MSMBuilder
  • Installation
    • Python Prerequisites
    • Install Python and Python Packages
    • Download and Install MSMBuilder
  • Tutorial : Introduction and Alanine Dipeptide
    • Overview of MSM Construction
    • Alanine Dipeptide Tutorial
  • Tutorial : Additional Methods
    • Cluster your data using Ward’s algorithm and the RMSD metric
    • Estimate a rate matrix using SCRE
  • MSMBuilder Commands
    • msmb
    • ConvertDataToHDF.py
    • CreateAtomIndices.py
    • Cluster.py
    • Assign.py / AssignHierarchical.py
    • CalculateImpliedTimescales.py
    • PlotImpliedTimescales.py
    • BuildMSM.py
    • GetRandomConfs.py
    • CalculateClusterRadii.py
    • CalculateRMSD.py
    • CalculateProjectRMSD.py
    • CalculateTPT.py
    • SavePDBs.py
    • PCCA.py
    • BACE_Coarse_Graining.py
  • Frequently Asked Questions
  • What’s New
    • 2.8 Changelog
    • 2.6 Changelog
    • 2.5.1 Changelog
    • 2.5 Changelog
    • 2.0.4 Changelog
    • 2.0.3 Changelog
    • 2.0.2 Changelog
    • 2.0.1 Changelog
  • Contributing
    • Submitting a bug report
    • How to contribute
  • Time-Structure Based Independent Component Analysis (tICA)
    • Introduction
    • Selection of tICA Parameters
    • Understanding the tICs
    • Drawbacks of tICA
  • Calculation of Autocorrelation Functions
  • Maximum-Likelihood Reversible Transition Matrix
  • msmbuilder.MSMLib
  • msmbuilder.msm_analysis
  • msmbuilder.assigning
  • msmbuilder.clustering
  • msmbuilder.drift
  • msmbuilder.cfep
  • msmbuilder.SCRE
  • msmbuilder.reduce.tICA
 
MSMBuilder
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