XmlConvert: An XML Expression
of Macromolecular Structure Data

The OpenMMS Toolkit
Release V_1_5_1

Introduction

XmlConvert is a tool for translating mmCIF formatted data files into XML files.

The default regression test of the conversion program can be run using the script $(TOP_DIR)/run/{unix,nt}/xmlconv with no command line arguments. The make script will place three example converted data files: 1xy2.xml and 3ebx.xml and 4hhb.xml in the openmms/data/xml directory.

An attempt was made to match the XML as closely as was practical to the mmCIF dictionary, yet still make use of XML's capabilities. However, because of the way in which XML is specified, in a few cases format changes were necessary. The XML schema for the translation is available at http://deposit.pdb.org/pdbML/pdbx-v0.905.xsd

An early experimental form of an XML translation is also available as the XMC format. This program can be executed with the command cif2xmc command in the the openmms/run/unix subdirectory. In the data files, the data ordering used by Peter Murray-Rust in CML is employed; that is, data is grouped by items in "columns" rather that the SQL record style where data is grouped by "rows". Files written in XMC format are much smaller in size than the standard (XmlConvert) files since they have only a single open and close tag for an entire column of data. To help ease problems associated with this formatting, a "length" attribute is written in the opening tag so that an xml parser can insure that the correct number of "rows" are present in the PCDATA.


OpenMMS was designed and written by Douglas S. Greer
SDSC/UCSD, 9500 Gilman Drive, La Jolla, CA 92093, USA
Copyright © 2001,  All rights reserved.