Re: [Jmol-developers] Re: [Jmol-users] hbonds in Jmol

[Miguel H. <mi...@ho...>]

Peter,

As you know, .pdb files normally don't contain either hydrogens or bond
order.

Therefore, when you see a C-O you don't know if it is a C=O or a C-O-H

Can the code currently in CDK deal with this?


> If not I suggest this shouldn't be a Jmol
> function but a CDK plugin (e.g. addMissingH with CDK)
In general, I agree.

RasMol/Chime includes some simple H-bond detection for a few special cases
(protein backbones & 'classic' DNA)

So we have been looking for something 'simple' to put in Jmol to support
existing scripts that use the 'hbonds on' command.

Any complicated hbond calculations should certainly happen in the context
of CDK.

> 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.
That sounds like the right approach.

> I'd ask on CCL if anyone has an
>  opensource tool to calculate H-bonds and what are the most widely used
> approaches.
What is CCL?

Miguel

>