On 01/28/2015 08:23 PM, Robert Hanson wrote: > In terms of parsers for *all *the information in an mmCIF file, there are > several out there. I happen to think Jmol's is the best. It's > Java/JavaScript; there are C++ versions as well. Basically, when you load > JSmol, you have a complete CIF parser right there in the DOM. Why write a > new one? > The parser wouldn't be used within a browser but to fill our database with data extracted from all PDB entries. To minimize the amount of time and work needed to switch to mmCIF files it would be best to have a parser in Perl since I havn't done any Java or C++ programming yet. The only Perl parser I found was the STAR package which leaves most of the parsing effort to the user of the package as far as I could tell from reading the documentation and doing some tests.
Maybe I have missed it but I didn't have the impression that most of the information within the PDB file header is readily available and usable in Jmol. But even if this would be the case my experience with using Jmol for generating images for about 100,000 PDB entries wouldn't make it my first choice as a PDB file parser for the JenaLib database. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 ------------------------------------------------------------------------------ Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
