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.