MSL Objects

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MSL Objects

Molecular representation objects

  • The AtomContainer: a simple, light containers for the molecules represented internally just as an array of Atom objects.
  • The System: a structured, hierarchical representation of the molecules. It contains Chain objects (which contain residues and then atoms). More complex, powerful object than the AtomContiner, supports energy calculations
    • The Chain: a polypeptide chain. Takes a letter as an identifier ("A", "B") as in a PDB file. It contains Position objects
      • The Position: a position in the Chain (i.e. 37 in a PDB file). It contains Residue objects (also called identities). It may contain multiple alternative identities (ILE, ALA, etc) but only one is active at the time.
        • The Residue: a specific residue type (i.e. "ALA", "LEU"), also referred as "identity". It contains AtomGroups. The AtomGroup contains Atom objects.
          • The AtomGroup: group of atoms, generally used when MSL reads the topology of a macromolecule from CHARMM input files (groups in CHARMM are sets of atoms that sum to integer charge).
            • The Atom: an atom. It has a name ("CA", "CB"), element, and coordinates (CartesianPoint objects). Atoms may have multiple alternative cordinates, but only one active at the time.
              • The CartesianPoint: not strictly part of the molecular representation but the CartesianPoint (the coordinates) is at the bottom of the object hierarchy

Geometry

  • Transforms

Selection

  • AtomSelection
  • Predicate
  • Selectable


Energetics

  • CharmmAngleInteraction
  • CharmmBondInteraction
  • CharmmDihedralInteraction
  • CharmmElectrostaticInteraction
  • CharmmEnergy
  • CharmmImproperInteraction
  • CharmmParameterReader
  • CharmmSystemBuilder
  • CharmmTopologyReader
  • CharmmTopologyResidue
  • CharmmUreyBradleyInteraction
  • CharmmVdwInteraction
  • EnergySet
  • EnergeticAnalysis
  • Interaction
  • PairwiseEnergyCalculator

SASA

  • SasaAtom
  • SasaCalculator

Molecule I/O

  • File
  • PDBFormat
  • PDBReader
  • PDBWriter
  • Reader
  • Writer

Rotamer library management

  • RotamerLibrary
  • RotamerLibraryReader
  • RotamerLibraryWriter



To be classified

  • Atom3DGrid
  • AtomAngleRelationship
  • AtomBondBuilder
  • AtomDihedralRelationship
  • AtomDistanceRelationship
  • AtomGeometricRelationship
  • AtomicPairwiseEnergy
  • AtomPointerVector
  • BackRub
  • BBQTable
  • BBQTableReader
  • BBQTableWriter
  • CartesianGeometry
  • CCD
  • ChiStatistics
  • CoiledCoils
  • CoordAxes
  • CrystalLattice
  • DeadEndElimination
  • Enumerator
  • EnvironmentDatabase
  • EnvironmentDescriptor
  • FourBodyInteraction
  • Frame
  • GSLMinimizer
  • Hash
  • HBond_LJGaussianInteraction
  • Helanal
  • HelixFusion
  • HelixGenerator
  • IcEntry
  • IcTable
  • InterfaceResidueDescriptor
  • LinearProgrammingOptimization
  • Line
  • LogicalParser
  • Matrix
  • MIDReader
  • Minimizer
  • MoleculeInterfaceDatabase
  • MonteCarloOptimization
  • MslExceptions
  • MslTools
  • OptionParser
  • PDBFragments
  • PhiPsiReader
  • PhiPsiStatistics
  • PolymerSequence
  • Position
  • PotentialTable
  • PrincipleComponentAnalysis
  • PSFReader
  • PyMolVisualization
  • Quaternion
  • Quench
  • RandomNumberGenerator
  • RandomSeqGenerator
  • Real
  • RegEx
  • ResiduePairTable
  • ResiduePairTableReader
  • ResidueSelection
  • ResidueSubstitutionTable
  • ResidueSubstitutionTableReader
  • RotamerLibraryBuilder
  • SelfPairManager
  • SphericalPoint
  • SurfaceAreaAndVolume
  • SurfaceSphere
  • Symmetry
  • SystemRotamerLoader
  • TBDReader
  • ThreeBodyInteraction
  • Timer
  • Tree
  • triple
  • TwoBodyDistanceDependentPotentialTable
  • TwoBodyInteraction
  • UserDefinedEnergy
  • UserDefinedEnergySetBuilder
  • UserDefinedInteraction