David W.H. Swenson
David W.H. Swenson
This is a really simple PR aiming to add support for `residue.is_nucleic` and `'nucleic'/'is_nucleic` as special query strings (like `'protein'`) in the atom selection language. Main question: Is there any...
My problem: OpenPathSampling allows users to define stable states and order parameters in terms of MSMBuilder featurizers, and to perform sampling using OpenMM for the dynamics. This combination is currently...
Far from urgent, but since at some point I'll probably steal the version div from here to use in the OpenPathSampling docs, I thought I'd see if you can fix...
I'm writing an OpenPathSampling engine to wrap the OpenMMTools `MCMCSampler`. This will allow users to do path sampling of Monte Carlo "trajectories." This came out of a user question in...
If I do "1.5 cycles" of serialization (i.e., serialize, deserialize the resulting dict, reserialize the result of that) I would expect that the dict for the originally serialized object would...
Currently, leaving an empty `google_analytics_key` (or not having it in your `_config.yml` at all) still builds the `` block for Google Analytics, because the value of `site.google_analytics_key` is `nil`, not...
I'm planning to rename the `master` branch here to `main`. My thoughts on this are fully discussed in https://github.com/openpathsampling/openpathsampling/issues/956, so I won't repeat them here. With the exceptions of Contact...
It might be nice to add a `ContactTrajectory` class. This would store a separate (single frame) contact map for each time slice. Then you could do interesting things like create...
***Current status (tl;dr for users):*** For a single-frame contact map, you should use `ContactFrequency` with a single-frame trajectory. ```python #cmap = ContactMap(traj, frame=0) # old cmap = ContactFrequency(traj[0]) # new...
To handle contact pairs, we frequently use dictionaries/counters where the keys are a `frozenset` of the indices. This gets very annoying to deal with, especially when writing unit tests (so...