Difference between revisions of "Documentation"
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=== Geometry === | === Geometry === | ||
| + | * Transforms | ||
| + | |||
| + | === Selection === | ||
| + | * AtomSelection | ||
| + | * Predicate | ||
| + | * Selectable | ||
| + | |||
=== Energetics === | === Energetics === | ||
| + | * CharmmAngleInteraction | ||
| + | * CharmmBondInteraction | ||
| + | * CharmmDihedralInteraction | ||
| + | * CharmmElectrostaticInteraction | ||
| + | * CharmmEnergy | ||
| + | * CharmmImproperInteraction | ||
| + | * CharmmParameterReader | ||
| + | * CharmmSystemBuilder | ||
| + | * CharmmTopologyReader | ||
| + | * CharmmTopologyResidue | ||
| + | * CharmmUreyBradleyInteraction | ||
| + | * CharmmVdwInteraction | ||
| + | * EnergySet | ||
| + | * EnergeticAnalysis | ||
| + | * Interaction | ||
| + | * PairwiseEnergyCalculator | ||
| + | |||
| + | === SASA=== | ||
| + | * SasaAtom | ||
| + | * SasaCalculator | ||
| + | |||
| + | === Molecule I/O === | ||
| + | * File | ||
| + | * PDBFormat | ||
| + | * PDBReader | ||
| + | * PDBWriter | ||
| + | * Reader | ||
| + | * Writer | ||
| + | |||
| + | === Rotamer library management === | ||
| + | * RotamerLibrary | ||
| + | * RotamerLibraryReader | ||
| + | * RotamerLibraryWriter | ||
| + | |||
| + | |||
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* AtomAngleRelationship | * AtomAngleRelationship | ||
* AtomBondBuilder | * AtomBondBuilder | ||
| − | |||
* AtomDihedralRelationship | * AtomDihedralRelationship | ||
* AtomDistanceRelationship | * AtomDistanceRelationship | ||
* AtomGeometricRelationship | * AtomGeometricRelationship | ||
| − | |||
| − | |||
* AtomicPairwiseEnergy | * AtomicPairwiseEnergy | ||
* AtomPointerVector | * AtomPointerVector | ||
| − | |||
* BackRub | * BackRub | ||
* BBQTable | * BBQTable | ||
| Line 37: | Line 75: | ||
* BBQTableWriter | * BBQTableWriter | ||
* CartesianGeometry | * CartesianGeometry | ||
| − | |||
* CCD | * CCD | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
* ChiStatistics | * ChiStatistics | ||
* CoiledCoils | * CoiledCoils | ||
| Line 57: | Line 81: | ||
* CrystalLattice | * CrystalLattice | ||
* DeadEndElimination | * DeadEndElimination | ||
| − | |||
| − | |||
* Enumerator | * Enumerator | ||
* EnvironmentDatabase | * EnvironmentDatabase | ||
* EnvironmentDescriptor | * EnvironmentDescriptor | ||
| − | |||
* FourBodyInteraction | * FourBodyInteraction | ||
* Frame | * Frame | ||
| Line 73: | Line 94: | ||
* IcEntry | * IcEntry | ||
* IcTable | * IcTable | ||
| − | |||
* InterfaceResidueDescriptor | * InterfaceResidueDescriptor | ||
* LinearProgrammingOptimization | * LinearProgrammingOptimization | ||
| Line 86: | Line 106: | ||
* MslTools | * MslTools | ||
* OptionParser | * OptionParser | ||
| − | |||
| − | |||
* PDBFragments | * PDBFragments | ||
| − | |||
| − | |||
* PhiPsiReader | * PhiPsiReader | ||
* PhiPsiStatistics | * PhiPsiStatistics | ||
| Line 96: | Line 112: | ||
* <strike>Position</strike> | * <strike>Position</strike> | ||
* PotentialTable | * PotentialTable | ||
| − | |||
* PrincipleComponentAnalysis | * PrincipleComponentAnalysis | ||
* PSFReader | * PSFReader | ||
| Line 104: | Line 119: | ||
* RandomNumberGenerator | * RandomNumberGenerator | ||
* RandomSeqGenerator | * RandomSeqGenerator | ||
| − | |||
* Real | * Real | ||
* RegEx | * RegEx | ||
| − | |||
* ResiduePairTable | * ResiduePairTable | ||
* ResiduePairTableReader | * ResiduePairTableReader | ||
| Line 114: | Line 127: | ||
* ResidueSubstitutionTableReader | * ResidueSubstitutionTableReader | ||
* RotamerLibraryBuilder | * RotamerLibraryBuilder | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
* SelfPairManager | * SelfPairManager | ||
* SphericalPoint | * SphericalPoint | ||
| Line 125: | Line 132: | ||
* SurfaceSphere | * SurfaceSphere | ||
* Symmetry | * Symmetry | ||
| − | |||
* SystemRotamerLoader | * SystemRotamerLoader | ||
* TBDReader | * TBDReader | ||
* ThreeBodyInteraction | * ThreeBodyInteraction | ||
* Timer | * Timer | ||
| − | |||
* Tree | * Tree | ||
* triple | * triple | ||
| Line 138: | Line 143: | ||
* UserDefinedEnergySetBuilder | * UserDefinedEnergySetBuilder | ||
* UserDefinedInteraction | * UserDefinedInteraction | ||
| − | |||
Revision as of 22:03, 15 February 2010
Contents
MSL Documentation
Getting started
Examples of simple programs that illustrate how to use different features of the library are provided in the Tutorial.
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
- 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
- Transforms
Selection
- AtomSelection
- Predicate
- Selectable
Energetics
- CharmmAngleInteraction
- CharmmBondInteraction
- CharmmDihedralInteraction
- CharmmElectrostaticInteraction
- CharmmEnergy
- CharmmImproperInteraction
- CharmmParameterReader
- CharmmSystemBuilder
- CharmmTopologyReader
- CharmmTopologyResidue
- CharmmUreyBradleyInteraction
- CharmmVdwInteraction
- EnergySet
- EnergeticAnalysis
- Interaction
- PairwiseEnergyCalculator
SASA
- SasaAtom
- SasaCalculator
Molecule I/O
- File
- PDBFormat
- PDBReader
- PDBWriter
- Reader
- Writer
Rotamer library management
- RotamerLibrary
- RotamerLibraryReader
- RotamerLibraryWriter
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
- FourBodyInteraction
- 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
Position- PotentialTable
- PrincipleComponentAnalysis
- PSFReader
- PyMolVisualization
- Quaternion
- Quench
- RandomNumberGenerator
- RandomSeqGenerator
- Real
- RegEx
- ResiduePairTable
- ResiduePairTableReader
- ResidueSelection
- ResidueSubstitutionTable
- ResidueSubstitutionTableReader
- RotamerLibraryBuilder
- SelfPairManager
- SphericalPoint
- SurfaceAreaAndVolume
- SurfaceSphere
- Symmetry
- SystemRotamerLoader
- TBDReader
- ThreeBodyInteraction
- Timer
- Tree
- triple
- TwoBodyDistanceDependentPotentialTable
- TwoBodyInteraction
- UserDefinedEnergy
- UserDefinedEnergySetBuilder
- UserDefinedInteraction
