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‎.github/workflows/build.yaml‎

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name: Build
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on:
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push:
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tags:
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- 'v[0-9]+.[0-9]+.[0-9]+*'
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jobs:
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build_wheels:
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name: Build wheels for ${{ matrix.platform_id }}
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ ubuntu-latest, macos-latest, windows-latest ]
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include:
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- os: ubuntu-latest
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platform_id: manylinux_x86_64
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- os: macos-latest
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platform_id: macosx
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- os: windows-latest
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platform_id: win_amd64
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steps:
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- uses: actions/checkout@v4
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- name: Set up MSVC environment (Windows)
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if: runner.os == 'Windows'
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uses: ilammy/msvc-dev-cmd@v1
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with:
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arch: x64
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- name: Setup Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.9"
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- name: Build wheels
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uses: pypa/cibuildwheel@v2.23.3
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env:
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CIBW_BUILD_VERBOSITY: 1
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CIBW_ARCHS: ${{ runner.os == 'macOS' && 'universal2' || 'auto64' }}
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- uses: actions/upload-artifact@v4
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with:
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name: cibw-wheels-${{ matrix.platform_id }}-${{ strategy.job-index }}
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path: ./wheelhouse/*.whl
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build_sdist:
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name: Build source distribution
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: true
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- uses: actions/setup-python@v5
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name: Install Python
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with:
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python-version: '3.13'
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- run: python -m pip install build
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- name: Build sdist
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run: python -m build --sdist
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- uses: actions/upload-artifact@v4
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with:
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name: cibw-sdist
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path: dist/*.tar.gz
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upload_pypi:
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needs: [ build_sdist, build_wheels ]
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runs-on: ubuntu-latest
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if: startsWith(github.ref, 'refs/tags/')
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permissions:
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id-token: write
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steps:
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- name: Download all distribution files
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uses: actions/download-artifact@v4
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with:
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pattern: cibw-*
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path: dist/
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merge-multiple: true
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- name: List files in dist
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run: ls -lR dist/
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- name: Publish package to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1

‎CMakeLists.txt‎

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# CMakeLists.txt
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cmake_minimum_required(VERSION 3.15)
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project(vcon_py C)
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# Ensure we compile as C99 (code uses classic C interfaces)
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set(CMAKE_C_STANDARD 99)
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set(CMAKE_C_STANDARD_REQUIRED ON)
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include_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/vconpy/vcon)
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add_executable(vcon
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${CMAKE_CURRENT_SOURCE_DIR}/src/vconpy/vcon/Vcontacts-v1-2.c
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)
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if(MSVC)
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target_compile_options(vcon PRIVATE /O2)
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else()
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target_compile_options(vcon PRIVATE -O3)
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target_link_libraries(vcon PRIVATE m)
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endif()
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# Install
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include(GNUInstallDirs)
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install(TARGETS vcon
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RUNTIME DESTINATION ${CMAKE_INSTALL_PREFIX}/bin
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)
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# Install Python module files
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install(FILES
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${CMAKE_CURRENT_SOURCE_DIR}/src/vconpy/__init__.py
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${CMAKE_CURRENT_SOURCE_DIR}/src/vconpy/vcontacts_wrapper.py
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DESTINATION ${CMAKE_INSTALL_PREFIX}
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)

‎README.md‎

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# vcontacts-wrapper (vconpy)
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A lightweight Python package to prepare arguments and run **Vcontacts**,
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a tool to compute surface areas in contact using the constrained Voronoi procedure from the paper:
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> **Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure**
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> (doi: [10.1093/bioinformatics/18.10.1365](https://doi.org/10.1093/bioinformatics/18.10.1365))
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This wrapper makes it easy to call the `Vcontacts` executables (`vcon_surfaces` or `vcon_nrgten`) directly from Python, capture their output, and optionally parse `.vcon` files into Python dictionaries.
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---
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## Installation
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```bash
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pip install vcon-py
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```
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---
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## Example Usage
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```python
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from vconpy import run_vcon
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# Run Vcontacts
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result_surfaces = run_vcon(
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"/path/to/receptor.pdb",
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vcon_type="surfaces"
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)
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# Run Vcontacts and return a dictionary instead of outputting a file
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result_nrgten = run_vcon(
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"/path/to/receptor.pdb",
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as_dictionary=True
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)
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# NRGTEN requires setting showbonded as True
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result_nrgten = run_vcon(
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"/path/to/receptor.pdb",
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as_dictionary=True,
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showbonded=True
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)
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print(result_nrgten.surface_dictionary) # dict of atom-atom contact areas
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```
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---
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## Arguments
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| Argument | Type | Description | Default |
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|------------------|--------|----------------------------------------------------------------------------------------------------------------------------------|--------------|
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| `pdb_filename` | `str` | Path to the input PDB file. | **Required** |
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| `showbonded` | `bool` | If `True`, include covalently bonded atoms in the contacts (`-all` flag). | `False` |
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| `normalize` | `bool` | If `True`, normalize contacts to percent of total contact area. Otherwise, contacts are given in SAS units (Ų). (`-norm` flag). | `False` |
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| `planedef` | `str` | Plane definition for analysis. Options: `X` (extended radical plane), `R` (radical plane), `B` (bisecting plane). | `None` |
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| `as_dictionary` | `bool` | If `True`, returns a Python dictionary. The `.vcon` file is deleted after parsing. | `False` |
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---
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## Returns
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The function returns a `VconResult` namedtuple with the following fields:
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| Field | Type | Description |
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|----------------------|--------|------------------------------------------------------------------------|
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| `vcon_filename` | `str` | Path to the generated `.vcon` file. |
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| `surface_dictionary` | `dict` | Dictionary of atom-atom contact areas (only if `as_dictionary=True`). |
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| `stdout` | `str` | Standard output from the Vcontacts process. |
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| `stderr` | `str` | Standard error from the Vcontacts process. |
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| `returncode` | `int` | Exit code from the Vcontacts process. |
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---
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## Raises
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| Error | Condition |
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|-------------|---------------------------------------------------------------------------|
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| `ValueError` | Raised if the input file does not exist, or if `vcon_type` is invalid. |
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| `VconError` | Raised if the Vcontacts executable is missing, not executable, or fails. |
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---

‎pyproject.toml‎

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[build-system]
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requires = [
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"scikit-build-core",
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"setuptools_scm[toml]>=6.2"
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]
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build-backend = "scikit_build_core.build"
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[project]
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name = "vcon-py"
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dynamic = ["version"]
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description = "Python wheels and a wrapper for Vcontacts, a tool to compute surface areas in contact using the constrained Voronoi procedure."
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authors = [
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{name = "Thomas DesCôteaux"},
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{name = "Rafael Najmanovich", email = "rafael.najmanovich@umontreal.ca"},
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]
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classifiers = [
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'Intended Audience :: Science/Research',
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'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
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'Natural Language :: English',
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]
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readme = "README.md"
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requires-python = ">=3.9"
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[project.urls]
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Homepage = "https://github.com/NRGlab"
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Documentation = "https://github.com/NRGlab/vcon-py/blob/main/README.md"
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Repository = "https://github.com/NRGlab/vcon-py"
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Issues = "https://github.com/NRGlab/vcon-py/issues"
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[tool.scikit-build]
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wheel.install-dir = "vconpy"
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wheel.py-api = "py3"
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metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"
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cmake.build-type = "Release"
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[tool.setuptools.packages.find]
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include = ["vconpy","vconpy.*"]
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[tool.setuptools_scm]
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[tool.cibuildwheel]
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build = "cp39-*"
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skip = [
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"*-win32",
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"*-manylinux_i686",
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"*-musllinux*",
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]
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environment-pass = ["CIBW_BUILD"]

‎src/vconpy/__init__.py‎

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from .vcontacts_wrapper import run_vcon

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