Sim stores universe kwargs if possible; refactored atomselections to address confusing API #55
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
The MDAnalysis.Universe does not currently hold onto its kwargs, so this is dependent on a small upstream change.
This will remove the universe definition for the Sim
We will encourage setting a Sim universe directly with an existing Universe, with the hope that we can eventually hide UniverseDefinition. At the moment, though, we leave it exposed for any manual interventions that can't be handled from the Universe itself. Also, AtomSelection getitem no longer returns an AtomGroup, but instead gives back the definition of the selection (that which was stored). It is possible to store only strings or numpy arrays of atom indices, or tuples/lists of these in any combination. One cannot directly store AtomGroups, but can store atom indices with `AG.indices`. Getting back an AtomGroup from the stored definition requires using the `create` method. This makes it clear that a new AtomGroup is being generated, and that there is a cost to this.
dotsdl
changed the title
|
@orbeckst if you get to this before @richardjgowers, you're welcome to merge. I'm itching to get this released so we can go from there. |
|
For the future: I would add an optional arg to ag = s.atomselections.create('lid', 'protein and resid 122:159')which would be equivalent to s.atomselections['lid'] = 'protein and resid 122:159'
ag = s.atomselections.create('lid') |
|
I haven't tested the PR but I am happy with the API changes. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Addresses concerns in #48 and #54. Fixes #25 pending upstream MDAnalysis/mdanalysis#813.
We will encourage setting a Sim universe directly with an existing Universe, with the hope that we can eventually hide UniverseDefinition. At the moment, though, we leave it exposed for any manual interventions that can't be handled from the Universe itself.
Also, AtomSelection getitem no longer returns an AtomGroup, but instead gives back the definition of the selection (that which was stored). It is possible to store only strings or numpy arrays of atom indices,
or tuples/lists of these in any combination. One cannot directly store AtomGroups, but can store atom indices with
AG.indices.Getting back an AtomGroup from the stored definition requires using the
createmethod. This makes it clear that a new AtomGroup is being generated, and that there is a cost to this.