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

Wed, 21 October 2020 09:15

nbehrnd
Messages: 241
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 701 times)
Attachment: test_in_DW.png
(Size: 17.33KB, Downloaded 1368 times)
Attachment: untitled_molecule_file.dwar
(Size: 2.07KB, Downloaded 706 times)
Attachment: test_import.png
(Size: 21.64KB, Downloaded 1236 times)
Attachment: untitled_molecule_file.png
(Size: 7.32KB, Downloaded 1450 times)

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[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

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