CompoundSystem Class Reference

Derived class of MolecularMechanicsSystem that knows how to model molmodel Compounds. More...

#include <CompoundSystem.h>

Inheritance diagram for CompoundSystem:

List of all members.

Public Member Functions
	SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE (CompoundSystem, CompoundIndex)
	Compound::Index type is an integer index into subcompounds of a Compound.
	CompoundSystem ()
	default constructor
	~CompoundSystem ()
	destructor
void	adoptCompound (Compound &child, const Transform &compoundTransform=Transform())
	Install a new Compound into this system.
void	modelCompounds ()
	Instantiate simbody MobilizedBodies representing the adopted Compounds.
size_t	getNumCompounds () const
const Compound &	getCompound (CompoundIndex i) const
Compound &	updCompound (CompoundIndex i)

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Detailed Description

Derived class of MolecularMechanicsSystem that knows how to model molmodel Compounds.

Todo:

merge this class with MolecularMechanicsSystem

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Constructor & Destructor Documentation

CompoundSystem

(

)

[inline]

default constructor

~CompoundSystem

(

)

[inline]

destructor

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Member Function Documentation

void adoptCompound	(	Compound &	child,
		const Transform &	compoundTransform = Transform()
	)			[inline]

Install a new Compound into this system.

We take over ownership of the Compound's representation from the given handle, leaving that handle as a reference to our new Compound. It is an error if the given handle wasn't the owner of the Compound.

Parameters:

	child	Compound to be incorporated
	compoundTransform	location and orientation of the Compound

References PIMPLHandle< HANDLE, IMPL, PTR >::disown(), Compound::getTopLevelTransform(), Compound::setMultibodySystem(), and Compound::setTopLevelTransform().

Referenced by LigandDroplet::LigandDroplet(), Protein::Protein(), and WaterDroplet::WaterDroplet().

const Compound& getCompound

(

CompoundIndex

i

)

const [inline]

Returns:

read-only reference to an adopted Compound

Parameters:

i

integer index of Compound

Referenced by PeriodicPdbWriter::handleEvent().

size_t getNumCompounds

(

)

const [inline]

Returns:

number of top-level Compounds adopted by this CompoundSystem

Referenced by PeriodicPdbWriter::handleEvent(), LigandDroplet::LigandDroplet(), and WaterDroplet::WaterDroplet().

void modelCompounds

(

)

Instantiate simbody MobilizedBodies representing the adopted Compounds.

SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE	(	CompoundSystem	,
		CompoundIndex
	)

Compound::Index type is an integer index into subcompounds of a Compound.

It is NOT instrinsic to the subcompound, but represents the relationship between a subcompound and precisely one of its parent compounds.

Compound& updCompound

(

CompoundIndex

i

)

[inline]

Returns:

mutable reference to an adopted Compound

Parameters:

i

integer index of Compound

Referenced by LigandDroplet::LigandDroplet(), and WaterDroplet::WaterDroplet().

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

• CompoundSystem.h