J. Cheminf. 2011, 3, 33

Table Of Contents

Previous topic

Reaction formats

Next topic

MDL RXN format (rxn)

This Page

CML Reaction format (cmlr)

A minimal implementation of the CML Reaction format

This implementation uses libxml2.

Write Options

1 output CML1 (rather than CML2)
a output array format for atoms and bonds
l molecules NOT in MoleculeList
h use hydrogenCount for all hydrogens
x omit XML declaration
r omit rate constant data
N <prefix> add namespace prefix to elements
M add obr prefix on non-CMLReact elements
p add properties to molecules


The implementation of this format which reads and writes to and from OBReaction objects is fairly minimal at present. (Currently the only other reaction format in OpenBabel is RXN.) During reading, only the elements <reaction>, <reactant>, <product> and <molecule> are acted upon (the last through CML). The molecules can be collected together in a list at the start of the file and referenced in the reactant and product via e.g. <molecule ref=”mol1”>.

On writing, the list format can be specified with the -xl option. The list containers are <moleculeList> and <reactionList> and the overall wrapper is <mechanism>. These are non-standard CMLReact element names and would have to be changed (in the code) to <list>,<list> and <cml> if this was unacceptable.