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CIF/STAR file support for Python

Project description

PyCIFRW Readme


PyCIFRW provides support for reading and writing CIF (Crystallographic
Information Format) files using Python. It was developed at the
Australian National Beamline Facility (ANBF), run by the Australian
Synchrotron Research Program (ASRP), as part of a larger project to
provide CIF input/output capabilities for data collection. It is
now (Jan 2015) maintained and developed within the Australian Nuclear Science and
Technology Organisation (ANSTO).


The CIF 1.1 and 2.0 working specifications were used as a reference,

PyCifRW has been tested on the IUCr sample CIF trip files located at and fails or
successfully reads as it is supposed to (note that ciftest5 contains
characters now forbidden in CIFs).

Supported Platforms

PyCIFRW is written entirely in Python. While this makes parsing of large
CIF files rather slow, it should run wherever Python runs. The latest version
has been tested on Linux and Windows 7.

The source code of a C extension module is also included in the distribution.
This module accelerates CIF file reading. From time to time
system-dependent installation packages are generated containing precompiled
versions of this module.


The following are some of the key files included in PyCIFRW:

Original files: Defines the CifFile module for Python
CifFile.nw Noweb file from which is obtained
CifFile.html Programming notes for CifFile derived also from
CifFile.nw Defines the StarFile module on which CifFiles are built
StarFile.nw Noweb file from which is obtained
StarFile.html Programming notes for also derived from StarFile.nw Cif parser for version n_n automatically generated by Yapps2
YappsStarParser.html Programming notes for the grammar
YappsStarParser.nw Literate format grammar with notes from which grammars are
Makefile How to derive .html, .py and .g files from .nw files Compiled Python extension module for Linux

drel/ Routines for processing dREL methods
Files derived from other programs: Yapps3 runtime support (modified part of the
Yapps3 distribution)




See the various files in the docs directory for details of the interface.
Essentially, CIF files look like python dictionaries, with each
entry in the dictionary corresponding to a data block. The blocks
themselves are also dictionaries, with each data name being a
single entry in the dictionary, so for example,
cf['si_std']['_diffrn_meas_wavelength'] will return the value of
_diffrn_meas_wavelength in the data block named si_std of the Cif file object


To read in a CIF:
>> from CifFile import CifFile
>> cf = CifFile.ReadCif('jun_01_2.cif')

to access information in a CIF

>> wav = cf['si_std']['_diffrn_meas_wavelength']

to set a value

>> cf['si_std']['_diffrn_meas_wavelength'] = 1.54

Extra programs

The "Programs" directory contains program "" which
validates a data files against data dictionaries. Execute this file
without arguments for a help message.

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