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Rendering structures from SMILES [message #263] Wed, 05 April 2017 19:28 Go to next message
jwfeng is currently offline  jwfeng
Messages: 4
Registered: March 2017
Junior Member
Hi,

My SD file contains SD tag with SMILES strings as values. Is there a way to render them as structures in DW? Attached is a simple example of what I want to do. The Structure column display what's in the MOL block, the r-group smiles column should render the SMILES string as a structure instead of displaying it as text.

Thanks,

JW


JW Feng
Re: Rendering structures from SMILES [message #264 is a reply to message #263] Wed, 05 April 2017 21:13 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 151
Registered: June 2014
Senior Member
Hi JW, if you open a text file (TAB or comma delimited) then DataWarrior automatically analyses all columns, whether they contain SMILES and adds structure columns for every valid SMILES column. SD-Files typically contain only one structure, which is shown as structure column. It would be possible to use the SMILES recognition mechanism also for SD-files, but currently, there is no straight-forward way. What you coulr do, however, is to create a macro, that after opening the SD-file does these tasks:
- (if you don't have any unique compound-IDs, then create a new column with row-numbers
- saves the file
- removes the structure column
- save as text file (TAB delimited)
- open the text file to automatically create structure columns for your SMILES columns
- save again as dwar
- open the original file
- merge with the new dwar that contains structure column for every SMILES using the compound-IDs as merge-keys
Does that solve the issue?

Thomas
Re: Rendering structures from SMILES [message #267 is a reply to message #264] Mon, 01 May 2017 07:25 Go to previous message
jwfeng is currently offline  jwfeng
Messages: 4
Registered: March 2017
Junior Member
Hi Thomas,

Thanks for the different options. I will convert my SD file into a tab separated file where the first column stores SMILES string of the SD structure. The remaining columns will store SD fields.

I like to store SMILES strings in SD tag where those SMILES could be substructures, near neighbors, or molecular match pairs.

JW


JW Feng
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