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
Docs
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msmbuilder.clustering
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msmbuilder.clustering
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BaseFlatClusterer
Clarans
Hierarchical
HybridKMedoids
KCenters
concatenate_prep_trajectories
unconcatenate_trajectory
concatenate_trajectories
deterministic_subsample
stochastic_subsample
p_norm