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Re: [Scaffoldhunter-users] [Scaffoldhunter-devel] How to find the exact input molecules?
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From: Till S. <til...@tu...> - 2015-09-29 08:24:52
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Hi, you can configure the tooltip delay under "session -> preferences -> general configuration" searching is not implemented yet, but you can sort the table view by a property and find the desired molecule thereby. The views selection is synchonised. Therefore, it is possible to select the appropriate molecule(s) in the table view and your will find them highlighted in the scaffoldtreeview, too. Viele Grüße Till Am Montag, 28. September 2015, 11:19:03 schrieben Sie: > 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 > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------------ > > > > > > > > > > > > _______________________________________________ > > > > > > 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 > > -- 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 |
