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Re: Molecule Displayed Incorrectly [message #963 is a reply to message #959]

Sun, 21 June 2020 14:11

thomas
Messages: 740
Registered: June 2014

Senior Member

Thank you for reporting this issue. There was indeed a bug in the charge neutralization part of the structure normalization, which takes place when importing structures from SD-Files or SMILES. This is fixed in the current development update. However, still DataWarrior doesn't show the structure as in mol.png, because DataWarrior normalizes and canonicalizes structures during the import. Part of the normalization is to neutralize charges as much as possible, meaning to move protons from protonated and positively charged atoms (e.g. ammonium) to negatively charged hetero atoms where possible.

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[Message index]

		Molecule Displayed Incorrectly By: sbembenek18 on Thu, 18 June 2020 22:48
		Re: Molecule Displayed Incorrectly By: thomas on Sun, 21 June 2020 14:11
		Re: Molecule Displayed Incorrectly By: sbembenek18 on Fri, 03 July 2020 23:26

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