diffpy.structure 1.2b2

Crystal structure container and parsers for structure formats.

storage and manipulation of crystal structure data

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, xyz. It provides conversion between fractional and absolute Cartesian coordinates, functions for symmetry expansion from 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.

To learn more about diffpy.Structure library, see the examples in the source repository and the user manual at http://diffpy.github.io/diffpy.Structure.

REQUIREMENTS

The diffpy.Structure requires Python 2.6 or 2.7 and the following software:

• setuptools - software distribution tools for Python

• NumPy - numerical mathematics and fast array operations for Python

On Ubuntu Linux the required software can be easily installed using the system package manager:

sudo aptitude install python-setuptools python-numpy

For Mac OS X machine with the MacPorts package manager the installation command is

sudo port install python27 py27-setuptools py27-numpy

When installing with MacPorts, make sure the MacPorts bin directory is the first in the system PATH and that python27 is selected as the default Python version in MacPorts:

sudo port select --set python python27

For other Linux distributions use their respective package manager; note the packages may have slightly different names. diffpy.Structure depends also on the PyCifRW library, which should get automatically deployed as a part of the installation process.

INSTALLATION

Use easy_install to download and install the latest release from Python Package Index

sudo easy_install diffpy.Structure

diffpy.Structure is also included in the DiffPy-CMI release bundle of Python libraries for structure analysis at http://www.diffpy.org.

If you prefer to install from sources, make sure all required software packages are in place and then run

sudo python setup.py install

By default the files are installed in the system directories, which are only writeable by the root user. See the usage info from ./setup.py install --help for options to install as a normal user under different location. Note that installation to non-standard directories may require adjustments to the PATH and PYTHONPATH environment variables. The installation integrity can be verified by changing to the HOME directory and running

python -m diffpy.Structure.tests.run

DEVELOPMENT

diffpy.Structure is an open-source software developed as a part of the DiffPy-CMI complex modeling initiative at the Brookhaven National Laboratory. The diffpy.Structure sources are hosted at https://github.com/diffpy/diffpy.Structure.

Feel free to fork the project and contribute. To install diffpy.Structure in a development mode, where the sources are directly used by Python rather than copied to a system directory, use

python setup.py develop --user

ACKNOWLEDGEMENT

Space group codes in spacegroupmod.py and mmlibspacegroups.py originate from the pymmlib project, http://pymmlib.sourceforge.net.

CONTACTS

For more information on diffpy.Structure please visit the project web-page

http://www.diffpy.org/

or email Prof. Simon Billinge at [e-mail].