openmolecules.org Forum: Bug Reports » Molecule Displayed Incorrectly

Home » DataWarrior » Bug Reports » Molecule Displayed Incorrectly

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

Molecule Displayed Incorrectly [message #959]

Thu, 18 June 2020 22:48

sbembenek18
Messages: 62
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 621 times)
Attachment: mol_dw_error.sdf
(Size: 1.71KB, Downloaded 620 times)

Report message to a moderator

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

Sun, 21 June 2020 14:11

thomas
Messages: 741
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.

Report message to a moderator

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

Fri, 03 July 2020 23:26

sbembenek18
Messages: 62
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"

Report message to a moderator

Previous Topic:	Aromaticity perception
Next Topic:	Uncaught Exception:/ by zero error when using structure view.

Goto Forum:

-=] Back to Top [=-

[ Syndicate this forum (XML) ] [

] [

]

Current Time: Fri Jan 16 19:10:55 CET 2026

Total time taken to generate the page: 1.16638 seconds