3 Replies Latest reply on Oct 17, 2014 4:51 PM by Marcy Card

    Exporting lists of metabolites

    New User



      I am using the QSAR toolbox solely to predict microbial and rat liver S9 metabolites, but not doing any further profiling or QSARs built into the toolbox.  Based on one of the tutorial PDFs available on the website, I am doing metabolite predictions on the "input" tab by right-clicking on the SMILES string -> multiplication -> metabolism/transformations.  I need a list of the SMILES strings for the metabolites, and I know that I can grab the SMILES strings one-by-one by clicking on the SMILES string in the Documents panel and then copying the SMILES from the substance identity panel, but there are far too many to all do by hand like that.  So I would like to export a list of all of the SMILES strings.   


      I have found a similar discussion (Metabolites reporting) but that user was told to double-click on the metabolites list to get the profiling dialog box.  When I double-click on the lists of metabolites that I'm seeing, nothing happens.  In another discussion (SMILES Code (*.smi) created by the Rat liver S9 metabolism simulator) a user suggests that it's possible to export lists of SMILES in their "export Daylight.jpg" image, but I can't find how to get to get there.


      Thanks in advance for your help!

        • Re: Exporting lists of metabolites
          New User

          Ok, I figured out one way, but am curious if there are any more streamlined approaches.  For the sake of anyone else with this issue:  After the metabolites are calculated, in the tree click on the heading for the metabolites (which shows up between the SMILES for the parent and the list of SMILES for the metabolites), and the structure image in the big panel will have the number of metabolites in that category written in bold in one corner.  Double-click on the structure image, and a window of all of the metabolites will pop up, and it is possible to save a tab-delimited text file of SMILES strings from there. 


          The drawback here is that for multiple generations of metabolites, I have to save a SMILES file for every metabolite in every generation, and that becomes tedious very quickly.  At least this is still much faster than copying and pasting each SMILES string individually, but is it possible to accomplish this in a more elegant way?  Thanks!

          • Re: Exporting lists of metabolites
            New User

            Hi Marcy,


            To solve this issue, I use to perform metabolization on the "Profiling" tab instead of the "Input" tab. This will produce an output on the main screen, under the profiling node instead of the left pane. 


            After applying the desired simulator or observed metabolism, just expand the Profile>>Metabolism/Transformations>>"Applied simulator" on the main screen and you can simply double click in order to search or export to a .smi file all the created metabolites.


            Hop this helps.