Lex O'brien

No yet but I did move on so it became less relevant for me.

I have a similar problem. Here's an (almost) reprex: ``` import pyemma from pyemma.datasets.double_well_discrete import DoubleWell_Discrete_Data print(pyemma.__version__) dtraj = DoubleWell_Discrete_Data().generate_traj(10000) print('Bayesian HMM') mm = pyemma.msm.bayesian_hidden_markov_model(dtraj, nstates=2, lag=50, nsamples=500) ck_b =...

OK, I see what you're saying regarding the conceptual problem.

OK. I think I've found a bug but I don't think it's totally related to the issue here: ``` def _compute_observables(self, model, estimator, mlag=1): # for lag time 0 we...

you need to use the regex operator for this: ``` topology.select("resname =~ '^1Q5'") ``` note - the single quote marks around the expression.

This looks like an easy fix: ``` def _topology_from_subset(topology, atom_indices): ... for chain in topology._chains: newChain = newTopology.add_chain(chain_id=chain.chain_id) ``` I'm happy to submit a PR and a new test for...

> Does the spec offer any guidance? It doesn't look to me like it has any particular opinions on how chain IDs are preserved (or not) when slicing up a...

hey - I've almost got this working. I had to: - reinstall homebrew and make sure all the dependencies are in the right place. - clone the git repo and...

Actually - this still doesn't work. I'm at a loss.

Not a question - just adding my experience for other people to read here. I had a similar problem with the SmirnoffGenerator from openff: ```python from openmm import app, VerletIntegrator,...