Skip to content

[WIP] MDTraj analysis wrapper#1246

Open
MBartkowiakSTFC wants to merge 6 commits into
protosfrom
maciej/mdtraj-wrapper
Open

[WIP] MDTraj analysis wrapper#1246
MBartkowiakSTFC wants to merge 6 commits into
protosfrom
maciej/mdtraj-wrapper

Conversation

@MBartkowiakSTFC

Copy link
Copy Markdown
Collaborator

Description of work
This PR introduces a proof-of-concept analysis run where and MDANSE trajectory can be used as input for MDTraj.

mdtraj.Trajectory and its underlying Topology object are both created in memory from an instance of MDANSE.MolecularDynamics.Trajectory.

At the moment the main effort of enabling an MDTraj analysis in MDANSE is adding code that will convert the output of the analysis into a structure that can be written into an .mda file.

Fixes

  1. Added functions for building an MDTraj.Trajectory from an MDANSE Trajectory.
  2. Added MDTrajAnalysis, MDTrajAnalysisConfigurator and MDTrajAnalysisWidget to enable basic parameter input for MDTraj analysis runs.
  3. Implemented writeout function for hydrogen bond statistics using the Wernet-Nilsson method: https://www.mdtraj.org/1.9.8.dev0/api/generated/mdtraj.wernet_nilsson.html#

To test
Try running the only possible MDTraj analysis on different input trajectories.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant