Feature Requests item #953260, was opened at 2004-05-13 15:06 Message generated for change (Comment added) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=953260&group_id=23629
I did not know that CML had support for hbonds. It would be very easy to add support for this ... the infrastructure is already in place.
CML does not support Hbonds in the connection table. It puts too much effort on the reader to distinguish "non-covalent" bonds. However it is possible (though messy) to add <bond> elements outside the bondArray. I haven't done this myself. It could be something like:
<cml>
<molecule id="m1">
<atomArray>
<atom id="F1"/>
<atom id="H1"/>
</atomArray>
<bondArray>
<bond atomRefs2="F1 H1" order="1"/>
</bondArray>
</molecule>
<molecule id="m2">
<atomArray>
<atom id="F2" formalCharge="-1"/>
</atomArray>
<bondArray>... normal bonds </bondArray>
</molecule>
<bond atomRefs2="m1:H1 m2:F2" convention="foo:bar" order="hbond"/>
</cml>
What do people think of this? (It can also be generalised to intramolecular H-bonds). If there is strong support we can add a CML convention for Hbond as long as it is not used in connection tables
P.
Q: Do you know of a 'sprout' algorithm which will automatically add the hydrogen atoms?
I added the geometrical routines to CDK some time back. You still have to decide which atoms have H atoms and what the geometry is, but these routines will then give the coordinates
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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