| Re: Possible to create substructure SMILES column? [message #193 is a reply to message #192] |
Sat, 27 August 2016 09:08   |
thomas
Messages: 655
Registered: June 2014
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Senior Member |
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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
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