ChemCompt Class Reference

#include <ChemCompt.h>

Inheritance diagram for ChemCompt:

Collaboration diagram for ChemCompt:

Public Member Functions
	ChemCompt ()
virtual	~ChemCompt ()
double	getEntireVolume (const Eref &e) const
virtual double	vGetEntireVolume () const =0
void	setEntireVolume (const Eref &e, double volume)
double	getOneVoxelVolume (const Eref &e, unsigned int voxel) const
void	setOneVoxelVolume (const Eref &e, unsigned int voxel, double volume)
unsigned int	getDimensions () const
virtual unsigned int	innerGetDimensions () const =0
void	setMethod (string method)
string	getMethod () const
vector< double >	getStencilRate (unsigned int row) const
virtual vector< double >	innerGetStencilRate (unsigned int row) const =0
	Virtual func for getting stencil rates for the derived classes.
vector< unsigned int >	getStencilIndex (unsigned int row) const
vector< double >	getVoxelVolume () const
	Returns vector of all voxel volumes in compartment.
virtual const vector< double > &	vGetVoxelVolume () const =0
	Virtual func so that derived classes can pass voxel volume back.
vector< double >	getVoxelMidpoint () const
	Returns vector of all voxel midpoints in compartment.
virtual const vector< double > &	vGetVoxelMidpoint () const =0
	Virtual func so that derived classes can return voxel midpoint.
void	setVolumeNotRates (double volume)
virtual bool	vSetVolumeNotRates (double volume)=0
	Virtual function for actually doing this.
void	buildDefaultMesh (const Eref &e, double volume, unsigned int numEntries)
virtual void	innerBuildDefaultMesh (const Eref &e, double volume, unsigned int numEntries)=0
void	handleNodeInfo (const Eref &e, unsigned int numNodes, unsigned int numThreads)
virtual void	innerHandleNodeInfo (const Eref &e, unsigned int numNodes, unsigned int numThreads)=0
void	resetStencil ()
virtual void	innerResetStencil ()=0
unsigned int	getNumEntries () const
virtual unsigned int	innerGetNumEntries () const =0
void	setNumEntries (unsigned int num)
virtual void	innerSetNumEntries (unsigned int n)=0
MeshEntry *	lookupEntry (unsigned int index)
void	getChildConcs (const Eref &e, vector< double > &childConcs) const
unsigned int	setChildConcs (const Eref &e, const vector< double > &childConcs, unsigned int start) const
void	buildJunction (ChemCompt *other, vector< VoxelJunction > &ret)
virtual void	matchMeshEntries (const ChemCompt *other, vector< VoxelJunction > &ret) const =0
virtual double	nearest (double x, double y, double z, unsigned int &index) const =0
virtual void	indexToSpace (unsigned int index, double &x, double &y, double &z) const =0
void	flipRet (vector< VoxelJunction > &ret) const
	Utility function for swapping first and second in VoxelJunctions.
virtual unsigned int	getMeshType (unsigned int fid) const =0
virtual unsigned int	getMeshDimensions (unsigned int fid) const =0
	Virtual function to return dimensions of specified entry.
virtual double	getMeshEntryVolume (unsigned int fid) const =0
	Virtual function to return volume of mesh Entry.
virtual void	setMeshEntryVolume (unsigned int fid, double volume)
virtual vector< double >	getCoordinates (unsigned int fid) const =0
	Virtual function to return coords of mesh Entry.
virtual vector< unsigned int >	getNeighbors (unsigned int fid) const =0
	Virtual function to return info on Entries connected to this one.
virtual vector< double >	getDiffusionArea (unsigned int fid) const =0
	Virtual function to return diffusion X-section area per neighbor.
virtual vector< double >	getDiffusionScaling (unsigned int fid) const =0
	Virtual function to return scale factor for diffusion. 1 here.
virtual double	extendedMeshEntryVolume (unsigned int fid) const =0
	Volume of mesh Entry including abutting diff-coupled voxels.
virtual void	clearExtendedMeshEntryVolume ()=0
	clear out extended mesh entries for rebuilding.
virtual unsigned int	getStencilRow (unsigned int meshIndex, const double entry, const unsigned int colIndex) const =0
virtual void	extendStencil (const ChemCompt *other, const vector< VoxelJunction > &vj)=0
Static Public Member Functions
static double	distance (double x, double y, double z)
static SrcFinfo1< vector < double > > *	voxelVolOut ()
static const Cinfo *	initCinfo ()

Detailed Description

The ChemCompt represents a chemically identified compartment. This may be spatially extended, and may even be discontinuous. The same set of reactions and molecules populates any given compartment. Examples of compartments might be: nucleus, cell membrane, early endosomes, spine heads. Connects to one or more 'Geometry' elements to define its boundaries.

Constructor & Destructor Documentation

ChemCompt::ChemCompt ( )

ChemCompt::~ChemCompt ( ) [virtual]

Member Function Documentation

void ChemCompt::buildDefaultMesh	(	const Eref &	e,
		double	volume,
		unsigned int	numEntries
	)

buildDefaultMesh tells the ChemCompt to make a standard mesh partitioning with the specified total volume and the specified number of subdivisions. For example, a CubeMesh of volume 8 and subdivisions 8 would make a 2x2x2 mesh. This function is specialized in each derived class.

References innerBuildDefaultMesh().

Referenced by initCinfo().

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void ChemCompt::buildJunction	(	ChemCompt *	other,
		vector< VoxelJunction > &	ret
	)

Wrapper function to buld junction between two meshes, and to extend the meshes so that their stencils also handle update to the voxels abutting the boundary on the neighbor mesh.

virtual void ChemCompt::clearExtendedMeshEntryVolume ( ) [pure virtual]

clear out extended mesh entries for rebuilding.

Implemented in MeshCompt.

double ChemCompt::distance	(	double	x,
		double	y,
		double	z
	)			`[static]`

Referenced by CylMesh::nearest(), and CubeMesh::nearest().

virtual double ChemCompt::extendedMeshEntryVolume ( unsigned int fid ) const [pure virtual]

Volume of mesh Entry including abutting diff-coupled voxels.

Implemented in CubeMesh, CylMesh, MeshCompt, NeuroMesh, PsdMesh, and SpineMesh.

virtual void ChemCompt::extendStencil	(	const ChemCompt *	other,
		const vector< VoxelJunction > &	vj
	)			`[pure virtual]`

Function to add voxels for boundaries. This is done so that the solver can do reaction-diffusion computations on the entire mesh including voxels of neighboring solvers abutting the boundary. It uses these to stitch together the computations that span multiple solvers and compartments.

void ChemCompt::flipRet ( vector< VoxelJunction > & ret ) const

Utility function for swapping first and second in VoxelJunctions.

void ChemCompt::getChildConcs	(	const Eref &	e,
		vector< double > &	childConcs
	)			const

Recursively traverses all children, depth_first, scooping up concentration terms: conc and concInit for pools, Kf and Kb for Reacs, and Km for enzymes. These are inserted in order into the vector of childConcs. Does not traverse into children of other ChemCompts

Referenced by CylMesh::setDiffLength(), setEntireVolume(), CylMesh::setR0(), CylMesh::setR1(), CylMesh::setX0(), CylMesh::setX1(), CylMesh::setY0(), CylMesh::setY1(), CylMesh::setZ0(), and CylMesh::setZ1().

virtual vector< double > ChemCompt::getCoordinates ( unsigned int fid ) const [pure virtual]

Virtual function to return coords of mesh Entry.

Implemented in CubeMesh, CylMesh, NeuroMesh, PsdMesh, and SpineMesh.

Referenced by MeshEntry::getCoordinates().

virtual vector< double > ChemCompt::getDiffusionArea ( unsigned int fid ) const [pure virtual]

Virtual function to return diffusion X-section area per neighbor.

Implemented in CubeMesh, CylMesh, NeuroMesh, PsdMesh, and SpineMesh.

Referenced by MeshEntry::getDiffusionArea().

virtual vector< double > ChemCompt::getDiffusionScaling ( unsigned int fid ) const [pure virtual]

Virtual function to return scale factor for diffusion. 1 here.

Implemented in CubeMesh, CylMesh, NeuroMesh, PsdMesh, and SpineMesh.

Referenced by MeshEntry::getDiffusionScaling().

unsigned int ChemCompt::getDimensions ( ) const

Returns # of dimensions of mesh. This is 3 for cube, and 1 for cylinder or neurons.

References innerGetDimensions().

Referenced by initCinfo(), testCubeMesh(), and testCubeMeshExtendStencil().

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double ChemCompt::getEntireVolume ( const Eref & e ) const

Returns volume, area, or length of compartment, depending on dimensionality.

References vGetEntireVolume().

Referenced by initCinfo().

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virtual unsigned int ChemCompt::getMeshDimensions ( unsigned int fid ) const [pure virtual]

Virtual function to return dimensions of specified entry.

Implemented in CubeMesh, CylMesh, NeuroMesh, PsdMesh, and SpineMesh.

Referenced by MeshEntry::getDimensions().

virtual double ChemCompt::getMeshEntryVolume ( unsigned int fid ) const [pure virtual]

Virtual function to return volume of mesh Entry.

Implemented in CubeMesh, CylMesh, NeuroMesh, PsdMesh, and SpineMesh.

Referenced by getOneVoxelVolume(), and MeshEntry::getVolume().

virtual unsigned int ChemCompt::getMeshType ( unsigned int fid ) const [pure virtual]

Virtual function to return MeshType of specified entry.

Implemented in CubeMesh, CylMesh, NeuroMesh, PsdMesh, and SpineMesh.

Referenced by MeshEntry::getMeshType().

string ChemCompt::getMethod ( ) const

virtual vector< unsigned int > ChemCompt::getNeighbors ( unsigned int fid ) const [pure virtual]

Virtual function to return info on Entries connected to this one.

Implemented in MeshCompt.

Referenced by MeshEntry::getNeighbors(), and getStencilIndex().

unsigned int ChemCompt::getNumEntries ( ) const

Returns the number of MeshEntries on this ChemCompt

References innerGetNumEntries().

Referenced by initCinfo().

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double ChemCompt::getOneVoxelVolume	(	const Eref &	e,
		unsigned int	voxel
	)			const

Returns volume of specified voxel

References getMeshEntryVolume().

Referenced by initCinfo().

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vector< unsigned int > ChemCompt::getStencilIndex ( unsigned int row ) const

Function to return the stencil indices used in the diffusion calculations for voxelized compartments. Refers to the getNeighbors virtual function.

References getNeighbors().

Referenced by initCinfo().

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vector< double > ChemCompt::getStencilRate ( unsigned int row ) const

Function to return the stencil values used in the diffusion calculations for voxelized compartments.

References innerGetStencilRate().

Referenced by initCinfo().

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virtual unsigned int ChemCompt::getStencilRow	(	unsigned int	meshIndex,
		const double **	entry,
		const unsigned int **	colIndex
	)			const `[pure virtual]`

Function to look up scale factor derived from area and length of compartment junction, for all the mesh entries connected to the specified one. Modeled on equivalent function in SparseMatrix. meshIndex: index of reference mesh entry entry: array of values of scale factor colIndex: array of relative indices for each entry. The values returned here are the offset from the meshIndex. Returns number of entries and colIndexes. For a 1-D mesh, there will be 2 except at boundaries For a 2-D mesh, there will be 4 except at boundaries For a 3-D mesh, there will be 6 except at boundaries For a neuromesh, there will be a variable number depending on branching. For a CylMesh there are 2 except at boundaries.

Implemented in MeshCompt.

vector< double > ChemCompt::getVoxelMidpoint ( ) const

Returns vector of all voxel midpoints in compartment.

References vGetVoxelMidpoint().

Referenced by initCinfo().

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vector< double > ChemCompt::getVoxelVolume ( ) const

Returns vector of all voxel volumes in compartment.

References vGetVoxelVolume().

Referenced by initCinfo().

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void ChemCompt::handleNodeInfo	(	const Eref &	e,
		unsigned int	numNodes,
		unsigned int	numThreads
	)

References innerHandleNodeInfo().

Referenced by initCinfo().

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virtual void ChemCompt::indexToSpace	(	unsigned int	index,
		double &	x,
		double &	y,
		double &	z
	)			const `[pure virtual]`

Converts specified index to xyz coords of middle of voxel Values out of range return original xyz

Implemented in CubeMesh, CylMesh, NeuroMesh, PsdMesh, and SpineMesh.

const Cinfo * ChemCompt::initCinfo ( ) [static]

Reimplemented in CubeMesh, CylMesh, NeuroMesh, PsdMesh, and SpineMesh.

References buildDefaultMesh(), getDimensions(), getEntireVolume(), getNumEntries(), getOneVoxelVolume(), getStencilIndex(), getStencilRate(), getVoxelMidpoint(), getVoxelVolume(), handleNodeInfo(), Neutral::initCinfo(), MeshEntry::initCinfo(), lookupEntry(), resetStencil(), setEntireVolume(), setNumEntries(), setOneVoxelVolume(), setVolumeNotRates(), and voxelVolOut().

Referenced by SpineMesh::initCinfo(), PsdMesh::initCinfo(), NeuroMesh::initCinfo(), CylMesh::initCinfo(), and CubeMesh::initCinfo().

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virtual void ChemCompt::innerBuildDefaultMesh	(	const Eref &	e,
		double	volume,
		unsigned int	numEntries
	)			`[pure virtual]`

Implemented in CubeMesh, CylMesh, NeuroMesh, PsdMesh, and SpineMesh.

Referenced by buildDefaultMesh().

virtual unsigned int ChemCompt::innerGetDimensions ( ) const [pure virtual]

Implemented in CubeMesh, CylMesh, NeuroMesh, PsdMesh, and SpineMesh.

Referenced by getDimensions().

virtual unsigned int ChemCompt::innerGetNumEntries ( ) const [pure virtual]

Implemented in CubeMesh, CylMesh, NeuroMesh, PsdMesh, and SpineMesh.

Referenced by getNumEntries().

virtual vector< double > ChemCompt::innerGetStencilRate ( unsigned int row ) const [pure virtual]

Virtual func for getting stencil rates for the derived classes.

Implemented in MeshCompt.

Referenced by getStencilRate().

virtual void ChemCompt::innerHandleNodeInfo	(	const Eref &	e,
		unsigned int	numNodes,
		unsigned int	numThreads
	)			`[pure virtual]`

Implemented in CubeMesh, CylMesh, NeuroMesh, PsdMesh, and SpineMesh.

Referenced by handleNodeInfo().

virtual void ChemCompt::innerResetStencil ( ) [pure virtual]

Implemented in MeshCompt.

Referenced by resetStencil().

virtual void ChemCompt::innerSetNumEntries ( unsigned int n ) [pure virtual]

Implemented in CubeMesh, CylMesh, NeuroMesh, PsdMesh, and SpineMesh.

Referenced by setNumEntries().

MeshEntry * ChemCompt::lookupEntry ( unsigned int index )

Returns the matched lookupEntry

Referenced by initCinfo().

virtual void ChemCompt::matchMeshEntries	(	const ChemCompt *	other,
		vector< VoxelJunction > &	ret
	)			const `[pure virtual]`

Returns the meshIndices (NOT spatial indices) of all adjacent mesh entry pairs on ether side of the (self, other) junction. meshIndices are the indices that look up entries in the vector of pools. spatialIndices are (iz * ny + iy) * nx + ix, that is, a linear conversion of cartesian spatial indices. So, for two touching cubes, the return vector is the paired meshIndices on either side of the plane of contact. If one mesh has a finer mesh than the other, or if there are more than one contact points from self to other (for example, at a corner), then we just have multiple pairs using the same meshIndex of the repeated voxel.

virtual double ChemCompt::nearest	(	double	x,
		double	y,
		double	z,
		unsigned int &	index
	)			const `[pure virtual]`

Returns distance and index of nearest mesh entry. Computes each mesh entry position as its geometric centre. If the current location is not inside a valid mesh entry, distance returned is negative.

Implemented in CubeMesh, CylMesh, NeuroMesh, PsdMesh, and SpineMesh.

void ChemCompt::resetStencil ( )

Reset stencil m_ to coreStencil_. This is needed as a prelude to rebuilding the junctions using extendStencil.

References innerResetStencil().

Referenced by initCinfo().

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unsigned int ChemCompt::setChildConcs	(	const Eref &	e,
		const vector< double > &	childConcs,
		unsigned int	start
	)			const

Recursively traverses all children, depth_first, restoring concentration terms as scooped up by getChildConcs. Does conc and concInit for pools, Kf and Kb for Reacs, and Km for enzymes. These are restored in order into the vector of childConcs. Does not traverse into children of other ChemCompts.

Referenced by setEntireVolume().

void ChemCompt::setEntireVolume	(	const Eref &	e,
		double	volume
	)

This is a little nasty. It calls buildDefaultMesh with the current numEntries. Should not be used if the mesh has been changed to something more interesting. Perhaps I need to do something like changeVolOfExistingMesh.

References Eref::dataIndex(), Eref::element(), getChildConcs(), Element::getMsgTargets(), setChildConcs(), vGetVoxelVolume(), voxelVolOut(), and vSetVolumeNotRates().

Referenced by initCinfo().

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void ChemCompt::setMeshEntryVolume	(	unsigned int	fid,
		double	volume
	)			`[virtual]`

Virtual function to assign volume of mesh Entry. Does nothing in most cases, but is operational in SpineMesh and PsdMesh.

Reimplemented in PsdMesh, and SpineMesh.

Referenced by setOneVoxelVolume().

void ChemCompt::setMethod ( string method )

Hint to system indicating method to be used on this compartment. Defaults to blank, which then leaves the decision to the calling function. Doesn't do anything unless the ChemCompt is parsed by the SimManager.

void ChemCompt::setNumEntries ( unsigned int num )

Dummy function. The numEntries is only set by other functions that define compartment decomposition.

References innerSetNumEntries().

Referenced by initCinfo().

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void ChemCompt::setOneVoxelVolume	(	const Eref &	e,
		unsigned int	voxel,
		double	volume
	)

References setMeshEntryVolume().

Referenced by initCinfo().

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void ChemCompt::setVolumeNotRates ( double volume )

Returns true on success. Changes volume but does not notify any child objects. For some classes, this only works if the ChemCompt has just one voxel. It will return false if it can't handle it. This function will invalidate any concentration term in the model. If you don't know why you would want to do this, then you shouldn't use this function.,

References vSetVolumeNotRates().

Referenced by initCinfo().

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