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- MSL Objects:Enumerator
- MSL Objects:EnvironmentDatabase
- MSL Objects:EnvironmentDescriptor
- MSL Objects:File
- MSL Objects:FourBodyInteraction
- MSL Objects:Frame
- MSL Objects:GSLMinimizer
- MSL Objects:HBond LJGaussianInteraction
- MSL Objects:Hash
- MSL Objects:Helanal
- MSL Objects:HelixFusion
- MSL Objects:HelixGenerator
- MSL Objects:IcEntry
- MSL Objects:IcTable
- MSL Objects:Interaction
- MSL Objects:InterfaceResidueDescriptor
- MSL Objects:Line
- MSL Objects:LinearProgrammingOptimization
- MSL Objects:LogicalParser
- MSL Objects:MIDReader
- MSL Objects:Matrix
- MSL Objects:Minimizer
- MSL Objects:MoleculeInterfaceDatabase
- MSL Objects:MonteCarloOptimization
- MSL Objects:MslExceptions
- MSL Objects:MslTools
- MSL Objects:OneBodyInteraction
- MSL Objects:OptionParser
- MSL Objects:PDBFormat
- MSL Objects:PDBFragments
- MSL Objects:PDBReader
- MSL Objects:PDBWriter
- MSL Objects:PSFReader
- MSL Objects:PairwiseEnergyCalculator
- MSL Objects:PhiPsiReader
- MSL Objects:PhiPsiStatistics
- MSL Objects:PolymerSequence
- MSL Objects:Position
- MSL Objects:PotentialTable
- MSL Objects:Predicate
- MSL Objects:PrincipleComponentAnalysis
- MSL Objects:PyMolVisualization
- MSL Objects:PythonMSL
- MSL Objects:Quaternion
- MSL Objects:Quench
- MSL Objects:RandomNumberGenerator
- MSL Objects:RandomSeqGenerator
- MSL Objects:Reader
- MSL Objects:Real
- MSL Objects:RegEx