Difference between revisions of "Documentation"

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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:AtomContainer|AtomContainer]]''': a simple, light containers for the molecules represented internally just as an array of '''Atom''' objects.
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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: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
 
*** 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 ===
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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
 
* <strike>CartesianPoint</strike>
 
* 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