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

[Jing Lu <aj...@gm...>]

Thanks, Till and Shamshad,

Ctrl-M is very helpful and also the tooltip dialog. But, I need to wait for
a while for tooltip to show up. I also find the table view useful as I need
to find a particular molecule. Does Scaffold Hunter have function for
searching?


Best,
Jing

On Mon, Sep 28, 2015 at 5:56 AM, Till Schäfer <til...@tu...
> wrote:

> Dear Jing,
>
> As Shamshad already said, the Scaffold Tree View only displays scaffolds
> of the imported molecules, but you can toggle the display of the molecules
> which are assigned to the scaffold nodes. If you like to learn more about
> the chemical purpose of the scaffold tree you can read the publication [1].
> The molecules are shown directly in other views such as the heatmap, table,
> dendrogram and plot view.
>
>
>
> To keep track of your imported data, you have to do two steps:
>
> 1. Ensure that you import the ID as a property together with your
> molecules (see the manual.pdf file contained in the Scaffold Hunter zip
> bundle for further details)
>
> 2. Configure the Tool-Tip-Dialog to display them (Menu: Session ->
> Configure Tooltip) or use the table view
>
>
>
> The ID will be not displayed for scaffolds but for molecules, as the
> scaffolds are generated and not contained in the input data.
>
>
>
> If you are importing smiles data, Scaffold Hunter re-generates the smiles
> in order to calculate canonical smiles (to keep track of the molecules).
> This smiles might be different from your input data, as there may exist
> different correct smiles for a single molecule. If you want to keep your
> old smiles string, please import it as a property. You will then be able to
> see both, the canonical smiles generated from Scaffold Hunter and the
> original smiles from your imported data.
>
>
>
> @Shamshad: thx for explaining the scaffold tree
>
>
>
> Regards,
>
> Till
>
>
>
> [1] Interactive exploration of chemical space with Scaffold Hunter
> Stefan Wetzel, Karsten Klein, Steffen Renner, Daniel Rauh, Tudor I. Oprea,
> Petra Mutzel, Herbert Waldmann
> Nature Chemical Biology, 2009, 5, 581-583
>
>
>
> Am Samstag, 26. September 2015, 23:31:53 schrieb Shamshad Alam:
>
> > 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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>
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>
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>
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>
> > >
>
> > >
>
> >
>
> >
>
> >
>
> --
>
> Dipl.-Inf. Till Schäfer
>
> TU Dortmund University
>
> Chair 11 - Algorithm Engineering
>
> Otto-Hahn-Str. 14 / Room 237
>
> 44227 Dortmund, Germany
>
>
>
> e-mail: til...@cs...
>
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>
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>
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>
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