[MDAKit / Hackathon] Molecular volume and surface analysis

[IAlibay]

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:

• C-library: https://github.com/mittinatten/freesasa
• Python bindings: https://github.com/freesasa/freesasa-python

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)