diffpy.structure 3.4.0

Crystal structure container and parsers for structure formats.

Crystal structure container and parsers for structure formats.

The diffpy.structure package provides objects for storing atomic coordinates, displacement parameters and other crystal structure data. diffpy.structure supports import and export of structure data in several structure formats such as CIF, PDB, and xyz. It provides conversion between fractional and absolute Cartesian coordinates, functions for symmetry expansion of atom sites in the asymmetric unit and generation of symmetry constraints for atom positions and displacement parameters. diffpy.structure includes definitions of all space groups in over 500 symmetry settings.

For more information about the diffpy.structure library, please consult our online documentation.

Citation

If you use this program for a scientific research that leads to publication, we ask that you acknowledge use of the program by citing the following paper in your publication:

P. Juhás, C. L. Farrow, X. Yang, K. R. Knox and S. J. L. Billinge, Complex modeling: a strategy and software program for combining multiple information sources to solve ill posed structure and nanostructure inverse problems, Acta Crystallogr. A 71, 562-568 (2015).

Installation

The preferred method is to use Miniconda Python and install from the “conda-forge” channel of Conda packages.

To add “conda-forge” to the conda channels, run the following in a terminal.

conda config --add channels conda-forge

We want to install our packages in a suitable conda environment. The following creates and activates a new environment named diffpy.structure_env

conda create -n diffpy.structure_env diffpy.structure
conda activate diffpy.structure_env

To confirm that the installation was successful, type

python -c "import diffpy.structure; print(diffpy.structure.__version__)"

The output should print the latest version displayed on the badges above.

If the above does not work, you can use pip to download and install the latest release from Python Package Index. To install using pip into your diffpy.structure_env environment, type

pip install diffpy.structure

If you prefer to install from sources, after installing the dependencies, obtain the source archive from GitHub. Once installed, cd into your diffpy.structure directory and run the following

pip install .

This package also provides command-line utilities. To check the software has been installed correctly, type

diffpy.structure --version

You can also type the following command to verify the installation.

python -c "import diffpy.structure; print(diffpy.structure.__version__)"

To view the basic usage and available commands, type

diffpy.structure -h

Getting Started

You may consult our online documentation for tutorials and API references.

Support and Contribute

Diffpy user group is the discussion forum for general questions and discussions about the use of diffpy.structure. Please join the diffpy.structure users community by joining the Google group. The diffpy.structure project welcomes your expertise and enthusiasm!

If you see a bug or want to request a feature, please report it as an issue and/or submit a fix as a PR. You can also post it to the Diffpy user group.

Feel free to fork the project and contribute. To install diffpy.structure in a development mode, with its sources being directly used by Python rather than copied to a package directory, use the following in the root directory

pip install -e .

To ensure code quality and to prevent accidental commits into the default branch, please set up the use of our pre-commit hooks.

1. Install pre-commit in your working environment by running conda install pre-commit.

2. Initialize pre-commit (one time only) pre-commit install.

Thereafter your code will be linted by black and isort and checked against flake8 before you can commit. If it fails by black or isort, just rerun and it should pass (black and isort will modify the files so should pass after they are modified). If the flake8 test fails please see the error messages and fix them manually before trying to commit again.

Improvements and fixes are always appreciated.

Before contributing, please read our Code of Conduct.

Contact

For more information on diffpy.structure please visit the project web-page or email the maintainer``Simon Billinge([e-mail])``.

Acknowledgements

diffpy.structure is built and maintained with scikit-package.

Space group codes in spacegroupmod.py and mmlibspacegroups.py originate from the pymmlib project.

Less common settings of space groups were generating using the Computational Crystallography Toolbox.

diffpy.structure is built and maintained with scikit-package.