Dear Jake,

Thank you very much, the example files now run. From the examples it is
fairly clear how to setup the molecule templates and the reaction map
files, I only have a few questions to ask concerning setting up a new type
of reaction. Is there maybe documentation explaining the work of these

yes, you can currently find the doc page at /doc/src/fix_bond_react.txt (in
the pull request)

also, I would definitely be interested in feedback about the clarity of the
doc page

In case not, let me just list the couple of questions I have:

- What is the role of the equivalences section in the map file?

this relates each atom in the pre-reacted template to its corresponding
atom in the post-reacted template (using template IDs). in my experience of
modifying molecule templates, 'atom 1' of the pre-reacted template usually
corresponds to 'atom 1' of the post-reacted template, but this might not
always be the case

- In the data template, what is the purpose of the Coords section, and
what configuration is expected to be given using the coordinate values?

bond/react ignores the 'coords' section of molecule template files

- In case of reaction, is there a way to output or access the IDs of the
atoms that have reacted?

no, but this could be an interesting feature request. what would be your
use for this? currently, you could dump the bond topology or atom types and
search for changes