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| | Examples of simple programs that illustrate how to use different features of the library are provided in the '''[[Tutorial]]'''. | | Examples of simple programs that illustrate how to use different features of the library are provided in the '''[[Tutorial]]'''. |
| | | | |
| − | === Molecular representation objects === | + | === MSL Objects === |
| − | * The '''[[MSL Objects:AtomContainer|AtomContainer]]''': a simple, light containers for the molecules represented internally just as an array of '''Atom''' objects.
| + | A description of the objects and link to the source code on SourceForge is provided in the [[MSL Objects]] section |
| − | * The '''[[MSL Objects:System|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 '''[[MSL Objects:Chain|Chain]]''': a polypeptide chain. Takes a letter as an identifier ("A", "B") as in a PDB file. It contains '''Position''' objects
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| − | *** The '''[[MSL Objects:Position|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 '''[[MSL Objects:Residue|Residue]]''': a specific residue type (i.e. "ALA", "LEU"), also referred as "identity". It contains '''AtomGroups'''. The AtomGroup contains '''Atom''' objects.
| |
| − | ***** The '''[[MSL Objects:AtomGroup|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 '''[[MSL Objects:Atom|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 '''[[MSL Objects:CartesianPoint|CartesianPoint]]''': not strictly part of the molecular representation but the CartesianPoint (the coordinates) is at the bottom of the object hierarchy
| |
| − | | |
| − | === Geometry ===
| |
| − | * Transforms
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| − | | |
| − | === Selection ===
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| − | * AtomSelection
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| − | * Predicate
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| − | * Selectable
| |
| − | | |
| − | | |
| − | === Energetics ===
| |
| − | * CharmmAngleInteraction
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| − | * CharmmBondInteraction
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| − | * CharmmDihedralInteraction
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| − | * CharmmElectrostaticInteraction
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| − | * CharmmEnergy
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| − | * CharmmImproperInteraction
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| − | * CharmmParameterReader
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| − | * CharmmSystemBuilder
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| − | * CharmmTopologyReader
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| − | * CharmmTopologyResidue
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| − | * CharmmUreyBradleyInteraction
| |
| − | * CharmmVdwInteraction
| |
| − | * EnergySet
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| − | * EnergeticAnalysis
| |
| − | * Interaction
| |
| − | * PairwiseEnergyCalculator
| |
| − | | |
| − | === SASA===
| |
| − | * SasaAtom
| |
| − | * SasaCalculator
| |
| − | | |
| − | === Molecule I/O ===
| |
| − | * File
| |
| − | * PDBFormat
| |
| − | * PDBReader
| |
| − | * PDBWriter
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| − | * Reader
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| − | * Writer
| |
| − | | |
| − | === Rotamer library management ===
| |
| − | * RotamerLibrary
| |
| − | * RotamerLibraryReader
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| − | * RotamerLibraryWriter
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| − | | |
| − | | |
| − | | |
| − | | |
| − | === To be classified ===
| |
| − | * Atom3DGrid
| |
| − | * AtomAngleRelationship
| |
| − | * AtomBondBuilder
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| − | * 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
| |
| − | * <strike>Position</strike>
| |
| − | * 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
| |
