MSL Objects - Revision history

Senes at 19:15, 16 March 2010

2010-03-16T19:15:40Z

Senes: /* Molecular representation objects */

2010-02-18T02:23:52Z

‎Molecular representation objects

Senes at 00:57, 18 February 2010

2010-02-18T00:57:25Z

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Senes at 15:42, 16 February 2010

2010-02-16T15:42:12Z

Senes: Created page with 'MSL Objects === Molecular representation objects === * The '''AtomContainer''': a simple, light containers for the molecules represented…'

2010-02-16T15:41:58Z

Created page with '<big>MSL Objects</big> === Molecular representation objects === * The '''AtomContainer''': a simple, light containers for the molecules represented…'

New page

<big>MSL Objects</big>

=== 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:System|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 '''[[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:Residue|Residue]]''': a specific residue type (i.e. "ALA", "LEU"), also referred as "identity". It contains '''AtomGroups'''. The AtomGroup contains '''Atom''' objects.
***** The '''[[MSL Objects:AtomGroup|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 '''[[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

=== 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
* <strike>Position</strike>
* 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

@@ Line 13: / Line 13: @@
 ****** 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
 === Geometry ===
@@ Line 28: / Line 29: @@
 * '''[[MSL Objects:CharmmDihedralInteraction|CharmmDihedralInteraction]]'''
 * '''[[MSL Objects:CharmmElectrostaticInteraction|CharmmElectrostaticInteraction]]'''
 * '''[[MSL Objects:CharmmEnergy|CharmmEnergy]]'''
 * '''[[MSL Objects:CharmmImproperInteraction|CharmmImproperInteraction]]'''
@@ Line 38: / Line 42: @@
 * '''[[MSL Objects:EnergySet|EnergySet]]'''
 * '''[[MSL Objects:EnergeticAnalysis|EnergeticAnalysis]]'''
 * '''[[MSL Objects:Interaction|Interaction]]'''
 * '''[[MSL Objects:PairwiseEnergyCalculator|PairwiseEnergyCalculator]]'''
 === SASA===
@@ Line 84: / Line 92: @@
 * '''[[MSL Objects:EnvironmentDatabase|EnvironmentDatabase]]'''
 * '''[[MSL Objects:EnvironmentDescriptor|EnvironmentDescriptor]]'''
 * '''[[MSL Objects:Frame|Frame]]'''
 * '''[[MSL Objects:GSLMinimizer|GSLMinimizer]]'''
@@ Line 133: / Line 140: @@
 * '''[[MSL Objects:SystemRotamerLoader|SystemRotamerLoader]]'''
 * '''[[MSL Objects:TBDReader|TBDReader]]'''
 * '''[[MSL Objects:Timer|Timer]]'''
 * '''[[MSL Objects:Tree|Tree]]'''
 * '''[[MSL Objects:triple|triple]]'''
 * '''[[MSL Objects:TwoBodyDistanceDependentPotentialTable|TwoBodyDistanceDependentPotentialTable]]'''
 * '''[[MSL Objects:UserDefinedEnergy|UserDefinedEnergy]]'''
 * '''[[MSL Objects:UserDefinedEnergySetBuilder|UserDefinedEnergySetBuilder]]'''
 * '''[[MSL Objects:UserDefinedInteraction|UserDefinedInteraction]]'''

← Older revision		Revision as of 15:42, 16 February 2010
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−	~~<big>MSL Objects</big>~~	+

	=== Molecular representation objects ===		=== Molecular representation objects ===

@@ Line 1: / Line 1: @@
 === Molecular representation objects ===
-* The '''[[MSL Objects:AtomContainer|AtomContainer]]''': a simple, light containers for the molecules represented internally just as an array of '''Atom''' objects.
+MSL contains two object for representing a macromolecule: the '''AtomContainer''' and the '''System'''.
-* The '''[[MSL Objects:System|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 '''[[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.