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Duplicate Molecules [message #792]

Mon, 02 March 2020 00:30

sbembenek18
Messages: 62
Registered: April 2019

Member

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.

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Re: Duplicate Molecules [message #797 is a reply to message #792]

Mon, 02 March 2020 18:46

thomas
Messages: 731
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.

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Re: Duplicate Molecules [message #801 is a reply to message #797]

Wed, 04 March 2020 21:18

sbembenek18
Messages: 62
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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