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COD::CIF::Parser : an error‐correcting CIF parser for the Perl language
Author(s) -
Merkys Andrius,
Vaitkus Antanas,
Butkus Justas,
Okulič-Kazarinas Mykolas,
Kairys Visvaldas,
Gražulis Saulius
Publication year - 2016
Publication title -
journal of applied crystallography
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.429
H-Index - 162
ISSN - 1600-5767
DOI - 10.1107/s1600576715022396
Subject(s) - perl , computer science , parsing , python (programming language) , programming language , pipeline (software) , natural language processing
A syntax‐correcting CIF parser, COD::CIF::Parser , is presented that can parse CIF 1.1 files and accurately report the position and the nature of the discovered syntactic problems. In addition, the parser is able to automatically fix the most common and the most obvious syntactic deficiencies of the input files. Bindings for Perl, C and Python programming environments are available. Based on COD::CIF::Parser , the cod‐tools package for manipulating the CIFs in the Crystallography Open Database (COD) has been developed. The cod‐tools package has been successfully used for continuous updates of the data in the automated COD data deposition pipeline, and to check the validity of COD data against the IUCr data validation guidelines. The performance, capabilities and applications of different parsers are compared.