Iván Pulido
Iván Pulido
In a recent [PR](#528) it was noted that we are testing against deprecated python versions. And it was suggested that we should follow the policies in https://numpy.org/neps/nep-0029-deprecation_policy.html as a project...
While trying to read an incomplete simulation from an nc file I get ``` Exception: Non-global MBAR analysis not implemented yet. ``` which comes from https://github.com/choderalab/openmmtools/blob/master/openmmtools/multistate/multistateanalyzer.py#L878 I think we should...
[This test](https://github.com/choderalab/perses/blob/main/perses/tests/test_rest.py#L304) fails stochastically. Examples: https://github.com/choderalab/perses/runs/7844494466?check_suite_focus=true#step:9:444 https://github.com/choderalab/perses/runs/6692487797?check_suite_focus=true#step:9:438
https://github.com/choderalab/perses/blob/87bc1d00c6c087b0dc13b38f83f5e2c4d13e012d/perses/rjmc/atom_mapping.py#L283-L286 https://docs.eyesopen.com/toolkits/python/depicttk/OEDepictClasses/OE2DMolDisplayOptions.html#OEDepict::OE2DMolDisplayOptions::SetAromaticStyle
While running our benchmarks and generating results I have realized that we do not have an easy way to add a phase (i.e. `vacuum`, `solvent`, `complex`) to current finished simulations/results....
It has been reported in #1063 that some of the examples and data files in the `perses/data` directory might be broken. We should try to clean this directory and make...
While working in #1052 it was noted that adding the `allow_undefned_stereochemistry` flag when reading some of the test molecule files, was required for tests to pass. This raises the question...
While working on https://github.com/choderalab/perses/pull/1050 it was noted that we can increase the readability and reduce some of the redundant code if we make a factory pattern for the hybrid topology...
While working on #1007 it was noted that there is code in the tests that never gets executed but they might be a good starting point for new and useful...