title: COD::CIF::Parser: an error-correcting CIF parser for the Perl language.
abstract: 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 onCOD::CIF::Parser, thecod-toolspackage for manipulating the CIFs in the Crystallography Open Database (COD) has been developed. Thecod-toolspackage 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.
authors.affiliation: Vilnius University Institute of Biotechnology, Graiciuno 8, LT-02241 Vilnius, Lithuania.
authors.forename: Andrius
authors.initials: A
authors.lastname: Merkys
authors.affiliation: Vilnius University Institute of Biotechnology, Graiciuno 8, LT-02241 Vilnius, Lithuania.
authors.forename: Antanas
authors.initials: A
authors.lastname: Vaitkus
authors.affiliation: Time.ly Network Inc., 2nd Floor, 607 Front Street, Nelson, British Columbia, Canada V1L 4B6.
authors.forename: Justas
authors.initials: J
authors.lastname: Butkus
authors.affiliation: Vilnius University Institute of Biotechnology, Graiciuno 8, LT-02241 Vilnius, Lithuania.
authors.forename: Mykolas
authors.initials: M
authors.lastname: Okulič-Kazarinas
authors.affiliation: Vilnius University Institute of Biotechnology, Graiciuno 8, LT-02241 Vilnius, Lithuania.
authors.forename: Visvaldas
authors.initials: V
authors.lastname: Kairys
authors.affiliation: Vilnius University Institute of Biotechnology, Graiciuno 8, LT-02241 Vilnius, Lithuania; Vilnius University Faculty of Mathematics and Informatics, Naugarduko 24, LT-03225 Vilnius, Lithuania.
authors.forename: Saulius
authors.initials: S
authors.lastname: Gražulis
keywords: CIF parsers; Crystallography Open Database; Perl