pyDiSCaMB

Simple pybind11 wrapper to communicate with DiSCaMB from cctbx, built with scikit-build and cmake.

LICENSE NOTE

Recursive cloning installs the MATTS databank, which uses a license restricting commercial use. Building the project with the databank will include the databank in the built module, which should be taken into account if the build is distributed.

Installation

Tested on ubuntu, macOS, and windows, on python 3.9-3.12. Currently (June 2025) not available as pre-built packages, manual installation instructions follow:

Using Conda

A environment file is provided. You also need a C++ compiler, which is in a seperate file depending on your operating system. Replace the brackets below with the appropriate choice (e.g. compiler_macOS-latest.yml).

git clone --recursive [email protected]:viljarjf/pyDiSCaMB.git
conda create -f pyDiSCaMB/conda/dev_env.yml
conda env update --file pyDiSCaMB/conda/compiler_[any of "macOS", "ubuntu", "windows"]-latest.yml
conda activate pydiscamb-dev
pip install pyDiSCaMB/

Using Phenix

With Phenix, installation is even simpler:

git clone --recursive [email protected]:viljarjf/pyDiSCaMB.git
phenix.python -m pip install pyDiSCaMB/

Only tested on versions newer than around 2.0rc1-5500.

Example usage

from pydiscamb import DiscambWrapper

wrapper = DiscambWrapper.from_file("your_structure.cif")
wrapper.set_d_min(2.0)
f_calc = wrapper.f_calc()

# Now do what you want with the list of structure factors

Development

Feel free to open pull requests. Currently under development by Viljar Femoen.

Installation

Make a fork of https://github.com/viljarjf/pyDiSCaMB and use your new URL for cloning instead. Otherwise the instructions are like before.

To debug, install in an editable state:

pip install -e pyDiSCaMB/[dev]

This sets the Debug flag in cmake, allowing you to use e.g. gdb. Confirmed to work with both C++ and python breakpoints in WSL Ubuntu, using gdb and Python C++ Debugger for VS Code.

When opening a PR, the code will be checked with black and clang-format. Using pre-commit avoids having to fix the formatting afterwards. Set it up with:

cd pyDiSCaMB
pre-commit install

Testing

Performed automatically on multiple OSs and Python version for all pull requests. Can be done manually as follows:

pip install pytest
pytest pyDiSCaMB/

To avoid slow or very slow tests, instead run

pytest -m "not veryslow" pyDiSCaMB/

change "veryslow" for "slow" to avoid even more tests.