Difference between revisions of "MSL Objects"

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=== Molecular representation objects ===
 
=== Molecular representation objects ===
 
* The '''[[MSL Objects:AtomContainer|AtomContainer]]''': a simple, light containers for the molecules represented internally just as an array of '''Atom''' 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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=== Geometry ===
 
=== Geometry ===
* Transforms
+
* '''[[MSL Objects:Transforms|Transforms]]'''
  
 
=== Selection ===
 
=== Selection ===
* AtomSelection
+
* '''[[MSL Objects:AtomSelection|AtomSelection]]'''
* Predicate
+
* '''[[MSL Objects:Predicate|Predicate]]'''
* Selectable
+
* '''[[MSL Objects:Selectable|Selectable]]'''
  
  
 
=== Energetics ===
 
=== Energetics ===
* CharmmAngleInteraction
+
* '''[[MSL Objects:CharmmAngleInteraction|CharmmAngleInteraction]]'''
* CharmmBondInteraction
+
* '''[[MSL Objects:CharmmBondInteraction|CharmmBondInteraction]]'''
* CharmmDihedralInteraction
+
* '''[[MSL Objects:CharmmDihedralInteraction|CharmmDihedralInteraction]]'''
* CharmmElectrostaticInteraction
+
* '''[[MSL Objects:CharmmElectrostaticInteraction|CharmmElectrostaticInteraction]]'''
* CharmmEnergy
+
* '''[[MSL Objects:CharmmEnergy|CharmmEnergy]]'''
* CharmmImproperInteraction
+
* '''[[MSL Objects:CharmmImproperInteraction|CharmmImproperInteraction]]'''
* CharmmParameterReader
+
* '''[[MSL Objects:CharmmParameterReader|CharmmParameterReader]]'''
* CharmmSystemBuilder
+
* '''[[MSL Objects:CharmmSystemBuilder|CharmmSystemBuilder]]'''
* CharmmTopologyReader
+
* '''[[MSL Objects:CharmmTopologyReader|CharmmTopologyReader]]'''
* CharmmTopologyResidue
+
* '''[[MSL Objects:CharmmTopologyResidue|CharmmTopologyResidue]]'''
* CharmmUreyBradleyInteraction
+
* '''[[MSL Objects:CharmmUreyBradleyInteraction|CharmmUreyBradleyInteraction]]'''
* CharmmVdwInteraction
+
* '''[[MSL Objects:CharmmVdwInteraction|CharmmVdwInteraction]]'''
* EnergySet
+
* '''[[MSL Objects:EnergySet|EnergySet]]'''
* EnergeticAnalysis
+
* '''[[MSL Objects:EnergeticAnalysis|EnergeticAnalysis]]'''
* Interaction
+
* '''[[MSL Objects:Interaction|Interaction]]'''
* PairwiseEnergyCalculator
+
* '''[[MSL Objects:PairwiseEnergyCalculator|PairwiseEnergyCalculator]]'''
  
 
=== SASA===
 
=== SASA===
* SasaAtom
+
* '''[[MSL Objects:SasaAtom|SasaAtom]]'''
* SasaCalculator
+
* '''[[MSL Objects:SasaCalculator|SasaCalculator]]'''
  
 
=== Molecule I/O ===
 
=== Molecule I/O ===
* File
+
* '''[[MSL Objects:File|File]]'''
* PDBFormat
+
* '''[[MSL Objects:PDBFormat|PDBFormat]]'''
* PDBReader
+
* '''[[MSL Objects:PDBReader|PDBReader]]'''
* PDBWriter
+
* '''[[MSL Objects:PDBWriter|PDBWriter]]'''
* Reader
+
* '''[[MSL Objects:Reader|Reader]]'''
* Writer
+
* '''[[MSL Objects:Writer|Writer]]'''
  
 
=== Rotamer library management ===
 
=== Rotamer library management ===
* RotamerLibrary
+
* '''[[MSL Objects:RotamerLibrary|RotamerLibrary]]'''
* RotamerLibraryReader
+
* '''[[MSL Objects:RotamerLibraryReader|RotamerLibraryReader]]'''
* RotamerLibraryWriter
+
* '''[[MSL Objects:RotamerLibraryWriter|RotamerLibraryWriter]]'''
  
  
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=== To be classified ===
 
=== To be classified ===
* Atom3DGrid
+
* '''[[MSL Objects:Atom3DGrid|Atom3DGrid]]'''
* AtomAngleRelationship
+
* '''[[MSL Objects:AtomAngleRelationship|AtomAngleRelationship]]'''
* AtomBondBuilder
+
* '''[[MSL Objects:AtomBondBuilder|AtomBondBuilder]]'''
* AtomDihedralRelationship
+
* '''[[MSL Objects:AtomDihedralRelationship|AtomDihedralRelationship]]'''
* AtomDistanceRelationship
+
* '''[[MSL Objects:AtomDistanceRelationship|AtomDistanceRelationship]]'''
* AtomGeometricRelationship
+
* '''[[MSL Objects:AtomGeometricRelationship|AtomGeometricRelationship]]'''
* AtomicPairwiseEnergy
+
* '''[[MSL Objects:AtomicPairwiseEnergy|AtomicPairwiseEnergy]]'''
* AtomPointerVector
+
* '''[[MSL Objects:AtomPointerVector|AtomPointerVector]]'''
* BackRub
+
* '''[[MSL Objects:BackRub|BackRub]]'''
* BBQTable
+
* '''[[MSL Objects:BBQTable|BBQTable]]'''
* BBQTableReader
+
* '''[[MSL Objects:BBQTableReader|BBQTableReader]]'''
* BBQTableWriter
+
* '''[[MSL Objects:BBQTableWriter|BBQTableWriter]]'''
* CartesianGeometry
+
* '''[[MSL Objects:CartesianGeometry|CartesianGeometry]]'''
* CCD
+
* '''[[MSL Objects:CCD|CCD]]'''
* ChiStatistics
+
* '''[[MSL Objects:ChiStatistics|ChiStatistics]]'''
* CoiledCoils
+
* '''[[MSL Objects:CoiledCoils|CoiledCoils]]'''
* CoordAxes
+
* '''[[MSL Objects:CoordAxes|CoordAxes]]'''
* CrystalLattice
+
* '''[[MSL Objects:CrystalLattice|CrystalLattice]]'''
* DeadEndElimination
+
* '''[[MSL Objects:DeadEndElimination|DeadEndElimination]]'''
* Enumerator
+
* '''[[MSL Objects:Enumerator|Enumerator]]'''
* EnvironmentDatabase
+
* '''[[MSL Objects:EnvironmentDatabase|EnvironmentDatabase]]'''
* EnvironmentDescriptor
+
* '''[[MSL Objects:EnvironmentDescriptor|EnvironmentDescriptor]]'''
* FourBodyInteraction
+
* '''[[MSL Objects:FourBodyInteraction|FourBodyInteraction]]'''
* Frame
+
* '''[[MSL Objects:Frame|Frame]]'''
* GSLMinimizer
+
* '''[[MSL Objects:GSLMinimizer|GSLMinimizer]]'''
* Hash
+
* '''[[MSL Objects:Hash|Hash]]'''
* HBond_LJGaussianInteraction
+
* '''[[MSL Objects:HBond_LJGaussianInteraction|HBond_LJGaussianInteraction]]'''
* Helanal
+
* '''[[MSL Objects:Helanal|Helanal]]'''
* HelixFusion
+
* '''[[MSL Objects:HelixFusion|HelixFusion]]'''
* HelixGenerator
+
* '''[[MSL Objects:HelixGenerator|HelixGenerator]]'''
* IcEntry
+
* '''[[MSL Objects:IcEntry|IcEntry]]'''
* IcTable
+
* '''[[MSL Objects:IcTable|IcTable]]'''
* InterfaceResidueDescriptor
+
* '''[[MSL Objects:InterfaceResidueDescriptor|InterfaceResidueDescriptor]]'''
* LinearProgrammingOptimization
+
* '''[[MSL Objects:LinearProgrammingOptimization|LinearProgrammingOptimization]]'''
* Line
+
* '''[[MSL Objects:Line|Line]]'''
* LogicalParser
+
* '''[[MSL Objects:LogicalParser|LogicalParser]]'''
* Matrix
+
* '''[[MSL Objects:Matrix|Matrix]]'''
* MIDReader
+
* '''[[MSL Objects:MIDReader|MIDReader]]'''
* Minimizer
+
* '''[[MSL Objects:Minimizer|Minimizer]]'''
* MoleculeInterfaceDatabase
+
* '''[[MSL Objects:MoleculeInterfaceDatabase|MoleculeInterfaceDatabase]]'''
* MonteCarloOptimization
+
* '''[[MSL Objects:MonteCarloOptimization|MonteCarloOptimization]]'''
* MslExceptions
+
* '''[[MSL Objects:MslExceptions|MslExceptions]]'''
* MslTools
+
* '''[[MSL Objects:MslTools|MslTools]]'''
* OptionParser
+
* '''[[MSL Objects:OptionParser|OptionParser]]'''
* PDBFragments
+
* '''[[MSL Objects:PDBFragments|PDBFragments]]'''
* PhiPsiReader
+
* '''[[MSL Objects:PhiPsiReader|PhiPsiReader]]'''
* PhiPsiStatistics
+
* '''[[MSL Objects:PhiPsiStatistics|PhiPsiStatistics]]'''
* PolymerSequence
+
* '''[[MSL Objects:PolymerSequence|PolymerSequence]]'''
* <strike>Position</strike>
+
* '''[[MSL Objects:PotentialTable|PotentialTable]]'''
* PotentialTable
+
* '''[[MSL Objects:PrincipleComponentAnalysis|PrincipleComponentAnalysis]]'''
* PrincipleComponentAnalysis
+
* '''[[MSL Objects:PSFReader|PSFReader]]'''
* PSFReader
+
* '''[[MSL Objects:PyMolVisualization|PyMolVisualization]]'''
* PyMolVisualization
+
* '''[[MSL Objects:Quaternion|Quaternion]]'''
* Quaternion
+
* '''[[MSL Objects:Quench|Quench]]'''
* Quench
+
* '''[[MSL Objects:RandomNumberGenerator|RandomNumberGenerator]]'''
* RandomNumberGenerator
+
* '''[[MSL Objects:RandomSeqGenerator|RandomSeqGenerator]]'''
* RandomSeqGenerator
+
* '''[[MSL Objects:Real|Real]]'''
* Real
+
* '''[[MSL Objects:RegEx|RegEx]]'''
* RegEx
+
* '''[[MSL Objects:ResiduePairTable|ResiduePairTable]]'''
* ResiduePairTable
+
* '''[[MSL Objects:ResiduePairTableReader|ResiduePairTableReader]]'''
* ResiduePairTableReader
+
* '''[[MSL Objects:ResidueSelection|ResidueSelection]]'''
* ResidueSelection
+
* '''[[MSL Objects:ResidueSubstitutionTable|ResidueSubstitutionTable]]'''
* ResidueSubstitutionTable
+
* '''[[MSL Objects:ResidueSubstitutionTableReader|ResidueSubstitutionTableReader]]'''
* ResidueSubstitutionTableReader
+
* '''[[MSL Objects:RotamerLibraryBuilder|RotamerLibraryBuilder]]'''
* RotamerLibraryBuilder
+
* '''[[MSL Objects:SelfPairManager|SelfPairManager]]'''
* SelfPairManager
+
* '''[[MSL Objects:SphericalPoint|SphericalPoint]]'''
* SphericalPoint
+
* '''[[MSL Objects:SurfaceAreaAndVolume|SurfaceAreaAndVolume]]'''
* SurfaceAreaAndVolume
+
* '''[[MSL Objects:SurfaceSphere|SurfaceSphere]]'''
* SurfaceSphere
+
* '''[[MSL Objects:Symmetry|Symmetry]]'''
* Symmetry
+
* '''[[MSL Objects:SystemRotamerLoader|SystemRotamerLoader]]'''
* SystemRotamerLoader
+
* '''[[MSL Objects:TBDReader|TBDReader]]'''
* TBDReader
+
* '''[[MSL Objects:ThreeBodyInteraction|ThreeBodyInteraction]]'''
* ThreeBodyInteraction
+
* '''[[MSL Objects:Timer|Timer]]'''
* Timer
+
* '''[[MSL Objects:Tree|Tree]]'''
* Tree
+
* '''[[MSL Objects:triple|triple]]'''
* triple
+
* '''[[MSL Objects:TwoBodyDistanceDependentPotentialTable|TwoBodyDistanceDependentPotentialTable]]'''
* TwoBodyDistanceDependentPotentialTable
+
* '''[[MSL Objects:TwoBodyInteraction|TwoBodyInteraction]]'''
* TwoBodyInteraction
+
* '''[[MSL Objects:UserDefinedEnergy|UserDefinedEnergy]]'''
* UserDefinedEnergy
+
* '''[[MSL Objects:UserDefinedEnergySetBuilder|UserDefinedEnergySetBuilder]]'''
* UserDefinedEnergySetBuilder
+
* '''[[MSL Objects:UserDefinedInteraction|UserDefinedInteraction]]'''
* UserDefinedInteraction
 

Revision as of 00:57, 18 February 2010

Molecular representation objects

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