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COD::CIF::Parser: an error-correcting CIF parser for the Perl language.

Andrius Merkys1, Antanas Vaitkus1, Justas Butkus2

  • 1Vilnius University Institute of Biotechnology, Graiciuno 8, LT-02241 Vilnius, Lithuania.

Journal of Applied Crystallography
|March 4, 2016
PubMed
Summary
This summary is machine-generated.

A new syntax-correcting CIF parser, COD::CIF::Parser, can identify and fix syntax errors in CIF 1.1 files. This tool enhances data integrity for the Crystallography Open Database (COD) through the cod-tools package.

Keywords:
CIF parsersCrystallography Open DatabasePerl

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Area of Science:

  • Crystallography
  • Computational Chemistry
  • Materials Science

Background:

  • Crystallographic Information Files (CIF) are crucial for data exchange in crystallography.
  • Existing CIF parsers may struggle with syntactic errors, hindering data processing.
  • Automated data deposition and validation require robust parsing tools.

Purpose of the Study:

  • To introduce COD::CIF::Parser, a novel syntax-correcting CIF parser.
  • To enable automatic correction of common syntactic deficiencies in CIF files.
  • To develop and evaluate the cod-tools package for CIF manipulation within the Crystallography Open Database (COD).

Main Methods:

  • Development of COD::CIF::Parser with syntax error detection and correction capabilities.
  • Implementation of bindings for Perl, C, and Python programming environments.
  • Integration of the parser into the cod-tools package for COD data management.

Main Results:

  • The parser accurately identifies and reports syntactic problems in CIF 1.1 files.
  • Automatic correction of common CIF syntax errors is achieved.
  • The cod-tools package has been successfully applied to automated COD data updates and validation.

Conclusions:

  • COD::CIF::Parser provides a robust solution for handling syntactic issues in CIF files.
  • The cod-tools package enhances the reliability of data in the Crystallography Open Database.
  • This work facilitates automated data deposition and validation processes in crystallography.