The CIF (Crystallographic Information File) format, a subset of STAR (Self-defining Text Archival and Retrieval format), is suitable for archiving all types of text and numerical data, in any order. CIF's usefulness derives from its generality, upward compatibility, and flexibility. Recently, the RCSB released a set of simple object-oriented Perl modules and scripts for parsing STAR-compliant data files and dictionaries like mmCIF. Users with a working knowledge of Perl and a basic familiarity with CIF or other STAR-compliant data file formats will benefit from these tools. Modules included in this distribution are:
STAR::Parser Perl extension for parsing STAR-compliant files (with no nested loops)
STAR::DataBlock class and object methods for dealing with DataBlock objects created by STAR::Parser, for such tasks as reading objects from disk or querying their data structures
STAR::Dictionary a subclass of STAR::DataBlock, which supports all methods from STAR::DataBlock, as well as the additional method get_save_blocks
STAR::Writer provides several methods for writing STAR::DataBlocks as files in different formats
STAR::Checker contains the checker object, with methods for checking DataBlock object against STAR rules and against a specified dictionary
STAR::Filter contains the filter object for filtering DataBlock objects
The included scripts are a mixture of basic utility scripts (e.g., parse.pl or check.pl) and very simplistic examples that are meant to test certain methods in the modules (e.g., create.pl). Users can also write their own custom scripts.
To download these modules or for more information, please refer to the documentation at http://pdb.sdsc.edu/STAR/.
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics:
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