cbc-univie / transformato

Set up relative free energy calculations using a common scaffold

https://cbc-univie.github.io/transformato/

MIT License

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update the handling of lp to the current parmed version #89

Closed JohannesKarwou closed 2 years ago

JohannesKarwou commented 2 years ago

parmed now supports lonepairs and we are no longer relying on our own forked version. If LPs are part of the dummy region electrostatics are turned off together with the other dummy atoms. More is not necessary since they do not have any LJ interactions and can be never the terminal dummy atom since they are always connected to a chlorine or bromine atom.

codecov-commenter commented 2 years ago

Codecov Report

Merging #89 (96de628) into master (00da6aa) will decrease coverage by 0.67%. The diff coverage is 87.33%.

Additional details and impacted files

JohannesKarwou commented 2 years ago

I added this pull request (https://github.com/wiederm/transformato/pull/90) into the current one to get one working branch. Pull request https://github.com/wiederm/transformato/pull/90 is about integrating the ProposeMutationRouteASFE from the annihilation.py into the ProposeMutationRoute from the mutation.py file