Re: [Scaffoldhunter-devel] How to find the exact input molecules?

[Shamshad A. <sha...@gm...>]

Hi Jing,

I contributed to scaffold hunter a year ago and worked on some feature
requests.

As far as I know scaffolds are generated by pruning terminal chains and
thereafter cycles. So SMILE string is likely to differ from original
molecules.

>>  How to keep track of the exact molecule?
Tree view only shows scaffolds by default. If you want to see molecules
too, press Ctrl + M, or in Tree menu check 'Show Scaffold Molecules'. I
guess it might help you.

>> Does Scaffold Hunter convert the original input molecules to a scaffold
first?
It does when you generate scaffold tree.

>> Because, when I was checking the leaf nodes, the structure does not
really exist in my input file. How to interpret that?
In scaffold view at the leaf node what you see may exist as a substructure
of one or more molecules.

I hope it will help you and clear your some doubts. If you have any further
queries let us know.


Cheers,
Shamshad

On Sat, Sep 26, 2015 at 9:29 PM, Jing Lu <aj...@gm...> wrote:

> Dear Scaffold Hunter developers,
>
>
> Sorrry to send this again. But, I am not sure where to ask questions. I
> try to put ligand id to tooltip to keep track of each molecule. It seems
> like impossible. Moreover, I find Scaffold Hunter changes the SMILE string
> I put in the input file. How to keep track of the exact molecule?
>
> Does Scaffold Hunter convert the original input molecules to a scaffold
> first? Because, when I was checking the leaf nodes, the structure does not
> really exist in my input file. How to inteperate that?
>
>
>
> Thanks,
> Jing
>
>
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Shamshad Alam
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