Hi Yurie,
Welcome to the mailing list!
The "Weights" property is used to define the position of the feature. A
feature is defined by a query and it's position is calculated by doing a
weighted average of the atoms matching that query. The "Weights" are the
values used in the weighted average.
In the example you give:
DefineFeature AcidicGroup [C,S](=[O,S,P])-[O;H1,H0&-1]
Family NegIonizable
Weights 1.0,1.0,1.0
EndFeature
the AcidicGroup is defined by three atoms (because there are there atoms in
the SMARTS). The "Weights" field says that the position of the feature is
defined by a weighted average of the positions of the three atoms with all
weights equal to 1.
I hope this helps.
Sorry that this isn't in the documentation.
Best,
-greg
On Fri, Oct 11, 2019 at 3:22 AM Yurie Kim <gimyu...@outlook.com> wrote:
> Hello everyone,
>
> This is a person who is very new to RDkit, even more I have no knowledge
> of Python language.
> At the moment, boldly I am trying to write fdef file and am in the process
> of studying what "Greg Landrum" had written previously.
>
> Before I even fire away question, I wish to share some of excerpt of his
> coding to you. So you see what I am talking about.
>
> ------------------------------------------------------------
>
> DefineFeature AcidicGroup [C,S](=[O,S,P])-[O;H1,H0&-1]
>
> Family NegIonizable
>
> Weights 1.0,1.0,1.0
>
> EndFeature
>
> AtomType Carbon_NotDouble [C;!$(C=*)]
>
> AtomType BasicNH2 [$([N;H2&+0][{Carbon_NotDouble}])]
> -------------------------------------------------------------
>
> I think I understand what 'AtomType', 'DefineFeature', and 'Family' are.
> They are syntax to define atom, chemical feature and chemical group. And I
> think you can come up with any name you want after those syntax.
> Caveat for me is.... I have no idea what to put after 'Weights' syntax.
> I understand that you put either 1.0 or multiple 1.0s along with commas,
> but I have no clue what that even means.
> I need some experts out in the community to advise me.
> For those of you who are experts, I know that this is very trivial thing,
> but novice like me I am quite lost. If you could guide me through, it will
> be a great help:)
>
> With sincere heart,
>
> From Yurie T. Kim
>
>
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> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
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>
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