Difference between revisions of "MSL Objects"
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| − | + | === Molecular representation objects === | |
| + | MSL contains two object for representing a macromolecule: the '''AtomContainer''' and the '''System'''. | ||
| + | |||
| + | |||
| + | * The '''[[MSL Objects:AtomContainer|AtomContainer]]''' is a simple, light containers for the molecules represented internally just as an array of '''Atom''' objects. | ||
| + | |||
| − | + | * 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:System|System]]''' | ||
** 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 | ||
| + | |||
=== 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:CharmmEEF1Interaction|CharmmEEF1Interaction]]''' |
| − | * CharmmImproperInteraction | + | * '''[[MSL Objects:CharmmEEF1RefInteraction|CharmmEEF1RefInteraction]]''' |
| − | * CharmmParameterReader | + | * '''[[MSL Objects:CharmmEEF1ParameterReader|CharmmEEF1ParameterReader]]''' |
| − | * CharmmSystemBuilder | + | * '''[[MSL Objects:CharmmEnergy|CharmmEnergy]]''' |
| − | * CharmmTopologyReader | + | * '''[[MSL Objects:CharmmImproperInteraction|CharmmImproperInteraction]]''' |
| − | * CharmmTopologyResidue | + | * '''[[MSL Objects:CharmmParameterReader|CharmmParameterReader]]''' |
| − | * CharmmUreyBradleyInteraction | + | * '''[[MSL Objects:CharmmSystemBuilder|CharmmSystemBuilder]]''' |
| − | * CharmmVdwInteraction | + | * '''[[MSL Objects:CharmmTopologyReader|CharmmTopologyReader]]''' |
| − | * EnergySet | + | * '''[[MSL Objects:CharmmTopologyResidue|CharmmTopologyResidue]]''' |
| − | * EnergeticAnalysis | + | * '''[[MSL Objects:CharmmUreyBradleyInteraction|CharmmUreyBradleyInteraction]]''' |
| − | * Interaction | + | * '''[[MSL Objects:CharmmVdwInteraction|CharmmVdwInteraction]]''' |
| − | * PairwiseEnergyCalculator | + | * '''[[MSL Objects:EnergySet|EnergySet]]''' |
| + | * '''[[MSL Objects:EnergeticAnalysis|EnergeticAnalysis]]''' | ||
| + | * '''[[MSL Objects:FourBodyInteraction|FourBodyInteraction]]''' | ||
| + | * '''[[MSL Objects:Interaction|Interaction]]''' | ||
| + | * '''[[MSL Objects:OneBodyInteraction|OneBodyInteraction]]''' | ||
| + | * '''[[MSL Objects:PairwiseEnergyCalculator|PairwiseEnergyCalculator]]''' | ||
| + | * '''[[MSL Objects:ThreeBodyInteraction|ThreeBodyInteraction]]''' | ||
| + | * '''[[MSL Objects:TwoBodyInteraction|TwoBodyInteraction]]''' | ||
=== 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]]''' |
| − | * | + | * '''[[MSL Objects:Frame|Frame]]''' |
| − | + | * '''[[MSL Objects:GSLMinimizer|GSLMinimizer]]''' | |
| − | * GSLMinimizer | + | * '''[[MSL Objects:Hash|Hash]]''' |
| − | * Hash | + | * '''[[MSL Objects:HBond_LJGaussianInteraction|HBond_LJGaussianInteraction]]''' |
| − | * HBond_LJGaussianInteraction | + | * '''[[MSL Objects:Helanal|Helanal]]''' |
| − | * Helanal | + | * '''[[MSL Objects:HelixFusion|HelixFusion]]''' |
| − | * HelixFusion | + | * '''[[MSL Objects:HelixGenerator|HelixGenerator]]''' |
| − | * HelixGenerator | + | * '''[[MSL Objects:IcEntry|IcEntry]]''' |
| − | * IcEntry | + | * '''[[MSL Objects:IcTable|IcTable]]''' |
| − | * IcTable | + | * '''[[MSL Objects:InterfaceResidueDescriptor|InterfaceResidueDescriptor]]''' |
| − | * InterfaceResidueDescriptor | + | * '''[[MSL Objects:LinearProgrammingOptimization|LinearProgrammingOptimization]]''' |
| − | * LinearProgrammingOptimization | + | * '''[[MSL Objects:Line|Line]]''' |
| − | * Line | + | * '''[[MSL Objects:LogicalParser|LogicalParser]]''' |
| − | * LogicalParser | + | * '''[[MSL Objects:Matrix|Matrix]]''' |
| − | * Matrix | + | * '''[[MSL Objects:MIDReader|MIDReader]]''' |
| − | * MIDReader | + | * '''[[MSL Objects:Minimizer|Minimizer]]''' |
| − | * Minimizer | + | * '''[[MSL Objects:MoleculeInterfaceDatabase|MoleculeInterfaceDatabase]]''' |
| − | * MoleculeInterfaceDatabase | + | * '''[[MSL Objects:MonteCarloOptimization|MonteCarloOptimization]]''' |
| − | * MonteCarloOptimization | + | * '''[[MSL Objects:MslExceptions|MslExceptions]]''' |
| − | * MslExceptions | + | * '''[[MSL Objects:MslTools|MslTools]]''' |
| − | * MslTools | + | * '''[[MSL Objects:OptionParser|OptionParser]]''' |
| − | * OptionParser | + | * '''[[MSL Objects:PDBFragments|PDBFragments]]''' |
| − | * PDBFragments | + | * '''[[MSL Objects:PhiPsiReader|PhiPsiReader]]''' |
| − | * PhiPsiReader | + | * '''[[MSL Objects:PhiPsiStatistics|PhiPsiStatistics]]''' |
| − | * PhiPsiStatistics | + | * '''[[MSL Objects:PolymerSequence|PolymerSequence]]''' |
| − | * PolymerSequence | + | * '''[[MSL Objects:PotentialTable|PotentialTable]]''' |
| − | * | + | * '''[[MSL Objects:PrincipleComponentAnalysis|PrincipleComponentAnalysis]]''' |
| − | + | * '''[[MSL Objects:PSFReader|PSFReader]]''' | |
| − | * PrincipleComponentAnalysis | + | * '''[[MSL Objects:PyMolVisualization|PyMolVisualization]]''' |
| − | * PSFReader | + | * '''[[MSL Objects:Quaternion|Quaternion]]''' |
| − | * PyMolVisualization | + | * '''[[MSL Objects:Quench|Quench]]''' |
| − | * Quaternion | + | * '''[[MSL Objects:RandomNumberGenerator|RandomNumberGenerator]]''' |
| − | * Quench | + | * '''[[MSL Objects:RandomSeqGenerator|RandomSeqGenerator]]''' |
| − | * RandomNumberGenerator | + | * '''[[MSL Objects:Real|Real]]''' |
| − | * RandomSeqGenerator | + | * '''[[MSL Objects:RegEx|RegEx]]''' |
| − | * Real | + | * '''[[MSL Objects:ResiduePairTable|ResiduePairTable]]''' |
| − | * RegEx | + | * '''[[MSL Objects:ResiduePairTableReader|ResiduePairTableReader]]''' |
| − | * ResiduePairTable | + | * '''[[MSL Objects:ResidueSelection|ResidueSelection]]''' |
| − | * ResiduePairTableReader | + | * '''[[MSL Objects:ResidueSubstitutionTable|ResidueSubstitutionTable]]''' |
| − | * ResidueSelection | + | * '''[[MSL Objects:ResidueSubstitutionTableReader|ResidueSubstitutionTableReader]]''' |
| − | * ResidueSubstitutionTable | + | * '''[[MSL Objects:RotamerLibraryBuilder|RotamerLibraryBuilder]]''' |
| − | * ResidueSubstitutionTableReader | + | * '''[[MSL Objects:SelfPairManager|SelfPairManager]]''' |
| − | * RotamerLibraryBuilder | + | * '''[[MSL Objects:SphericalPoint|SphericalPoint]]''' |
| − | * SelfPairManager | + | * '''[[MSL Objects:SurfaceAreaAndVolume|SurfaceAreaAndVolume]]''' |
| − | * SphericalPoint | + | * '''[[MSL Objects:SurfaceSphere|SurfaceSphere]]''' |
| − | * SurfaceAreaAndVolume | + | * '''[[MSL Objects:Symmetry|Symmetry]]''' |
| − | * SurfaceSphere | + | * '''[[MSL Objects:SystemRotamerLoader|SystemRotamerLoader]]''' |
| − | * Symmetry | + | * '''[[MSL Objects:TBDReader|TBDReader]]''' |
| − | * SystemRotamerLoader | + | * '''[[MSL Objects:Timer|Timer]]''' |
| − | * TBDReader | + | * '''[[MSL Objects:Tree|Tree]]''' |
| − | * | + | * '''[[MSL Objects:triple|triple]]''' |
| − | + | * '''[[MSL Objects:TwoBodyDistanceDependentPotentialTable|TwoBodyDistanceDependentPotentialTable]]''' | |
| − | * Tree | + | * '''[[MSL Objects:UserDefinedEnergy|UserDefinedEnergy]]''' |
| − | * triple | + | * '''[[MSL Objects:UserDefinedEnergySetBuilder|UserDefinedEnergySetBuilder]]''' |
| − | * TwoBodyDistanceDependentPotentialTable | + | * '''[[MSL Objects:UserDefinedInteraction|UserDefinedInteraction]]''' |
| − | * | ||
| − | |||
| − | * UserDefinedEnergySetBuilder | ||
| − | * UserDefinedInteraction | ||
Latest revision as of 19:15, 16 March 2010
Contents
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
- 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 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 Residue: a specific residue type (i.e. "ALA", "LEU"), also referred as "identity". It contains AtomGroups. The AtomGroup contains Atom 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 Chain: a polypeptide chain. Takes a letter as an identifier ("A", "B") as in a PDB file. It contains Position objects
Geometry
Selection
Energetics
- CharmmAngleInteraction
- CharmmBondInteraction
- CharmmDihedralInteraction
- CharmmElectrostaticInteraction
- CharmmEEF1Interaction
- CharmmEEF1RefInteraction
- CharmmEEF1ParameterReader
- CharmmEnergy
- CharmmImproperInteraction
- CharmmParameterReader
- CharmmSystemBuilder
- CharmmTopologyReader
- CharmmTopologyResidue
- CharmmUreyBradleyInteraction
- CharmmVdwInteraction
- EnergySet
- EnergeticAnalysis
- FourBodyInteraction
- Interaction
- OneBodyInteraction
- PairwiseEnergyCalculator
- ThreeBodyInteraction
- TwoBodyInteraction
SASA
Molecule I/O
Rotamer library management
To be classified
- Atom3DGrid
- AtomAngleRelationship
- AtomBondBuilder
- AtomDihedralRelationship
- AtomDistanceRelationship
- AtomGeometricRelationship
- AtomicPairwiseEnergy
- AtomPointerVector
- BackRub
- BBQTable
- BBQTableReader
- BBQTableWriter
- CartesianGeometry
- CCD
- ChiStatistics
- CoiledCoils
- CoordAxes
- CrystalLattice
- DeadEndElimination
- Enumerator
- EnvironmentDatabase
- EnvironmentDescriptor
- Frame
- GSLMinimizer
- Hash
- HBond_LJGaussianInteraction
- Helanal
- HelixFusion
- HelixGenerator
- IcEntry
- IcTable
- InterfaceResidueDescriptor
- LinearProgrammingOptimization
- Line
- LogicalParser
- Matrix
- MIDReader
- Minimizer
- MoleculeInterfaceDatabase
- MonteCarloOptimization
- MslExceptions
- MslTools
- OptionParser
- PDBFragments
- PhiPsiReader
- PhiPsiStatistics
- PolymerSequence
- PotentialTable
- PrincipleComponentAnalysis
- PSFReader
- PyMolVisualization
- Quaternion
- Quench
- RandomNumberGenerator
- RandomSeqGenerator
- Real
- RegEx
- ResiduePairTable
- ResiduePairTableReader
- ResidueSelection
- ResidueSubstitutionTable
- ResidueSubstitutionTableReader
- RotamerLibraryBuilder
- SelfPairManager
- SphericalPoint
- SurfaceAreaAndVolume
- SurfaceSphere
- Symmetry
- SystemRotamerLoader
- TBDReader
- Timer
- Tree
- triple
- TwoBodyDistanceDependentPotentialTable
- UserDefinedEnergy
- UserDefinedEnergySetBuilder
- UserDefinedInteraction
