OpenMMS toolkit

Description

OpenMMS is a toolkit for creating efficient representations of macromolecular structure data in several common formats.

The OpenMMS Toolkit contains software for translating protein and nucleic acid macromolecular structure data stored in the mmCIF format into CORBA, XML and SQL-relational-database expressions. This translation is driven by a central metamodel based on the ontology contained in the mmCIF dictionary. All of the software for the metamodel and for generating the translated expressions is written in Java and is included with this distribution.

Distribution

If you wish to install and use this software you should download the most up-to-date version from the above Web site. The links below are to copies which are suitable for browsing or for use if the primary Web site is not available. However, they may be out of date and lack the full functionality of the latest version.

Status

OpenMMS is available from the San Diego Supercomputer Center site of the Research Collaboratory for Structural Bioinformatics (RCSB) but is no longer actively supported. There is however an OpenMMS Users Group web site. The version distributed here is 1.5.1 of 2001.

Language and platform

The software is written in Java for cross-platform implementation. Most executables require only a Java Runtime Environment; users wishing to load MMS data into a relational database may also require a specific JDBC Driver for the particular database they are using.

Documentation

  • Installation: For Unix-type installations, copy the gzipped tar file OpenMMS-1.5.1_Std.tar.gz into an empty directory; uncompress using gzip and extract files using the Unix tar utility.
     cp OpenMMS-1.5.1_Std.tar.gz /g/h/i; cd /g/h/i
    gunzip OpenMMS-1.5.1_Std.tar.gz; tar xvf OpenMMS-1.5.1_Std.tar More information:
  • Documentation Index 
  • README 
  • Overview 
  • OpenMMS API specification

Terms and conditions of use

Copyright in the software © The Regents of the University of California
Author: Douglas S. Greer

Use of this software is governed by the UCSD copyright licence. Queries concerning any other use should be directed to the Technology Transfer Office, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0910, USA. Phone: +1 (619) 534-5815, FAX: +1 (619) 534-7345.

References

Greer, D. S. (2000). Macromolecular structure RFP Response, revised submission. http://openmms.sdsc.edu/OpenMMS-1.5.1_Std/openmms/docs/specs/lifesci_00-11-01.pdf.

Greer, D. S., Westbrook, J. D. & Bourne, P. E. (2002). An ontology driven architecture for derived representations of macromolecular structure. Bioinformatics, 18, 1280-1281. [CrossRef]