Charlie Jeynes Posted January 5, 2021 Share Posted January 5, 2021 HI I want to export all my structures in a column in SMILES notation how do I do this please it's not obvious thanks Link to comment Share on other sites More sharing options...
Donald Johnson Posted January 6, 2021 Share Posted January 6, 2021 Is the TIBCO Spotfire Lead Discovery https://docs.tibco.com/products/tibco-spotfire-lead-discovery Link to comment Share on other sites More sharing options...
Charlie Jeynes Posted January 6, 2021 Author Share Posted January 6, 2021 HI Don I have TIBCO spotfire Analyst 7.12.0 yes I did read this document manual before - so it seems i can export the column which contains the rendered chemicals as images in .sdf format - which I suppose contains the SMILES (sorry i'm a bit new to this field) EDITED: yes I see now - I was getting confused because my structures are saved as mdl mol files - i need to convert them to SMILES - I can easily do this (in python or ChemDraw or something) - but can I do the conversion easily on the column in SpotFire It would be nice to be able to export the table (containing other information about the molecule) as a csv, with the SMILES notation in the row - i'm guessing this isn't an option Link to comment Share on other sites More sharing options...
Donald Johnson Posted January 7, 2021 Share Posted January 7, 2021 Are you using a PerkinElmer Product They have a home page here: https://community.spotfire.com/wiki/perkinelmer with contact information at the bottom Link to comment Share on other sites More sharing options...
Gerard Conway 2 Posted January 7, 2021 Share Posted January 7, 2021 Hi Charlie, If you are working with PerkinElmer's Lead Discovery product then there are a series of Chemical Functions available which can be used as part of Calculated Columns. Insert -> Calcualted Column, and you will see the Chemical Functions category, there is Convert function that allows you to convert to multiple chemical formats, for instance SMILES notation to be generated and exported: Chemical function: Convert(Arg1, Arg2) Convert Arg1 molecule to the MimeType of Arg2. Below MimeTypes can be defined in Arg2: - CDX - CDXML - Molfile - SMILES Example: Convert([structure], "SMILES"). This will produce a new SMILES column in your Data Table. You can then use standard export features to export the SMILES. Hope that helps, Gerard Link to comment Share on other sites More sharing options...
Donald Johnson Posted January 7, 2021 Share Posted January 7, 2021 Thanks, Gerard! Link to comment Share on other sites More sharing options...
Charlie Jeynes Posted January 13, 2021 Author Share Posted January 13, 2021 great thanks Gerard that worked a treat!! probably was in the manual somewhere but it wasn't obvious to me as a newbie user thanks Charlie Link to comment Share on other sites More sharing options...
Recommended Posts
Create an account or sign in to comment
You need to be a member in order to leave a comment
Create an account
Sign up for a new account in our community. It's easy!
Register a new accountSign in
Already have an account? Sign in here.
Sign In Now