MSMBuilder 3

Abstract

This document is a collaborative wiki page for brainstorming the direction of new development efforts towards msmbuilder 3.

Overall Goals

• Enhanced usability
  • Robust
  • Informative error messages
  • Sanity checking of inputs in library functions
• Better error analysis
  • Bayesian methods?
  • Add script for Nina's method
• New visualization tools
  • Plot eigenvector components by state index?
  • Plot eigenvector components by observables?
• Clean up code
  • Rewrite the Trajectory code.
    • "Smart" slicing and keeping track of the time index of every frame.
    • Use new PDB reader
  • DRY the scripts. To the extent that they are "thin" wrappers for library functions, can they be auto-generated?
  • Rewrite all of the non-RMSD C code (asa, rg, etc) in cython.
• Improve documentation
  • Bring the latex tutorial onto readthedocs.org
  • Increase the amount of narrative content on readthedocs.org
• New test systems and benchmarks
  • Muller potential (?)
  • BPTI (?)

Questions

• Should all of the scripts be accessible under a single command?

  • $ msmbuilder cluster
  • $ msmbuilder setup
  • $ msmbuilder assign
  • RTM prefers yes.

• Is it time to re-work our "best practices" to better include conformational change? TICA?

• Should we reorganize the directory layout of the source code? Currently we have two main directories, src/python and src/ext. If you look at how a project like numpy or scipy is organized, the directory structure is by logical grouping instead. Like package/subpackage. It's not based on what language the code is in. This is, in RTM's opinion, related to the idea of bringing the current c code into cython and making it more "public" and robust.