What’s New

2.8 Changelog

  • Ported code to use MDTraj. This eliminates the need for MSMBuilder to directly handle the loading and saving of trajectories, and gives us much more cross-format support.
  • New sphinx documentation

2.6 Changelog

  • Migrated from SVN to Github for version control. The source code can now be found at https://github.com/SimTk/msmbuilder
  • Renamed all the functions in MSMLib to be pep8 compliant. Aliases have been added for the old names. Note: Trajectory.py is still not pep8 compliant, but will be fixed by release 3.0.
  • Split MSMLib into 2 files: MSMLib and msm_analysis. msm_analysis contains all the code for analyzing MSMs (eigenvector calculation, sampling, etc). MSMLib contains code for building models, while msm_analysis contains code for working with models.
  • Removed AssignMPI.py
  • Added more unit tests and Travis automated unit testing.
  • Updated most of MSMBuilder to be PEP8 compliant.
  • Rewrote code for estimating reversible maximum likelihood count matrix. The new code should be faster and easier to read.
  • New code implementing min-cut/max-flow cut-based reaction coordinate learning from MSMs (cfep.py). Beta version.
  • New code for the computation of MSM hub scores.
  • Switched to YAML for storing project information.
  • Added script RebuildProject.py to construct YAML ProjectInfo file.
  • Deleted the Serializer class.
  • New msmbuilder.io module for storing output.
  • Added support for the BACE coarse graining algorithm.
  • Better error checking for assignments arrays.
  • Updates to tutorials.
  • Rewrote lumping code for improved readability.

2.5.1 Changelog

  • Updates to tutorials.
  • Moved Ward clustering and SCRE to AdvancedMethods tutorial.

2.5 Changelog

  • The libraries are distance metric agnostic, you can use your own new distance metric without having to change the clustering/assignment code.
  • Dihedral, Contact (residues and/or atoms), hybrid distance metric code
  • New clustering algorithms (CLARANS / subsampled CLARANS)
  • Flux-based PCCA+.
  • Support for Hierarchical Clustering (e.g. Ward).
  • SCRE rate matrix estimation.

2.0.4 Changelog

  • Improvements in PCCA, PCCA+ lead to better macrostate definition.

2.0.3 Changelog

  • Bug fix: In ConvertDataToHDF, the Stride option was not being used for non-FAH style datasets.
  • Fixed unicode strings were causing scipy issues on certain platforms.

2.0.2 Changelog

  • Fixed issue with AtomIndices in UpdateProjectToHDF
  • Using dtype=’int’ for Assignments, consistent throughout MSMBuilder.
  • CalculateImpliedTimescales now allows users to exit through control+C
  • Fixed some tabbing issues in MSMLib.py

2.0.1 Changelog

  • Fixed a bug in ConvertProjectToHDF that prevented MSMBuilder from seeing multiple XTC files in a single directory.
  • Fixed carriage return issues in UpdateProjectToHDF
  • Fixed minor bugs in Project class.
  • If Project cannot find its PDB, it also will look in the current directory. This helps when the absolute path of a Project changes.
  • Unit tests.
  • Removed unnecessary files, reducing the package size to 10MB.
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