Documentation

From MSL-Libraries
Revision as of 17:13, 15 February 2010 by Senes (talk | contribs) (To be classified)
Jump to navigationJump to search

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 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

Energetics

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