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SphericalBox Class Reference
[Components]

#import <SphericalBox.h>

Inheritance diagram for SphericalBox:

AdObject < AdSystemDataSource > < AdDataSourceDelegation > < AdGridDelegate > < AdMemento > < AdCreation > < AdEnvironmentObservation > < AdDynamicsDataSource > < AdBondedTopologyDataSource > < AdNonbondedTopologyDataSource >

List of all members.


Detailed Description

SphericalBox creates and manages a collection of molecules of a given type in a spherical volume. The type of molecule and its topology is defined by the dataSource which must conform to the AdSystemDataSource protocol. SphericalBox creates the collection by using an AdGrid instance to create a (cartesian) grid inside the volume. The number of molecules to be placed in the volume is calculated from the density parameter. Once the number of molecules is known SphericalBox replecates the information in its dataSource that many times and uses the grid points created by AdGrid as initial positions for the molecules. The molecules are randomly oriented when first placed.

SphericalBox conforms to AdSystemDataSource and forms the basis of solvent systems in Adun. Aswell as creating a solvent system it also provides methods that allow you to insert and extract other systems into/from the solvent volume eliminating and creating solvent molecules as necessary.

Todo:
We can refactor the non grid delegate parts to the superclass and then subclasses can just implement the grid delegate methods
Todo:
Move expandInterTable code to a function in Base
Todo:
Calculate the grid spacing correctly
Todo:
Provide a more complete initialiser: initWithEnvironment:density:dimensions
Bug:
Environment observation - variable dependants not updated
Bug:
Dependants dict not encoded - Have to decided wheather this is the correct mechanism for dependant variable updating.
Todo:
Check how changing the system radius, speacing density etc would work
Todo:
Check obscured molecule maintainence

Definition at line 67 of file SphericalBox.h.


Public Member Functions

(BOOL) - _checkMolecule:against:withExclusionRadius: [implementation]
(int *) - _chooseGridPoints [implementation]
(void) - _cleanUp [implementation]
(void) - _clearCurrentSystem [implementation]
(void) - _createGrid [implementation]
(InterTable *) - _expandTable:times:indexColumns: [implementation]
(void) - _fullDecode: [implementation]
(void) - _fullEncodeWithCoder: [implementation]
(void) - _initialiseDependants [implementation]
(void) - _mementoDecode: [implementation]
(void) - _mementoEncodeWithCoder: [implementation]
(void) - _placeMoleculesAtSites: [implementation]
(void) - _populateBox [implementation]
(void) - _randomlyOrientMolecules [implementation]
(void) - _retrieveBondedInteractions [implementation]
(void) - _retrieveCoordinates [implementation]
(void) - _retrieveNonbondedInteractions [implementation]
(void) - _setCurrentSystem [implementation]
(void) - _useEnvironmentDefaults [implementation]
(BOOL) - allowsTranslation [implementation]
(int) - atomsPerMolecule
(id) - captureState [implementation]
(void) - captureStateWithArchiver:key: [implementation]
(Vector3D *) - cavityCentre [implementation]
(NSArray *) - cavityExtremes [implementation]
(double) - cavityVolume [implementation]
(NSValue *) - coordinates
(id) - dataSource [implementation]
(void) - dealloc [implementation]
(void) - deregisterWithEnvironment [implementation]
(void) - encodeWithCoder: [implementation]
(BOOL) - handlesTranslation [implementation]
(void) - hideMoleculesWithIndexes: [implementation]
(id) - init [implementation]
(id) - initWithCoder: [implementation]
(id) - initWithEnvironment: [implementation]
(id) - initWithEnvironment:observe: [implementation]
(BOOL) - isPointInCavity: [implementation]
(int) - numberOccludedMolecules
(int) - numberOfAtoms
(NSValue *) - objectValueForAccelerations: [implementation]
(NSArray *) - objectValueForAtomTypes: [implementation]
(NSDictionary *) - objectValueForBondedInteractions: [implementation]
(NSValue *) - objectValueForCoordinates: [implementation]
(NSArray *) - objectValueForNonbondedInteractions: [implementation]
(NSDictionary *) - objectValueForNonbondedInteractionTypes: [implementation]
(NSValue *) - objectValueForVelocities: [implementation]
(BOOL) - observesEnvironment [implementation]
(void) - registerWithEnvironment [implementation]
(void) - reloadData [implementation]
(void) - returnToState: [implementation]
(id) - setCaptureMethod: [implementation]
(void) - setDataSource: [implementation]
(void) - setEnvironment: [implementation]
(void) - setExclusionPoints:exclusionRadius:
(void) - setObservesEnvironment: [implementation]
(void) - synchroniseWithEnvironment [implementation]
(NSString *) - systemName [implementation]
(void) - updateDependantsOfKey: [implementation]
(void) - updateForKey:value:object: [implementation]
(BOOL) - updateOnTranslation [implementation]

The documentation for this class was generated from the following files:

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