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

[Till S. <til...@tu...>]

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*


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
> >
> >
> > ------------------------------------------------------------------------------
> >
> > _______________________________________________
> > Scaffoldhunter-devel mailing list
> > Sca...@li...
> > https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-devel
> >
> >
> 
> 
> 
-- 
Dipl.-Inf. Till Schäfer
TU Dortmund University
Chair 11 - Algorithm Engineering
Otto-Hahn-Str. 14 / Room 237
44227 Dortmund, Germany

e-mail: til...@cs...
phone: +49(231)755-7706
fax: +49(231)755-7740
web: http://ls11-www.cs.uni-dortmund.de/staff/schaefer
pgp: https://keyserver2.pgp.com/vkd/SubmitSearch.event?&&SearchCriteria=0xD84DED79