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#203 Perceive bonding is very slow if file contains many atoms

v_1.0.0
open
Konstantin Tokarev
Open Babel (3)
5
2012-09-12
2010-03-17
Konstantin Tokarev
No

When trying to open file (e.g., xyz) with a lot of atoms (e.g., ~1000, fragment of crystal structure), file opening tends to take forever. I've found that it's caused by perceiving bonds (disappears if I open file using Import dialog). However, I think for so large files user should be asked if he wants bonds perceiving

Discussion

  • Marcus D. Hanwell

    Marcus D. Hanwell - 2011-01-30

    I think this is a great suggestion. What I would love to see is just loading the file, and then perceiving bonds etc in a separate thread/process. I am going to put this into feature requests, I am sure you can take a look at this at some point. I often curse myself when I accidentally open a large file and perceive bonds.

     

  • Geoff Hutchison

    Geoff Hutchison - 2011-08-22

    At its root, this is a cheminformatics issue with Open Babel. I'd be happy to give some papers if someone wants to implement the more modern high-performance method.