Contents:
- BuildMacroMSM.py = Build a macrostate MSM.  First finds microstate transition matrix, thenlump into macrostates.
- BuildMacroMSMsVaryLagTime.py = Takes MSM built with BuildMacroMSM.py and determines implied timescales as vary lagtime so can find minimum lagtime that gives you a Markovian model.
- BuildMacroMSMwithNoeSampling.py = Like BuildMacroMSM.py but uses the Noe transition matrix sampling algorithm to determine the transition probability matrix.
- BuildMicroMSMsVaryLagTime.py = Build microstate MSMs with a series of different lagtimes to get implied timescales for each lagtime.  Use this information to determine appropriate number of states to use in macrostate MSM.
- DatabaseTools.py = Some methods for connecting to databases.
- FAHProj.py = Describes a general FAH project.
- GetMacroMSMPopStats.py = Uses bootstrapping on an MSM to get populstions of each state with errorbars.
- GetNoeMacroMSMPopStats.py = Use the Noe transition matrix sampling algorithm to get populations of states with errorbars.
- GetRandomConfsFromEachMacroState.py = Get n random conformations from each macrostate in a macrostate MSM.  Useful for shooting.
- MacroMSM.py = Code for building macrostate MSMs.
- MacroNoeMSM.py = Code for building macrostate MSMs using the Noe transition matrix sampling code.
- MicroMSM.py = Code for building microstate MSMs.
- NoeSampling.py = Noe transition matrix xampling code.
- SetupFAHProjClustering.py = Sets up the directories and input files for clustering a general FAH project.
- SetupSTProjClustering.py = Sets up the directories and input files for clustering an ST FAH project.
- STProj.py = Describes as ST FAH project.
- testFAH.py = Example script for setting up the clustering inputs for a general FAH project.
- testST.py = Example script for setting up the clustering inputs for an ST FAH project.