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Possible to create substructure SMILES column? [message #192] Thu, 25 August 2016 14:37 Go to next message
jowi is currently offline  jowi
Messages: 2
Registered: August 2016
Junior Member
Hi,

I have a collection of compounds with molecular weights of approx 400 Da, all with SMILES structures.
To visualize the effect of certain structural decorations on my parameter of interest, I would like to use the 2D plot and the structure as a label. However, the plot becomes rather messy with only a few compounds. Therefore, I would like to only use sub-structures in the plot.

If I first filter my compound list on the shared common structure, is there any way to automatically create a new column with SMILES describing the rest of the molecules?

To increase the level of complexity, all my SMILES structures are not written in the same way.

Any input is appreciated.

Thanks,
Jowi
Re: Possible to create substructure SMILES column? [message #193 is a reply to message #192] Sat, 27 August 2016 09:08 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 146
Registered: June 2014
Senior Member
Hi Jowi,

I don't see a straightforward solution. What may come close are any of these two procedures:

1: make a core-based or interactive (this is faster to use, because you select scaffolds rather than drawing them) SAR analysis to split the molecule structures into scaffold and substituent columns. Then you can use e.g. 4 substituent columns as labels decorating the actual marker. The marker itself could be colored or shaped by scaffold class.

2: Use 'Add Largest Fragment' to create a new column to be used for scaffold replacement
The for every scaffold:
1 - Use a filter on the original Structure column to show only molecules with that scaffold
2 - Copy scaffold in filter and open 'Search and replace' dialog
Select the new(!) Structure column, paste scaffold in 'Search' field, attach R-groups at every substituted position
In the 'Replace' field draw one C atom, change the C to a distinguishable atom e.g. V that supports higher valences
Attach the same R-groups to V, which you use in the 'Search' field.
Select 'Visible rows only' and click OK.
This way you replace all selected scaffold by a pseudo atom (V), which should result in smaller labels

Since the whole procedure is a little cumbersome, you may create a macro out of it if scaffolds don't change and you do this often.

Hope this helps,
Thomas
Re: Possible to create substructure SMILES column? [message #194 is a reply to message #193] Mon, 29 August 2016 08:10 Go to previous message
jowi is currently offline  jowi
Messages: 2
Registered: August 2016
Junior Member
Hi Thomas,

Many thanks for your quick help. Much appreciated!

Cheers,
Jowi
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