On Aug 30, 2007, at 8:14 AM, Peter Maas wrote:
>
> Hi all,
>
> Actually I had exactly the same behavour.
> The H-bond descriptor seems only the be working properly when you add
> implicite hydrogens (which is also stated in the documentation).
>
> Brings me to the question. How is this handled in the Descriptor
> Engine?
> Should one always add implicit or even explicit hydrogens to be on
> the save
> side?
> Are there descriptors which have problems with explicite hydrogens?
In general descriptors will remove H's if they are meant to work on a
H-depleted graph. I should probably check up on this.
> Also looked at the source code of Rajarshi Guha's Descriptor GUI. I
> can't
> find were the hydrogens are checked or added. I tried the H-bond Donor
> descriptor from this GUI but and it also return almost only ZERO's.
The descriptor GUI will not add/delete H's - for the case of 3D
structures the 3D desciptors will expect H's to be present and
topologicals will ignore the H's.
In general, it's best to supply molecules that have H's.
Now the problematic case I think is when you try and caculate H-bond
donor/acceptors. In this case you don't need 3D structures, but you'd
need H's. Are you supplying 3D structures? Or SMILES?
Implicit H's is an ongoing problem I think.
In the case of the H-bond descriptor IIRC the code is basically a set
of if/then's. It might be time to convert it to a SMARTS based form
which will be more reliable (though it doesn't necessarily remove the
implicit H problem)
-------------------------------------------------------------------
Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
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Science kind of takes the fun out of the portent business.
-Hobbes
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