Difference between revisions of "MSL Objects"
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=== Molecular representation objects === | === Molecular representation objects === | ||
| − | * The '''[[MSL Objects:AtomContainer|AtomContainer]]''' | + | MSL contains two object for representing a macromolecule: the '''AtomContainer''' and the '''System'''. |
| − | * The '''[[MSL Objects:System|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: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 === | ||
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* '''[[MSL Objects:CharmmDihedralInteraction|CharmmDihedralInteraction]]''' | * '''[[MSL Objects:CharmmDihedralInteraction|CharmmDihedralInteraction]]''' | ||
* '''[[MSL Objects:CharmmElectrostaticInteraction|CharmmElectrostaticInteraction]]''' | * '''[[MSL Objects:CharmmElectrostaticInteraction|CharmmElectrostaticInteraction]]''' | ||
| + | * '''[[MSL Objects:CharmmEEF1Interaction|CharmmEEF1Interaction]]''' | ||
| + | * '''[[MSL Objects:CharmmEEF1RefInteraction|CharmmEEF1RefInteraction]]''' | ||
| + | * '''[[MSL Objects:CharmmEEF1ParameterReader|CharmmEEF1ParameterReader]]''' | ||
* '''[[MSL Objects:CharmmEnergy|CharmmEnergy]]''' | * '''[[MSL Objects:CharmmEnergy|CharmmEnergy]]''' | ||
* '''[[MSL Objects:CharmmImproperInteraction|CharmmImproperInteraction]]''' | * '''[[MSL Objects:CharmmImproperInteraction|CharmmImproperInteraction]]''' | ||
| Line 33: | Line 42: | ||
* '''[[MSL Objects:EnergySet|EnergySet]]''' | * '''[[MSL Objects:EnergySet|EnergySet]]''' | ||
* '''[[MSL Objects:EnergeticAnalysis|EnergeticAnalysis]]''' | * '''[[MSL Objects:EnergeticAnalysis|EnergeticAnalysis]]''' | ||
| + | * '''[[MSL Objects:FourBodyInteraction|FourBodyInteraction]]''' | ||
* '''[[MSL Objects:Interaction|Interaction]]''' | * '''[[MSL Objects:Interaction|Interaction]]''' | ||
| + | * '''[[MSL Objects:OneBodyInteraction|OneBodyInteraction]]''' | ||
* '''[[MSL Objects:PairwiseEnergyCalculator|PairwiseEnergyCalculator]]''' | * '''[[MSL Objects:PairwiseEnergyCalculator|PairwiseEnergyCalculator]]''' | ||
| + | * '''[[MSL Objects:ThreeBodyInteraction|ThreeBodyInteraction]]''' | ||
| + | * '''[[MSL Objects:TwoBodyInteraction|TwoBodyInteraction]]''' | ||
=== SASA=== | === SASA=== | ||
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* '''[[MSL Objects:EnvironmentDatabase|EnvironmentDatabase]]''' | * '''[[MSL Objects:EnvironmentDatabase|EnvironmentDatabase]]''' | ||
* '''[[MSL Objects:EnvironmentDescriptor|EnvironmentDescriptor]]''' | * '''[[MSL Objects:EnvironmentDescriptor|EnvironmentDescriptor]]''' | ||
| − | |||
* '''[[MSL Objects:Frame|Frame]]''' | * '''[[MSL Objects:Frame|Frame]]''' | ||
* '''[[MSL Objects:GSLMinimizer|GSLMinimizer]]''' | * '''[[MSL Objects:GSLMinimizer|GSLMinimizer]]''' | ||
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* '''[[MSL Objects:SystemRotamerLoader|SystemRotamerLoader]]''' | * '''[[MSL Objects:SystemRotamerLoader|SystemRotamerLoader]]''' | ||
* '''[[MSL Objects:TBDReader|TBDReader]]''' | * '''[[MSL Objects:TBDReader|TBDReader]]''' | ||
| − | |||
* '''[[MSL Objects:Timer|Timer]]''' | * '''[[MSL Objects:Timer|Timer]]''' | ||
* '''[[MSL Objects:Tree|Tree]]''' | * '''[[MSL Objects:Tree|Tree]]''' | ||
* '''[[MSL Objects:triple|triple]]''' | * '''[[MSL Objects:triple|triple]]''' | ||
* '''[[MSL Objects:TwoBodyDistanceDependentPotentialTable|TwoBodyDistanceDependentPotentialTable]]''' | * '''[[MSL Objects:TwoBodyDistanceDependentPotentialTable|TwoBodyDistanceDependentPotentialTable]]''' | ||
| − | |||
* '''[[MSL Objects:UserDefinedEnergy|UserDefinedEnergy]]''' | * '''[[MSL Objects:UserDefinedEnergy|UserDefinedEnergy]]''' | ||
* '''[[MSL Objects:UserDefinedEnergySetBuilder|UserDefinedEnergySetBuilder]]''' | * '''[[MSL Objects:UserDefinedEnergySetBuilder|UserDefinedEnergySetBuilder]]''' | ||
* '''[[MSL Objects:UserDefinedInteraction|UserDefinedInteraction]]''' | * '''[[MSL Objects:UserDefinedInteraction|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
