openmolecules.org Forum: Functionality

Home » DataWarrior » Functionality » Duplicate Molecules

Show: Today's Messages :: Polls :: Message Navigator

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.

Report message to a moderator

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

Mon, 02 March 2020 18:46

thomas
Messages: 742
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.

Report message to a moderator

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.

Report message to a moderator

Previous Topic:	Hyperlinks
Next Topic:	New feature request: Autosave

Goto Forum:

-=] Back to Top [=-

[ Syndicate this forum (XML) ] [

] [

]

Current Time: Sun Mar 15 19:41:19 CET 2026

Total time taken to generate the page: 0.00662 seconds