Documentation

MSL Documentation

Getting started

Examples of simple programs that illustrate how to use different features of the library are provided in the Tutorial.

Molecular representation objects

• The System: contains the molecules in a structured, hierarchical way (chains, residues, atoms), more complex, powerful object, supports energy calculations
• The AtomContainer: a simpler, lighter containers for the molecules represented internally just as an array of Atoms
• The Chain: a polypeptide chain. Takes a letter as an identifier ("A", "B") as in a PDB file.
• The Position: a position in the Chain (i.e. 37 in a PDB file). It may contain multiple alternative residue types (but only one active at the time)
• The Residue: a specific residue type (i.e. "ALA", "LEU")
• The Atom: an atom. It has a name ("CA", "CB"), coordinates (potentially multiple, but only one active at the time), element, etc.

To be classified

• Atom3DGrid
• AtomAngleRelationship
• AtomBondBuilder
• AtomContainer
• AtomDihedralRelationship
• AtomDistanceRelationship
• AtomGeometricRelationship
• AtomGroup
• Atom
• AtomicPairwiseEnergy
• AtomPointerVector
• AtomSelection
• BackRub
• BBQTable
• BBQTableReader
• BBQTableWriter
• CartesianGeometry
• CartesianPoint
• CCD
• Chain
• CharmmAngleInteraction
• CharmmBondInteraction
• CharmmDihedralInteraction
• CharmmElectrostaticInteraction
• CharmmEnergy
• CharmmImproperInteraction
• CharmmParameterReader
• CharmmSystemBuilder
• CharmmTopologyReader
• CharmmTopologyResidue
• CharmmUreyBradleyInteraction
• CharmmVdwInteraction
• ChiStatistics
• CoiledCoils
• CoordAxes
• CrystalLattice
• DeadEndElimination
• EnergeticAnalysis
• EnergySet
• Enumerator
• EnvironmentDatabase
• EnvironmentDescriptor
• File
• FourBodyInteraction
• Frame
• GSLMinimizer
• Hash
• HBond_LJGaussianInteraction
• Helanal
• HelixFusion
• HelixGenerator
• IcEntry
• IcTable
• Interaction
• InterfaceResidueDescriptor
• LinearProgrammingOptimization
• Line
• LogicalParser
• Matrix
• MIDReader
• Minimizer
• MoleculeInterfaceDatabase
• MonteCarloOptimization
• MslExceptions
• MslTools
• OptionParser
• PairwiseEnergyCalculator
• PDBFormat
• PDBFragments
• PDBReader
• PDBWriter
• PhiPsiReader
• PhiPsiStatistics
• PolymerSequence
• Position
• PotentialTable
• Predicate
• PrincipleComponentAnalysis
• PSFReader
• PyMolVisualization
• Quaternion
• Quench
• RandomNumberGenerator
• RandomSeqGenerator
• Reader
• Real
• RegEx
• Residue
• ResiduePairTable
• ResiduePairTableReader
• ResidueSelection
• ResidueSubstitutionTable
• ResidueSubstitutionTableReader
• RotamerLibraryBuilder
• RotamerLibrary
• RotamerLibraryReader
• RotamerLibraryWriter
• SasaAtom
• SasaCalculator
• Selectable
• SelfPairManager
• SphericalPoint
• SurfaceAreaAndVolume
• SurfaceSphere
• Symmetry
• System
• SystemRotamerLoader
• TBDReader
• ThreeBodyInteraction
• Timer
• Transforms
• Tree
• triple
• TwoBodyDistanceDependentPotentialTable
• TwoBodyInteraction
• UserDefinedEnergy
• UserDefinedEnergySetBuilder
• UserDefinedInteraction
• Writer