#471 Patch that sets electron count for bond orders

Needs_Review
closed
master (162)
5
2012-10-28
2012-01-21
No

Rich made a strong point about file format limitations, and statement about decent electron counts for bonds:

http://depth-first.com/articles/2012/01/11/on-the-futility-of-extending-the-molfile-format/

Since the CDK supports this, I guess it was about time to actually start using it...

So, this patch automatically sets electron count when a particular bond order is chosen.

I prefer this in cdk-1.4.x as it should have set this from the start, and while the electron count = 0 right now, I doubt any code is in fact using it.

Still, being an API change, I prefer two reviewers.

Discussion

  • Rajarshi Guha

    Rajarshi Guha - 2012-01-21

    the first 2 patches look fine; but patch 3 seems to be corrupted as nothing gets downloaded

     
  • Egon Willighagen

    Downloading the 3rd patch works fine for me, but I had yesterday also trouble downloading a patch from SF, which only could be downloaded half.. I guess the same problem.

    But before we can continue this patch, we first need to resolve that debug logger thingy...

     
  • Egon Willighagen

    Rajarshi, I have uploaded a new 0002 and 0003 that no longer depends on the datadebug patch, by introducing a private helper method to set the electron counts based on the bond order.

     
  • Egon Willighagen

    Rajarshi, can you please check the updates?

    Also, let's just put this in master, not cdk-1.4.x...

     
  • Rajarshi Guha

    Rajarshi Guha - 2012-05-18

    OK, looks good now. Applied and pushed. Put it into master

     

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