prompt you to select which cavities to fill
+4. Prompt you for the number of water molecules per cavity
+5. Place waters using Monte Carlo sampling with clash detection
+6. Build explicit RDKit H-O-H waters and export a combined PDB
+7. Save the output to `./output/protein_filled.pdb`
+
+### Command-line Options
+
+```bash
+cavefiller [PROTEIN_FILE] [OPTIONS]
+```
+
+**Arguments:**
+- `PROTEIN_FILE`: Path to the protein PDB file (required)
+
+**Options:**
+- `--output-dir PATH`: Directory to save output files (default: `./output`)
+- `--probe-in FLOAT`: Probe In radius for cavity detection in Ångströms (default: 1.4)
+- `--probe-out FLOAT`: Probe Out radius for cavity detection in Ångströms (default: 4.0)
+- `--volume-cutoff FLOAT`: Minimum cavity volume to consider in Ų (default: 5.0)
+- `--auto-select`: Automatically select all cavities without user interaction
+- `--cavity-ids TEXT`: Comma-separated list of cavity IDs to fill (e.g., '1,2,3')
+- `--waters-per-cavity TEXT`: Comma-separated list of water counts (e.g., '10,15,20'), must match cavity-ids order
+- `--optimize-mmff94 / --no-optimize-mmff94`: Enable/disable MMFF94 with protein fixed (default: enabled)
+- `--mmff-max-iterations INTEGER`: Max MMFF94 iterations (default: 300)
+
+Recommended usage:
+- Prefer interactive/manual cavity and water-count selection over `--auto-select`. Auto-selection often overfills cavities with too many waters.
+- Keep `--optimize-mmff94` enabled (recommended) to refine water placement after Monte Carlo sampling.
+
+### Examples
+
+**Interactive cavity and water selection:**
+```bash
+cavefiller protein.pdb --output-dir results
+```
+
+**Auto-select all cavities with default water counts (not generally recommended):**
+```bash
+cavefiller protein.pdb --auto-select
+```
+
+**Fill specific cavities with specific water counts:**
+```bash
+cavefiller protein.pdb --cavity-ids "1,3,5" --waters-per-cavity "10,15,20"
+```
+
+**Custom cavity detection parameters:**
+```bash
+cavefiller protein.pdb --probe-in 1.2 --probe-out 5.0 --volume-cutoff 10.0
+```
+
+## Workflow
+
+1. **Cavity Detection**: The tool uses pyKVFinder to detect cavities in the input protein structure
+2. **Cavity Analysis**: Displays information about detected cavities (ID, volume, surface area)
+3. **Cavity Selection**: 
+   - Interactive mode: User selects cavities and specifies water counts
+   - Auto mode: All cavities are selected with automatic water count estimation
+   - Command-line mode: Specific cavities and water counts are pre-selected
+4. **Water Placement**: 
+   - Monte Carlo sampling places waters randomly in cavity
+   - Clash detection validates each position against protein atoms and other waters
+   - Uses Van der Waals radii for distance calculations
+5. **RDKit Water Construction**:
+   - Explicit H-O-H waters are generated with ideal geometry
+   - Waters include hydrogens and proper HOH residue records in the output PDB
+
+## Algorithm Details
+
+### Monte Carlo Sampling
+- Samples around cavity grid points with small local jitter
+- Validates position stays near cavity voxels (< 0.7 Å from a grid point)
+- Checks for clashes with protein atoms (minimum distance based on VDW radii)
+- Checks for clashes with other waters (minimum 2.7 Å separation)
+- Attempts up to 500 placements per water molecule
+
+### Clash Detection
+- Uses Van der Waals radii for different atom types (H, C, N, O, S, P)
+- Minimum water-protein distance: 2.35 Å
+- Minimum water-water distance: 2.7 Å
+- Tolerance of 0.5 Å for VDW overlap
+
+### RDKit Water Geometry
+- Creates proper H-O-H geometry for each water
+- Writes explicit HOH residues (O, H1, H2) into output PDB
+
+## Output
+
+The tool generates the following files in the output directory:
+
+- `protein_filled.pdb`: Protein structure with explicit water molecules in selected cavities
+
+## Dependencies
+
+- **typer**: CLI framework
+- **pyKVFinder**: Cavity detection
+- **rdkit**: Molecular manipulation and explicit water generation
+- **numpy**: Numerical operations
+- **biopython**: PDB file handling
+
+## Development
+
+### Running Tests
+
+```bash
+pip install -e ".[dev]"
+pytest
+```
+
+### Code Formatting
+
+```bash
+black cavefiller/
+ruff check cavefiller/
+```
+
+### Automated CI/CD and PyPI Publishing
+
+This repository includes GitHub Actions workflow at `.github/workflows/ci-cd.yml` that:
+- Runs `pytest` on every push to `main`
+- Runs `pytest` on every pull request targeting `main`
+- Builds package distributions after tests pass
+- Publishes to PyPI only when you push a version tag like `v0.1.1`
+
+#### One-time setup for automatic PyPI publishing
+
+1. Create a PyPI account at https://pypi.org and create your project once (or publish once manually so the name exists).
+2. In PyPI, open your project settings and add a **Trusted Publisher**:
+   - Owner: your GitHub username/org
+   - Repository: `Desperadus/CaveFiller`
+   - Workflow name: `CI/CD`
+   - Environment: leave empty (unless you choose to use one)
+3. In GitHub, ensure Actions are enabled for the repository.
+
+No PyPI API token secret is needed when using Trusted Publishing.
+
+#### Releasing a new version
+
+1. Bump version in both:
+   - `pyproject.toml` (`project.version`)
+   - `cavefiller/__init__.py` (`__version__`)
+2. Commit and push to `main`.
+3. Create and push a matching tag:
+
+```bash
+git tag v0.1.1
+git push origin v0.1.1
+```
+
+The workflow validates that the tag matches `pyproject.toml` (for example, tag `v0.1.1` must match version `0.1.1`) before publishing.
+
+## License
+
+See LICENSE file for details.
+
+## Citation
+
+If you use CaveFiller in your research, please cite:
+
+- pyKVFinder: Guerra et al. (2020) BMC Bioinformatics
+- RDKit: RDKit: Open-source cheminformatics; http://www.rdkit.org
+
+## Contributing
+
+Contributions are welcome! Please feel free to submit a Pull Request.

cavefiller-0.2.0/cavefiller/__init__.py

@@ -0,0 +1,3 @@
+"""CaveFiller - A tool to find and fill protein cavities with water molecules."""
+
+__version__ = "0.2.0"