API for pmda

The pmda package implements a simple map-reduce scheme for parallel trajectory analysis [Khoshlessan2017] and extends MDAnalysis [Gowers2016] [Michaud-Agrawal2011]. In order to make use of it, a user should be familiar with MDAnalysis.

Building blocks

Building new parallel analysis classes is easy with the pmda.custom.AnalysisFromFunction base class if you can formulate the problem as a calculation over one AtomGroup for a single frame. If your need more flexibility you can use the pmda.parallel.ParallelAnalysisBase.

• Parallel Analysis building blocks — pmda.parallel
• Parallel Analysis helper — pmda.custom
• Utility functions — pmda.util

Pre-defined parallel analysis tasks

pmda also has various predefined analysis tasks to use. They also function as examples for how to implement your own functions with pmda.parallel.ParallelAnalysisBase.

• Calculating Root-Mean-Square Deviations (RMSD) — pmda.rms
• Calculating Root-Mean-Square Fluctuations (RMSF) — pmda.rmsf
• Native contacts analysis — pmda.contacts
• Hydrogen Bond Analysis — pmda.hbond_analysis
• Radial Distribution Functions — pmda.rdf
• LeafletFinder Analysis tool — pmda.leaflet
• Generating Densities from Trajectories — pmda.density