Difference between revisions of "MSL Objects"

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(Created page with '<big>MSL Objects</big> === Molecular representation objects === * The '''AtomContainer''': a simple, light containers for the molecules represented…')
 
 
(3 intermediate revisions by the same user not shown)
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<big>MSL Objects</big>
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=== Molecular representation objects ===
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MSL contains two object for representing a macromolecule: the '''AtomContainer''' and the '''System'''.
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* The '''[[MSL Objects:AtomContainer|AtomContainer]]''' is a simple, light containers for the molecules represented internally just as an array of '''Atom''' objects.
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=== Molecular representation objects ===
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* The '''[[MSL Objects:System|System]]''' is a structured, hierarchical representation of the molecules, more complex, powerful object than the AtomContiner, supports energy calculations.  It contains '''Chain''' objects and a whole hierarchy all the way to the '''Atom''' and its coordinates.   
* The '''[[MSL Objects:AtomContainer|AtomContainer]]''': a simple, light containers for the molecules represented internally just as an array of '''Atom''' objects.
 
* 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: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: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: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: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
 
******* 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 ===
 
=== Geometry ===
* Transforms
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* '''[[MSL Objects:Transforms|Transforms]]'''
  
 
=== Selection ===
 
=== Selection ===
* AtomSelection
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* '''[[MSL Objects:AtomSelection|AtomSelection]]'''
* Predicate
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* '''[[MSL Objects:Predicate|Predicate]]'''
* Selectable
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* '''[[MSL Objects:Selectable|Selectable]]'''
  
  
 
=== Energetics ===
 
=== Energetics ===
* CharmmAngleInteraction
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* '''[[MSL Objects:CharmmAngleInteraction|CharmmAngleInteraction]]'''
* CharmmBondInteraction
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* '''[[MSL Objects:CharmmBondInteraction|CharmmBondInteraction]]'''
* CharmmDihedralInteraction
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* '''[[MSL Objects:CharmmDihedralInteraction|CharmmDihedralInteraction]]'''
* CharmmElectrostaticInteraction
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* '''[[MSL Objects:CharmmElectrostaticInteraction|CharmmElectrostaticInteraction]]'''
* CharmmEnergy
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* '''[[MSL Objects:CharmmEEF1Interaction|CharmmEEF1Interaction]]'''
* CharmmImproperInteraction
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* '''[[MSL Objects:CharmmEEF1RefInteraction|CharmmEEF1RefInteraction]]'''
* CharmmParameterReader
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* '''[[MSL Objects:CharmmEEF1ParameterReader|CharmmEEF1ParameterReader]]'''
* CharmmSystemBuilder
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* '''[[MSL Objects:CharmmEnergy|CharmmEnergy]]'''
* CharmmTopologyReader
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* '''[[MSL Objects:CharmmImproperInteraction|CharmmImproperInteraction]]'''
* CharmmTopologyResidue
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* '''[[MSL Objects:CharmmParameterReader|CharmmParameterReader]]'''
* CharmmUreyBradleyInteraction
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* '''[[MSL Objects:CharmmSystemBuilder|CharmmSystemBuilder]]'''
* CharmmVdwInteraction
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* '''[[MSL Objects:CharmmTopologyReader|CharmmTopologyReader]]'''
* EnergySet
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* '''[[MSL Objects:CharmmTopologyResidue|CharmmTopologyResidue]]'''
* EnergeticAnalysis
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* '''[[MSL Objects:CharmmUreyBradleyInteraction|CharmmUreyBradleyInteraction]]'''
* Interaction
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* '''[[MSL Objects:CharmmVdwInteraction|CharmmVdwInteraction]]'''
* PairwiseEnergyCalculator
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* '''[[MSL Objects:EnergySet|EnergySet]]'''
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* '''[[MSL Objects:EnergeticAnalysis|EnergeticAnalysis]]'''
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* '''[[MSL Objects:FourBodyInteraction|FourBodyInteraction]]'''
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* '''[[MSL Objects:Interaction|Interaction]]'''
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* '''[[MSL Objects:OneBodyInteraction|OneBodyInteraction]]'''
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* '''[[MSL Objects:PairwiseEnergyCalculator|PairwiseEnergyCalculator]]'''
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* '''[[MSL Objects:ThreeBodyInteraction|ThreeBodyInteraction]]'''
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* '''[[MSL Objects:TwoBodyInteraction|TwoBodyInteraction]]'''
  
 
=== SASA===
 
=== SASA===
* SasaAtom
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* '''[[MSL Objects:SasaAtom|SasaAtom]]'''
* SasaCalculator
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* '''[[MSL Objects:SasaCalculator|SasaCalculator]]'''
  
 
=== Molecule I/O ===
 
=== Molecule I/O ===
* File
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* '''[[MSL Objects:File|File]]'''
* PDBFormat
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* '''[[MSL Objects:PDBFormat|PDBFormat]]'''
* PDBReader
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* '''[[MSL Objects:PDBReader|PDBReader]]'''
* PDBWriter
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* '''[[MSL Objects:PDBWriter|PDBWriter]]'''
* Reader
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* '''[[MSL Objects:Reader|Reader]]'''
* Writer
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* '''[[MSL Objects:Writer|Writer]]'''
  
 
=== Rotamer library management ===
 
=== Rotamer library management ===
* RotamerLibrary
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* '''[[MSL Objects:RotamerLibrary|RotamerLibrary]]'''
* RotamerLibraryReader
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* '''[[MSL Objects:RotamerLibraryReader|RotamerLibraryReader]]'''
* RotamerLibraryWriter
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* '''[[MSL Objects:RotamerLibraryWriter|RotamerLibraryWriter]]'''
  
  
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=== To be classified ===
 
=== To be classified ===
* Atom3DGrid
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* '''[[MSL Objects:Atom3DGrid|Atom3DGrid]]'''
* AtomAngleRelationship
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* '''[[MSL Objects:AtomAngleRelationship|AtomAngleRelationship]]'''
* AtomBondBuilder
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* '''[[MSL Objects:AtomBondBuilder|AtomBondBuilder]]'''
* AtomDihedralRelationship
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* '''[[MSL Objects:AtomDihedralRelationship|AtomDihedralRelationship]]'''
* AtomDistanceRelationship
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* '''[[MSL Objects:AtomDistanceRelationship|AtomDistanceRelationship]]'''
* AtomGeometricRelationship
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* '''[[MSL Objects:AtomGeometricRelationship|AtomGeometricRelationship]]'''
* AtomicPairwiseEnergy
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* '''[[MSL Objects:AtomicPairwiseEnergy|AtomicPairwiseEnergy]]'''
* AtomPointerVector
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* '''[[MSL Objects:AtomPointerVector|AtomPointerVector]]'''
* BackRub
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* '''[[MSL Objects:BackRub|BackRub]]'''
* BBQTable
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* '''[[MSL Objects:BBQTable|BBQTable]]'''
* BBQTableReader
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* '''[[MSL Objects:BBQTableReader|BBQTableReader]]'''
* BBQTableWriter
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* '''[[MSL Objects:BBQTableWriter|BBQTableWriter]]'''
* CartesianGeometry
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* '''[[MSL Objects:CartesianGeometry|CartesianGeometry]]'''
* CCD
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* '''[[MSL Objects:CCD|CCD]]'''
* ChiStatistics
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* '''[[MSL Objects:ChiStatistics|ChiStatistics]]'''
* CoiledCoils
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* '''[[MSL Objects:CoiledCoils|CoiledCoils]]'''
* CoordAxes
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* '''[[MSL Objects:CoordAxes|CoordAxes]]'''
* CrystalLattice
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* '''[[MSL Objects:CrystalLattice|CrystalLattice]]'''
* DeadEndElimination
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* '''[[MSL Objects:DeadEndElimination|DeadEndElimination]]'''
* Enumerator
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* '''[[MSL Objects:Enumerator|Enumerator]]'''
* EnvironmentDatabase
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* '''[[MSL Objects:EnvironmentDatabase|EnvironmentDatabase]]'''
* EnvironmentDescriptor
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* '''[[MSL Objects:EnvironmentDescriptor|EnvironmentDescriptor]]'''
* FourBodyInteraction
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* '''[[MSL Objects:Frame|Frame]]'''
* Frame
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* '''[[MSL Objects:GSLMinimizer|GSLMinimizer]]'''
* GSLMinimizer
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* '''[[MSL Objects:Hash|Hash]]'''
* Hash
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* '''[[MSL Objects:HBond_LJGaussianInteraction|HBond_LJGaussianInteraction]]'''
* HBond_LJGaussianInteraction
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* '''[[MSL Objects:Helanal|Helanal]]'''
* Helanal
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* '''[[MSL Objects:HelixFusion|HelixFusion]]'''
* HelixFusion
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* '''[[MSL Objects:HelixGenerator|HelixGenerator]]'''
* HelixGenerator
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* '''[[MSL Objects:IcEntry|IcEntry]]'''
* IcEntry
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* '''[[MSL Objects:IcTable|IcTable]]'''
* IcTable
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* '''[[MSL Objects:InterfaceResidueDescriptor|InterfaceResidueDescriptor]]'''
* InterfaceResidueDescriptor
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* '''[[MSL Objects:LinearProgrammingOptimization|LinearProgrammingOptimization]]'''
* LinearProgrammingOptimization
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* '''[[MSL Objects:Line|Line]]'''
* Line
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* '''[[MSL Objects:LogicalParser|LogicalParser]]'''
* LogicalParser
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* '''[[MSL Objects:Matrix|Matrix]]'''
* Matrix
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* '''[[MSL Objects:MIDReader|MIDReader]]'''
* MIDReader
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* '''[[MSL Objects:Minimizer|Minimizer]]'''
* Minimizer
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* '''[[MSL Objects:MoleculeInterfaceDatabase|MoleculeInterfaceDatabase]]'''
* MoleculeInterfaceDatabase
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* '''[[MSL Objects:MonteCarloOptimization|MonteCarloOptimization]]'''
* MonteCarloOptimization
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* '''[[MSL Objects:MslExceptions|MslExceptions]]'''
* MslExceptions
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* '''[[MSL Objects:MslTools|MslTools]]'''
* MslTools
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* '''[[MSL Objects:OptionParser|OptionParser]]'''
* OptionParser
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* '''[[MSL Objects:PDBFragments|PDBFragments]]'''
* PDBFragments
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* '''[[MSL Objects:PhiPsiReader|PhiPsiReader]]'''
* PhiPsiReader
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* '''[[MSL Objects:PhiPsiStatistics|PhiPsiStatistics]]'''
* PhiPsiStatistics
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* '''[[MSL Objects:PolymerSequence|PolymerSequence]]'''
* PolymerSequence
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* '''[[MSL Objects:PotentialTable|PotentialTable]]'''
* <strike>Position</strike>
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* '''[[MSL Objects:PrincipleComponentAnalysis|PrincipleComponentAnalysis]]'''
* PotentialTable
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* '''[[MSL Objects:PSFReader|PSFReader]]'''
* PrincipleComponentAnalysis
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* '''[[MSL Objects:PyMolVisualization|PyMolVisualization]]'''
* PSFReader
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* '''[[MSL Objects:Quaternion|Quaternion]]'''
* PyMolVisualization
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* '''[[MSL Objects:Quench|Quench]]'''
* Quaternion
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* '''[[MSL Objects:RandomNumberGenerator|RandomNumberGenerator]]'''
* Quench
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* '''[[MSL Objects:RandomSeqGenerator|RandomSeqGenerator]]'''
* RandomNumberGenerator
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* '''[[MSL Objects:Real|Real]]'''
* RandomSeqGenerator
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* '''[[MSL Objects:RegEx|RegEx]]'''
* Real
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* '''[[MSL Objects:ResiduePairTable|ResiduePairTable]]'''
* RegEx
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* '''[[MSL Objects:ResiduePairTableReader|ResiduePairTableReader]]'''
* ResiduePairTable
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* '''[[MSL Objects:ResidueSelection|ResidueSelection]]'''
* ResiduePairTableReader
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* '''[[MSL Objects:ResidueSubstitutionTable|ResidueSubstitutionTable]]'''
* ResidueSelection
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* '''[[MSL Objects:ResidueSubstitutionTableReader|ResidueSubstitutionTableReader]]'''
* ResidueSubstitutionTable
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* '''[[MSL Objects:RotamerLibraryBuilder|RotamerLibraryBuilder]]'''
* ResidueSubstitutionTableReader
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* '''[[MSL Objects:SelfPairManager|SelfPairManager]]'''
* RotamerLibraryBuilder
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* '''[[MSL Objects:SphericalPoint|SphericalPoint]]'''
* SelfPairManager
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* '''[[MSL Objects:SurfaceAreaAndVolume|SurfaceAreaAndVolume]]'''
* SphericalPoint
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* '''[[MSL Objects:SurfaceSphere|SurfaceSphere]]'''
* SurfaceAreaAndVolume
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* '''[[MSL Objects:Symmetry|Symmetry]]'''
* SurfaceSphere
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* '''[[MSL Objects:SystemRotamerLoader|SystemRotamerLoader]]'''
* Symmetry
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* '''[[MSL Objects:TBDReader|TBDReader]]'''
* SystemRotamerLoader
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* '''[[MSL Objects:Timer|Timer]]'''
* TBDReader
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* '''[[MSL Objects:Tree|Tree]]'''
* ThreeBodyInteraction
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* '''[[MSL Objects:triple|triple]]'''
* Timer
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* '''[[MSL Objects:TwoBodyDistanceDependentPotentialTable|TwoBodyDistanceDependentPotentialTable]]'''
* Tree
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* '''[[MSL Objects:UserDefinedEnergy|UserDefinedEnergy]]'''
* triple
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* '''[[MSL Objects:UserDefinedEnergySetBuilder|UserDefinedEnergySetBuilder]]'''
* TwoBodyDistanceDependentPotentialTable
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* '''[[MSL Objects:UserDefinedInteraction|UserDefinedInteraction]]'''
* TwoBodyInteraction
 
* UserDefinedEnergy
 
* UserDefinedEnergySetBuilder
 
* UserDefinedInteraction
 

Latest revision as of 19:15, 16 March 2010

Molecular representation objects

MSL contains two object for representing a macromolecule: the AtomContainer and the System.


  • The AtomContainer is a simple, light containers for the molecules represented internally just as an array of Atom objects.


  • The System is a structured, hierarchical representation of the molecules, more complex, powerful object than the AtomContiner, supports energy calculations. It contains Chain objects and a whole hierarchy all the way to the Atom and its coordinates.
    • 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

Selection


Energetics

SASA

Molecule I/O

Rotamer library management



To be classified