Duplicate instances of `self._setup_complex_phase()` in relative_setup.py
zhang-ivy opened this issue · comments
I noticed that self._setup_complex_phase() is called twice.
- first time: https://github.com/choderalab/perses/blob/main/perses/app/relative_setup.py#L333 -- as noted in the comments, this call needs to happen before the system generator is created because for host guest systems, the host molecule needs to be supplied to when creating the system generator
- second time: https://github.com/choderalab/perses/blob/main/perses/app/relative_setup.py#L409 -- not sure if this is necessary, try removing it and seeing what happens?
Iván notes that this is not super high priority since we are in the midst of overhauling the API anyway
Yes,the comment on
perses/perses/app/relative_setup.py
Line 329 in ae55801
As a reference, when I worked in the refactor for the NEQ cycling protocol, the RelativeFEPSetup.__init__
method of is more organized and it's only setting up the phases at the end of it, as per
perses/perses/app/relative_setup.py
Line 349 in faac030