Difference between revisions of "Documentation"
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Revision as of 17:13, 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
Energetics
To be classified
- Atom3DGrid
- AtomAngleRelationship
- AtomBondBuilder
AtomContainer- AtomDihedralRelationship
- AtomDistanceRelationship
- AtomGeometricRelationship
- AtomGroup
Atom- AtomicPairwiseEnergy
- AtomPointerVector
- AtomSelection
- BackRub
- BBQTable
- BBQTableReader
- BBQTableWriter
- CartesianGeometry
CartesianPoint- CCD
Chain- CharmmAngleInteraction
- CharmmBondInteraction
- CharmmDihedralInteraction
- CharmmElectrostaticInteraction
- CharmmEnergy
- CharmmImproperInteraction
- CharmmParameterReader
- CharmmSystemBuilder
- CharmmTopologyReader
- CharmmTopologyResidue
- CharmmUreyBradleyInteraction
- CharmmVdwInteraction
- ChiStatistics
- CoiledCoils
- CoordAxes
- CrystalLattice
- DeadEndElimination
- EnergeticAnalysis
- EnergySet
- Enumerator
- EnvironmentDatabase
- EnvironmentDescriptor
- File
- FourBodyInteraction
- Frame
- GSLMinimizer
- Hash
- HBond_LJGaussianInteraction
- Helanal
- HelixFusion
- HelixGenerator
- IcEntry
- IcTable
- Interaction
- InterfaceResidueDescriptor
- LinearProgrammingOptimization
- Line
- LogicalParser
- Matrix
- MIDReader
- Minimizer
- MoleculeInterfaceDatabase
- MonteCarloOptimization
- MslExceptions
- MslTools
- OptionParser
- PairwiseEnergyCalculator
- PDBFormat
- PDBFragments
- PDBReader
- PDBWriter
- PhiPsiReader
- PhiPsiStatistics
- PolymerSequence
Position- PotentialTable
- Predicate
- PrincipleComponentAnalysis
- PSFReader
- PyMolVisualization
- Quaternion
- Quench
- RandomNumberGenerator
- RandomSeqGenerator
- Reader
- Real
- RegEx
Residue- ResiduePairTable
- ResiduePairTableReader
- ResidueSelection
- ResidueSubstitutionTable
- ResidueSubstitutionTableReader
- RotamerLibraryBuilder
- RotamerLibrary
- RotamerLibraryReader
- RotamerLibraryWriter
- SasaAtom
- SasaCalculator
- Selectable
- SelfPairManager
- SphericalPoint
- SurfaceAreaAndVolume
- SurfaceSphere
- Symmetry
System- SystemRotamerLoader
- TBDReader
- ThreeBodyInteraction
- Timer
- Transforms
- Tree
- triple
- TwoBodyDistanceDependentPotentialTable
- TwoBodyInteraction
- UserDefinedEnergy
- UserDefinedEnergySetBuilder
- UserDefinedInteraction
- Writer
