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| | === Getting started === | | === Getting started === |
| − | Examples of simple programs that illustrate how to use different features of the library are provided in the '''[[Tutorial]]'''.
| + | An introduction for first users and some simple programs that illustrate how to use different features of the library are provided in the '''[[Tutorial]]'''. |
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| − | === 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
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| − | ** 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.
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| − | **** 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.
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| − | ***** 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).
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| − | ****** 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.
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| − | ******* 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
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| − | === Geometry === | + | ===Distributed Programs=== |
| − | * Transforms
| + | A number of programs and utilities are distributed with MSL. Check the '''[[MSL Programs]]''' section. |
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| − | === Selection === | + | === MSL by example === |
| − | * AtomSelection
| + | A number of example on how to do simple or complex tasks: '''[[MSL by example]]''' |
| − | * Predicate
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| − | * Selectable
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| | | | |
| − | | + | === Developers of MSL === |
| − | === Energetics ===
| + | * '''[[Committing code to MSL]]''' |
| − | * CharmmAngleInteraction
| + | * '''[[Creating branches]]''' |
| − | * 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
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| − | * CharmmVdwInteraction
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| − | * EnergySet
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| − | * EnergeticAnalysis
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| − | * Interaction
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| − | * PairwiseEnergyCalculator
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| − | | |
| − | === SASA===
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| − | * SasaAtom
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| − | * SasaCalculator
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| − | | |
| − | === Molecule I/O ===
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| − | * File
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| − | * PDBFormat
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| − | * PDBReader
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| − | * PDBWriter
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| − | * Reader
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| − | * Writer
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| − | | |
| − | === Rotamer library management === | |
| − | * RotamerLibrary | |
| − | * RotamerLibraryReader
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| − | * RotamerLibraryWriter
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| − | | |
| − | | |
| − | | |
| − | | |
| − | === To be classified ===
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| − | * Atom3DGrid
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| − | * AtomAngleRelationship
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| − | * AtomBondBuilder
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| − | * AtomDihedralRelationship
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| − | * AtomDistanceRelationship
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| − | * AtomGeometricRelationship
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| − | * AtomicPairwiseEnergy
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| − | * AtomPointerVector
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| − | * BackRub
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| − | * BBQTable
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| − | * BBQTableReader
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| − | * BBQTableWriter
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| − | * CartesianGeometry
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| − | * CCD
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| − | * ChiStatistics
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| − | * CoiledCoils
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| − | * CoordAxes
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| − | * CrystalLattice
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| − | * DeadEndElimination
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| − | * Enumerator
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| − | * EnvironmentDatabase
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| − | * EnvironmentDescriptor
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| − | * FourBodyInteraction
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| − | * Frame
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| − | * GSLMinimizer
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| − | * Hash
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| − | * HBond_LJGaussianInteraction
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| − | * Helanal
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| − | * HelixFusion
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| − | * HelixGenerator
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| − | * IcEntry
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| − | * IcTable
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| − | * InterfaceResidueDescriptor
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| − | * LinearProgrammingOptimization
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| − | * Line
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| − | * LogicalParser
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| − | * Matrix
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| − | * MIDReader
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| − | * Minimizer
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| − | * MoleculeInterfaceDatabase
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| − | * MonteCarloOptimization
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| − | * MslExceptions
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| − | * MslTools
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| − | * OptionParser
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| − | * PDBFragments
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| − | * PhiPsiReader
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| − | * PhiPsiStatistics
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| − | * PolymerSequence
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| − | * <strike>Position</strike>
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| − | * PotentialTable
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| − | * PrincipleComponentAnalysis
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| − | * PSFReader
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| − | * PyMolVisualization
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| − | * Quaternion
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| − | * Quench
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| − | * RandomNumberGenerator
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| − | * RandomSeqGenerator
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| − | * Real
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| − | * RegEx
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| − | * ResiduePairTable
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| − | * ResiduePairTableReader
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| − | * ResidueSelection
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| − | * ResidueSubstitutionTable
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| − | * ResidueSubstitutionTableReader
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| − | * RotamerLibraryBuilder
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| − | * SelfPairManager
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| − | * SphericalPoint
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| − | * SurfaceAreaAndVolume
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| − | * SurfaceSphere
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| − | * Symmetry
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| − | * SystemRotamerLoader
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| − | * TBDReader
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| − | * ThreeBodyInteraction
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| − | * Timer
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| − | * Tree
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| − | * triple
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| − | * TwoBodyDistanceDependentPotentialTable
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| − | * TwoBodyInteraction
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| − | * UserDefinedEnergy
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| − | * UserDefinedEnergySetBuilder
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| − | * UserDefinedInteraction | |
