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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]]'''.
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An introduction for first users and some simple programs that illustrate how to use different features of the library are provided in the '''[[Tutorial]]'''.
  
=== Molecular representation objects ===
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=== MSL Objects ===
* The '''[[MSL Objects:System|System]]''': contains the molecules in a structured, hierarchical way (chains, residues, atoms), more complex, powerful object, supports energy calculations
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A description of the objects and link to the source code on SourceForge is provided in the '''[[MSL Objects]]''' section
* The '''[[MSL Objects:AtomContainer|AtomContainer]]''': a simpler, lighter containers for the molecules represented internally just as an array of Atoms
 
* The '''[[MSL Objects:Chain|Chain]]''': a polypeptide chain.  Takes a letter as an identifier ("A", "B") as in a PDB file.
 
* The '''[[MSL Objects:Position|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 '''[[MSL Objects:Residue|Residue]]''': a specific residue type (i.e. "ALA", "LEU")
 
* The '''[[MSL Objects:Atom|Atom]]''': an atom.  It has a name ("CA", "CB"), coordinates (potentially multiple, but only one active at the time), element, etc.
 
  
=== Geometry ===
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===Distributed Programs===
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A number of programs and utilities are distributed with MSL.  Check the '''[[MSL Programs]]''' section.
  
=== Energetics ===
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=== MSL by example ===
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A number of example on how to do simple or complex tasks: '''[[MSL by example]]'''
  
 
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=== Developers of MSL ===
=== To be classified ===
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* '''[[Committing code to MSL]]'''
* Atom3DGrid
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* '''[[Creating branches]]'''
* AtomAngleRelationship
 
* AtomBondBuilder
 
* <strike>AtomContainer</strike>
 
* AtomDihedralRelationship
 
* AtomDistanceRelationship
 
* AtomGeometricRelationship
 
* AtomGroup
 
* <strike>Atom</strike>
 
* AtomicPairwiseEnergy
 
* AtomPointerVector
 
* AtomSelection
 
* BackRub
 
* BBQTable
 
* BBQTableReader
 
* BBQTableWriter
 
* CartesianGeometry
 
* CartesianPoint
 
* CCD
 
* <strike>Chain</strike>
 
* 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
 
* <strike>Position</strike>
 
* PotentialTable
 
* Predicate
 
* PrincipleComponentAnalysis
 
* PSFReader
 
* PyMolVisualization
 
* Quaternion
 
* Quench
 
* RandomNumberGenerator
 
* RandomSeqGenerator
 
* Reader
 
* Real
 
* RegEx
 
* <strike>Residue</strike>
 
* ResiduePairTable
 
* ResiduePairTableReader
 
* ResidueSelection
 
* ResidueSubstitutionTable
 
* ResidueSubstitutionTableReader
 
* RotamerLibraryBuilder
 
* RotamerLibrary
 
* RotamerLibraryReader
 
* RotamerLibraryWriter
 
* SasaAtom
 
* SasaCalculator
 
* Selectable
 
* SelfPairManager
 
* SphericalPoint
 
* SurfaceAreaAndVolume
 
* SurfaceSphere
 
* Symmetry
 
* <strike>System</strike>
 
* SystemRotamerLoader
 
* TBDReader
 
* ThreeBodyInteraction
 
* Timer
 
* Transforms
 
* Tree
 
* triple
 
* TwoBodyDistanceDependentPotentialTable
 
* TwoBodyInteraction
 
* UserDefinedEnergy
 
* UserDefinedEnergySetBuilder
 
* UserDefinedInteraction
 
* Writer
 

Latest revision as of 01:25, 26 September 2013

MSL Documentation

Getting started

An introduction for first users and some simple programs that illustrate how to use different features of the library are provided in the Tutorial.

MSL Objects

A description of the objects and link to the source code on SourceForge is provided in the MSL Objects section

Distributed Programs

A number of programs and utilities are distributed with MSL. Check the MSL Programs section.

MSL by example

A number of example on how to do simple or complex tasks: MSL by example

Developers of MSL