search

MDAnalysis / UGM2023

Materials for the 2023 MDAnalysis User Group Meeting
Other
4 stars 10 forks source link

[MDAKit / Hackathon] Molecular volume and surface analysis #28

Open IAlibay opened 1 year ago

IAlibay commented 1 year ago

Overview

This is one of the most wanted analysis features missing in MDAnalysis.

It is often necessary to measure volume and surface area of a biomolecule or parts of it over an MD trajectory. MDAnalysis is currently lacking this important functionality. In this project you will implement an analysis class that calculates the molecular volume and area for an atomgroup as a function of time. See issue #2439.

The FreeSASA library appears to be a suitable tool to integrate into MDAnalysis. It comes under MIT license and has a C core and python bindings:

By default Lee & Richards' algorithm is used, but Shrake & Rupley's is also available.

Objectives

For this project you would

  1. Interface freesasa-python [Mitternacht 2016] with MDAnalysis: Find out how to pass information from MDAnalysis to freesasa so that it can compute areas and volumes.
  2. Write a SASAnalysis class using the AnalysisBase framework (see the [tutorial on writing your own trajectory analysis][UserGuide AnalysisBase].
  3. Create test cases (use existing files in MDA and run external implementation for reference)
  4. Benchmark performance

References

  1. Simon Mitternacht (2016) FreeSASA: An open source C library for solvent accessible surface area calculation. F1000Research 5:189 (doi: 10.12688/f1000research.7931.1)