On Tue, Jan 25, 2011 at 5:51 AM, Greg Landrum <[email protected]> wrote:
> The current release of the code doesn't really support this but it's
> one of those easy-to-add features that make sense to me. I just
> checked in some changes to the drawing code so that it supports the
> ignoreHs argument:
>
> [5]>>> Draw.ShowMol(mh,ignoreHs=True)
>
> or:
>
> [6]>>> Draw.MolToFile(mh,'blah.png',ignoreHs=True)
I downloaded the latest revision and tested it briefly.
While this change is doing a good job at removing H atoms from the
final image, they are still used to compute 2D coordinates so the
resulting depiction is often distorted; do you think adding the same
"IgnoreHs" parameter to AllChem.Compute2DCoords() would be much more
involved?
I've implemented a workaround in my code (store a map of {indexH:
indexNoH} pairs and use it to highlight the requested atom in the
hydrogen-free depiction) but a more proper solution would be probably
appreciated (not only by me :-) )
Cheers
G.
--
Gianluca Sforna
http://morefedora.blogspot.com
http://identi.ca/giallu - http://twitter.com/giallu
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