openmolecules.org Forum: Bug Reports

Home » DataWarrior » Bug Reports » Faulty SDF import (Incorrect determination of bonds)

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

Faulty SDF import [message #1087]

Mon, 19 October 2020 11:30

richards99
Messages: 42
Registered: May 2020
Location: UK

Member

Hi,
There are still issues with regards the import of SDF files and its interpretation of the bonding.
This time it is not down to specified aromatic bonds but simply kekulised bonds.

Take for instance this SMILES string of a protonated heterocycle.
CNC1=C2C=C3OCCOC3=CC2=[NH+]C=C1

When this is saved as an SDF file using Marvin for instance, and then imported into DataWarrior the bonding is completely wrong.
I have attached the SDF of this smiles string above.

The output it provides is attached
index.php?t=getfile&id=277&private=0

Attachment: Screenshot 2020-10-19 at 10.28.58.png
(Size: 21.46KB, Downloaded 1241 times)
Attachment: untitled_molecule_file.sdf
(Size: 1.58KB, Downloaded 677 times)

Report message to a moderator

[Message index]

		Faulty SDF import By: richards99 on Mon, 19 October 2020 11:30
		Re: Faulty SDF import By: richards99 on Mon, 19 October 2020 11:32
		Re: Faulty SDF import By: nbehrnd on Wed, 21 October 2020 09:15
		Re: Faulty SDF import By: richards99 on Wed, 21 October 2020 11:54
		Re: Faulty SDF import By: nbehrnd on Thu, 22 October 2020 12:28
		Re: Faulty SDF import By: thomas on Fri, 23 October 2020 10:13

Previous Topic:	Export of Chiral compounds
Next Topic:	3D structure display is lost after hovering over certain structures

Goto Forum:

-=] Back to Top [=-

[ Syndicate this forum (XML) ] [

] [

]

Current Time: Tue Jul 28 04:23:55 CEST 2026

Total time taken to generate the page: 0.00612 seconds