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Duplicate Molecules [message #792] Mon, 02 March 2020 00:30 Go to next message
sbembenek18 is currently offline  sbembenek18
Messages: 58
Registered: April 2019
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Before loading an SDF file into DW, I remove duplicate molecules via canonical smiles. However, in DW, when I do: Data->Merge Equivalent Rows->Structure, DW still says there's duplicates -- I am unclear as to how this is possible.
Re: Duplicate Molecules [message #797 is a reply to message #792] Mon, 02 March 2020 18:46 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 646
Registered: June 2014
Senior Member
This would mean that two different canonical SMILES are considered the same structure by DataWarrior. I cannot perceive of a reason for that. If you delete all unique rows from your file, then you retain all these cases. If you can send me some of them, I may have a more detailed explanation.
Re: Duplicate Molecules [message #801 is a reply to message #797] Wed, 04 March 2020 21:18 Go to previous message
sbembenek18 is currently offline  sbembenek18
Messages: 58
Registered: April 2019
Member
I see what it is now. I have molecules where nitrogen might be considered a stereocenter. So, whereas the program that wrote the SDF considers that there are distinct stereoisomers, DW does not. I think this is consistent with the challenges of assessing this for these molecules.
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