openmolecules.org Forum: Bug Reports

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

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

Re: Faulty SDF import [message #1089 is a reply to message #1088]

Wed, 21 October 2020 09:15

nbehrnd
Messages: 233
Registered: June 2019

Senior Member

My observation differs:

1) First I pasted the SMILES string into DW (5.2.1, natively Linux version [used in Debian 10 / unstable]) and obtained a pyridinium:

index.php?t=getfile&id=282&private=0

2) Then the .sdf provided by you (as generated by Marvin) was read by a separate, newly started instance of DW, again yielding a pyridinium:

index.php?t=getfile&id=284&private=0

which seems chemically plausible, matches (by constitution) both the former and the visual output when requesting OpenBabel (3.1.0) to visualize the .sdf as a .png:

index.php?t=getfile&id=285&private=0

Attachment: test.dwar
(Size: 1.62KB, Downloaded 404 times)
Attachment: test_in_DW.png
(Size: 17.33KB, Downloaded 728 times)
Attachment: untitled_molecule_file.dwar
(Size: 2.07KB, Downloaded 419 times)
Attachment: test_import.png
(Size: 21.64KB, Downloaded 609 times)
Attachment: untitled_molecule_file.png
(Size: 7.32KB, Downloaded 789 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: Mon Jul 07 03:42:32 CEST 2025

Total time taken to generate the page: 0.06217 seconds