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Explicit fragmentation between pairs of atoms with metals/ions fails #26

Closed cstein closed 6 years ago

cstein commented 7 years ago

The metals/ions are moved to the back of the file silently(?) due to OpenBabel and it's charge-models. However, the user is not notified of this change.

This issue can (and will be solved in different stages):

  1. provide textual information to the user that metal ions have been moved around.
  2. should the user provide some manual bond, be very explicit about this.
  3. eventually we should just remember the indices of where these atoms need to go instead of appending them.

items 1 and 2 above is quickly 'fixed'. number 3 above is fixed when 1.8 is released.

for now users should either shift indices in the configuration file or move the ions to the back of their file which will also serve as a workaround

Thanks to Morten Steen Nørby for notifying me of this.

cstein commented 7 years ago

The first two points in the opening post is now addressed. Will fix item number 3 when it is not past midnight because it needs some more brain.