openmolecules.org

 
Home » DataWarrior » Bug Reports » V3000 input (V3000 input with custom atom index can not be read)
V3000 input [message #14] Fri, 24 October 2014 09:54 Go to next message
bruno.b is currently offline  bruno.b
Messages: 11
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
Re: V3000 input [message #16 is a reply to message #14] Sun, 26 October 2014 01:10 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 151
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
Re: V3000 input [message #17 is a reply to message #16] Mon, 27 October 2014 16:00 Go to previous messageGo to next message
bruno.b is currently offline  bruno.b
Messages: 11
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
Re: V3000 input [message #19 is a reply to message #17] Wed, 05 November 2014 16:46 Go to previous message
thomas is currently offline  thomas
Messages: 151
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
Previous Topic: Saving Preferences in Linux - Solution
Next Topic: copy/paste from ChemBioDraw 14 to latest DW causes crash
Goto Forum:
  


Current Time: Wed Sep 19 22:08:28 CEST 2018

Total time taken to generate the page: 0.00479 seconds