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Molecule Displayed Incorrectly [message #959]

Thu, 18 June 2020 22:48

sbembenek18
Messages: 63
Registered: April 2019

Member

I've noticed in certain cases, DW will not correctly display the molecule. This appears to happen for 'non conventional' protomers mostly but not always. I've included an example. The attached molecule should appear as in the image. However, if you load the SDF in DW, you see that it does not appear this way.

Attachment: mol.png
(Size: 13.15KB, Downloaded 1079 times)
Attachment: mol_dw_error.sdf
(Size: 1.71KB, Downloaded 760 times)

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

Sun, 21 June 2020 14:11

thomas
Messages: 747
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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Re: Molecule Displayed Incorrectly [message #981 is a reply to message #963]

Fri, 03 July 2020 23:26

sbembenek18
Messages: 63
Registered: April 2019

Member

thanks. I appreciate why it is doing it. it could be useful to allow the user to change this default behavior so that DW displays the molecule "as is"

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