CIF Applications. IX. A new approach for representing and manipulating STAR files

Abstract

The Self-defining Text Archival and Retrieval (STAR) format provides a low-level data description from which Crystallographic Information Files (CIFs) are derived. STAR is independent of the two Dictionary Definition Languages (DDLs) currently used in crystallography, is used to represent scientific data beyond crystallographic data and is thus quite general. This paper describes an object-oriented approach to representing STAR files (00STAR) which is then used in several applications of importance to crystallographers. Applications are described for validating the integrity of STAR-compliant files, extracting subsets of data from STAR files and converting STAR files to HypcrText Markup Language (HTML) for use with a Web browser. SunOS 4.1 binaries, Objective-C source code and instructions for compiling and testing on other Unix-based hardware platforms are available via the World Wide Web from http:// www.sdsc.edu/pb/cif/OOSTAR.html.

iotbx.cif: a comprehensive CIF toolbox

“…Several CIF programming libraries have been developed for various languages and environments, including Fortran (Hall & Bernstein, 1996; Rodriguez-Carvajal & Gonzá lez-Platas, 2003), C (Ellis & Bernstein, 2001;Westbrook et al, 1997), Objective C (Chang & Bourne, 1998), .NET (Lin, 2010), Java (Day et al, 2011), Perl (Bluhm, 2000) and Python (Hester, 2006). Whilst there existed several partial CIF parsers within the cctbx, each hand-crafted to suit a specific task [separate tools for reading the PDB chemical components and CCP4 monomer libraries (Painter & Merritt, 2004); as part of the phenix.cif_as_mtz tool; for reading fcf reflection files as output by SHELXL (Sheldrick, 2008)], a comprehensive CIF parser that was tightly integrated with the rest of the library was conspicuously absent.…”

CIFXML: a schema and toolkit for managing CIFs in XML

“…Several excellent CIF parsers have been developed, but most of them store the parsed information (infoset) within the memory of the program and users will need to know the internals and language of each program to extract information. Programming libraries for working with CIF files have already been described for Fortran (Hall & Bernstein, 1996) and C, or variants (Westbrook et al, 1997;Hester, 2006), Python (Chang & Bourne, 1998;Edgington, 1997), and Perl (Bluhm, 2000).…”

ASTAR: a .NET class library for STAR/CIF manipulation

“…Programming libraries for manipulation of STAR/CIF files are available in various programming languages, including Fortran (Hall & Bernstein, 1996), C , Objective C (Chang & Bourne, 1998), Perl (Bluhm, 2000) and Python (Hester, 2006). These libraries can significantly ease the task of adding CIF or STAR functionality to software projects.…”