openmolecules.org Forum: Bug Reports

Home » DataWarrior » Bug Reports » V3000 input (V3000 input with custom atom index can not be read)

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

V3000 input [message #14]

Fri, 24 October 2014 09:54

bruno.b
Messages: 13
Registered: October 2014
Location: Germaniy

Junior Member

FYI, Data warrior cannot read the attached file. I think it is a valid V3000 file. Pubchem can read it.

Best regards,

Bruno

Attachment: abs_stereo_index.v3000.sdf
(Size: 0.73KB, Downloaded 959 times)

Report message to a moderator

Re: V3000 input [message #16 is a reply to message #14]

Sun, 26 October 2014 01:10

thomas
Messages: 722
Registered: June 2014

Senior Member

After a quick check it seems that in a V3 molfile atoms have to be in order, which they are not.
In any case DataWarrior should throw a reasonable error message, or should be kind enough to accept
atoms in any order. I will check and let you know.

Thanks for the question and kind regards, Thomas

Report message to a moderator

Re: V3000 input [message #17 is a reply to message #16]

Mon, 27 October 2014 16:00

bruno.b
Messages: 13
Registered: October 2014
Location: Germaniy

Junior Member

Hi Thomas,

according to the Symyx June 2010 documentation, the atom index can be any strictly positive number.

"Identifies atoms. The actual value of the index does not
matter as long as each index is unique to each atom. "

For the bonds:

"The actual value of the index does not matter as
long as all are unique."

I did not find comment about the order of the atom indices in the Symyx document.

Regards,

Bruno

Report message to a moderator

Re: V3000 input [message #19 is a reply to message #17]

Wed, 05 November 2014 16:46

thomas
Messages: 722
Registered: June 2014

Senior Member

Hi Bruno,

I checked myself and found the same thing. I will make sure, that this issue will be fixed in the next public DataWarrior release.

Kind regards,

Thomas

Report message to a moderator

Previous Topic:	Saving Preferences in Linux - Solution
Next Topic:	copy/paste from ChemBioDraw 14 to latest DW causes crash

Goto Forum:

-=] Back to Top [=-

[ Syndicate this forum (XML) ] [

] [

]

Current Time: Wed Feb 05 18:02:18 CET 2025

Total time taken to generate the page: 0.03179 seconds