On Aug 27, 2008, at 7:40 AM, Christian Grunwald wrote:
> Hi Thorsten,
>
> Thorsten Meinl <[EMAIL PROTECTED]> schrieb am 27.08.2008
> 12:13:58:
>
>>> just some comments from my side: First: Yes, it would be very
>>> useful to
>>> automatically add the hydrogens or to be able to configure the
> SDF_to_CDK
>>> node to do so. At least, there should be some kind of an error
>>> hint if
> the
>>> hydrogens are missing.
>> Already in the SDF->CDK node? I thought about adding them in the
>> XLogP
>> node if necessary. Are there any situations, where explicit hydrogens
>> can hurt? If not, then we can really do this upon conversion to CDK.
>
> I have just compared "Molecular Properties" results with and
> without use
> of the "Hydrogen Adder". There are differences regarding TPSA,
> Molweight,
> HB_Donors and even the number of rotatable bonds. That means that
> these
> module
> also use the structures as they are - without adding hydrogens.
> Therefore
> the
> SDF_CDK node should be used to add the hydrogens, or even the
> SDF_Reader.
I would suggest that hydrogens be added on loading (ie SDF_CDK node)
- as pointed out a number of methods will require explicit H's - and
though we can update some methods to make sure that they do it
themselves, currently this will lead to a performance hit. There are
plans for a cahcing scheme, so that these types of things do not
necessarily have to be recalculated all the time, but that's in the
future.
In general, adding explicit H's is not bad - many descriptors that do
not consider H's will simply remove them in a local copy.
But the advantages of adding explicit H's right up front are quite
big since a vairety of tasks (polarizability, SMARTS matching etc)
will require them
-------------------------------------------------------------------
Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84
-------------------------------------------------------------------
So the Zen master asked the hot-dog vendor,
"Can you make me one with everything?"
- TauZero on Slashdot
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
_______________________________________________
Cdk-user mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/cdk-user
