I have had email exchanges about chemical reactions in CML - I think it is useful to expose some of the points on this list.
The current state of play is:
* we have finalised a draft of CMLReact - a subset of CML elements, attributes and types. There is a draft manuscript shortly to be submitted for publication. Unfortunately some mainstream chemical publishers forbid any exposure of material prior to formal publication (and some forbid it afterwards). One editor even told us that sending preprints to individuals could vitiate publication. I and colleagues have and will continue to challenge this position publicly (e.g. at the forthcoming ACS meeting).
* the latest JUMBO (http://wwmm.ch.cam.ac.uk/moin/Jumbo4.6 - mail me if you have problems on this page) contains specifications for all CMLReact elements, attributes and types and considerable amounts of supporting examples. However their is no narrative.
* Gemma Holliday has tested the current design on an extensive set of enzyme reactions
* we have a number of collaborators who are helping us with examples and applications. We can always use more. The current areas - some at an early stage - include:
- combustion and atmospheric (including radicals, branched reactions, etc.)
- organic synthetic planning and recording
- organic reaction mechanisms
* There is an exciting new way of visualising reactions through animation (CMLSnap). This is as simple to create as conventional pictures of reactions (though it requires a change of view). See http://www.dspace.cam.ac.uk/handle/1810/746 where the full text and data of the paper is viewable (under the Internet Journal of Chemistry's enlightened position).
* There are some tools which generate CMLReact directly (though they have not had a chance to implement the full spec). They include:
- JChempaint
- Marvin
- BKChem
(please let us know if there are others we have missed and the state of their conformance)
* there are converters from legacy formats.
- RXN. A converter for this is bundled in JUMBO4.6. Note that this format can generate varying semantics ranging from giant molecules on either side of a reaction to separated molecules with or without atom mapping. We are not aware that RXN can support more that isolated single reactions, so it is not easy to chain them into a CML ReactionScheme
- ChemDraw. JUMBO4.6 contains a converter written to the spec on the CambridgeSoft pages. It offers no certainly of conformance, but seems to work. However as Chemdraw is a graphically oriented format it is often difficult to formalise the semantics for a given picture. Authors need to check that products and reactants (especially in multi step reactions) are faithfully labelled in the CML. Note also that Chemdraw frequently uses text to transmit chemical information (e.g. in groups or reagents and that it may be difficult to resolve these from the CML). Please use the latest CVS rather than the WWMM distrib as we have updated to the latest CDX pages
- SMILES. There are a number of SMILES2CML converts but I am not aware of any than manage reactions. It shouldn't be difficult - if someone has reactions in this format let me know and I'll see if I can hack some
* renderers. Laying our reactions without author coordinates is an art and we are at an early stage (e.g. with JChempaint. We would be happy for comments here). There are three cases:
- no coordinates at all
- coordinates for each molecule but no relative coordinates
- complete coordinates
it isn't always easy to distinguish between the last two. If there are no relative coordinates then a compact list of reactants probably horizontal, should be displayed and a similar set of products. For multistep reactions there is no simple answer but dot (the graph program) should give some fun and hopefully challenging layouts. (We have to get away from the tyranny of the printers)
The current state of renderers is:
- XSLT (bundled with Jumbo). Visually horrible but should give a faithful semantic representation. No editing facility
- JChempaint. Semantically aware, under current development
- Jmol. Can render reactions but not heavily used for CMLReact. We need to develop this.
- BKChem. Visually attractive and simple. No sure what the semantics are
- Marvin. not sure
Wish list:
Since there is very little effective interchange of chemical reactions in electronic form CMLReact has a lot of potential to do things properly. We would welcome:
- carefully constructed examples of reactions in CMLReact
- examples where CMLReact is unable to represent a major need
- new or enhanced editing tools
- new or enhanced renderers.
- new or enhanced converters
As JUMBO is OpenSource, anyone can play. However as the architecture is complex we ask people to mail us of any intended participation and contribution. JUMBO4.6 is offered as a maintenance branch so we don't see major additions to the spec and to the Tool functionality. However the converters and renderers are certainly open for enhancement as they are fairly independent of the architecture. [Note that the next development release of JUMBO is planned as JUMBO5. This will use Java 1.5, have full unit tests, have a slimmed down API for the DOM. Therefore architectural changes to JUMBO4.6 probably won't get incorporated, but bugfixes, wrappers and ancillary support will.]
P.
Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069
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