There are roughly three steps:
Determine precisely which atoms have hydrogens and which don't. If they are explicitly given, OK. If not I suggest this shouldn't be a Jmol function but a CDK plugin (e.g. addMissingH with CDK)
determine their coordinates. If they are already given, fine, else I have written a routine in CDK that does that. The problem comes with X-O-H bonds which can rotate around the X-O bond. This is a non-trivial problem. Again I think that should be delegated to another tool
Calculate which atoms are H-bonded. In principle this is very difficult as people will argue about what is and isn't an HBond. There are conferences on this subject. I worked actively in this area ca. 20-25 years ago. There *are* C-H...O bonds but they depend on the substituents of the C. There *are* bifurcated bonds. There are ...
There are two main strategies:
- a write a tool to calculate H-bonds from geometry. This will solve 80% of the problems quickly and you'll spend the next 5 years chasing down the rest.
- borrow someone else's algorithms (or better provide more than one).
I suggest the latter if it's easy to do. I'd ask on CCL if anyone has an opensource tool to calculate H-bonds and what are the most widely used approaches.
P.
this one might be helpful as well...
<http://cdk.sourceforge.net/api/org/openscience/cdk/tools/SaturationChecker. html>
at 12.20p EDT on 2003 December 08 Monday Miguel Howard said:
> > is this useful? > > <http://cdk.sourceforge.net/api/org/openscience/cdk/tools/HydrogenAdder.html> > > > > > > it is already a part of the cdk package from openscience, if that > > makes a difference. > > Actually, that makes a big difference. > > Egon is one of the principals CDK, and we will use CDK to get support > for more file types. > > Egon or Christoph will have to comment on how effective this would be with > ..pdb files that have neither hydrogens nor bond orders. > > > Miguel > > > >
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