On Mon, Apr 15, 2013 at 7:53 PM, JP <[email protected]> wrote:
> As a followup to this question - further questions/problems :)
>
> Why is AmideN (and SulfonamideN) defined in the BaseFeatures.fdef ? (I
> cannot understand how/where these two definitions are used).
They aren't currently being used. I guess they were probably used
earlier as part of the Donor definition (i.e. to define atoms that are
not donors).
> One of the H Bond Donor definitions is AtomType NDonor [$([Nv3](-C)(-C)-C)]
> :- but if a Nv3 is connected to 3 C - then there are no hydrogens. How is
> this a donor? The v3 according to daylight means "atom with bond orders
> totaling 3 (includes implicit H's)"
This is an "uncharged" feature definition and is, implicitly assuming
that a v3 N which is connected to three Cs would be protonated.
I should emphasize that the feature definitions in BaseFeatures.fdef
are really not very good. They are primarily provided as an example of
what an fdef file should look like.
> I had a look around and thought the
> Contrib/M_Kossner/BaseFeatures_DIP2_NoMicrospecies.fdef file looked more
> complete in terms of definition. Unfortunately this file does not load with
> BuildFeatureFactory (ValueError). Anyone knows the history of that file?
> Or why it came to being?
>
> FACTORY =
> ChemicalFeatures.BuildFeatureFactory("/opt/RDKit_2012_12_1/Contrib/M_Kossner/BaseFeatures_DIP2_NoMicrospecies.fdef")
> ValueError: pattern->getNumAtoms() != len(feature weight vector)
That was indeed a bug in the file, which is now fixed. Thanks for reporting it.
The file itself is an attempt at building a useable (=reasonably
complete) fdef file that Markus Kossner contributed a few years ago.
It's probably a better starting point than BaseFeatures.fdef is.
>
> Many thanks and sorry for the repeated emails,
No worries.
-greg
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