Stoich Class Reference

#include <Stoich.h>

Collaboration diagram for Stoich:

Public Member Functions
	Stoich ()
	~Stoich ()
void	setOneWay (bool v)
bool	getOneWay () const
unsigned int	getNumVarPools () const
	Returns number of local pools that are updated by solver.
unsigned int	getNumBufPools () const
	Returns number of local buffered pools.
unsigned int	getNumAllPools () const
unsigned int	getNumProxyPools () const
vector< unsigned int >	getPoolIdMap () const
void	setPath (const Eref &e, string path)
string	getPath (const Eref &e) const
void	setKsolve (Id v)
	assigns kinetic solver: Ksovle or GSSAsolve.
Id	getKsolve () const
void	setDsolve (Id v)
	assigns diffusion solver: Dsovle or a Gillespie voxel stepper
Id	getDsolve () const
void	setCompartment (Id v)
	assigns compartment occupied by Stoich.
Id	getCompartment () const
unsigned int	getNumRates () const
unsigned int	getNumCoreRates () const
const RateTerm *	rates (unsigned int i) const
	Utility function to return a rates_ entry.
const vector< RateTerm * > &	getRateTerms () const
	Returns a reference to the entire rates_ vector.
unsigned int	getNumFuncs () const
const FuncTerm *	funcs (unsigned int i) const
vector< int >	getMatrixEntry () const
vector< unsigned int >	getColIndex () const
vector< unsigned int >	getRowStart () const
vector< Id >	getProxyPools (Id i) const
int	getStatus () const
void	setElist (const Eref &e, const vector< ObjId > &elist)
void	locateOffSolverReacs (Id myCompt, vector< Id > &elist)
void	allocateObjMap (const vector< Id > &elist)
void	resizeArrays ()
	Using the computed array sizes, now allocate space for them.
void	allocateModelObject (Id id, vector< Id > &bufPools)
	Identifies and allocates objects in the Stoich.
void	allocateModel (const vector< Id > &elist)
	Calculate sizes of all arrays, and allocate them.
void	convertRatesToStochasticForm ()
void	buildXreacs (const Eref &e, Id otherStoich)
void	filterXreacs ()
void	scaleBufsAndRates (unsigned int index, double volScale)
	Used to handle run-time size updates for spines.
void	comptsOnCrossReacTerms (vector< pair< Id, Id > > &xr) const
void	setupCrossSolverReacVols () const
void	zombifyModel (const Eref &e, const vector< Id > &elist)
void	unZombifyModel ()
void	unZombifyPools ()
	unZombifies Pools. Helper for unZombifyModel.
void	zombifyChemCompt (Id compt)
unsigned int	convertIdToReacIndex (Id id) const
unsigned int	convertIdToPoolIndex (Id id) const
unsigned int	convertIdToFuncIndex (Id id) const
ZeroOrder *	makeHalfReaction (double rate, const vector< Id > &reactants)
	Utility function to make a half reac and return the rate term.
void	installReaction (Id reacId, const vector< Id > &subs, const vector< Id > &prds)
unsigned int	innerInstallReaction (Id reacId, const vector< Id > &subs, const vector< Id > &prds)
void	installMMenz (Id enzId, const vector< Id > &enzMolId, const vector< Id > &subs, const vector< Id > &prds)
void	installMMenz (MMEnzymeBase *meb, unsigned int rateIndex, const vector< Id > &subs, const vector< Id > &prds)
void	installEnzyme (Id enzId, Id enzMolId, Id cplxId, const vector< Id > &subs, const vector< Id > &prds)
void	installEnzyme (ZeroOrder r1, ZeroOrder r2, ZeroOrder *r3, Id enzId, Id enzMolId, const vector< Id > &prds)
void	installDummyEnzyme (Id enzId, Id enzMolId)
	This is used when the enzyme lacks sub or prd.
void	installAndUnschedFunc (Id func, Id pool)
void	installAndUnschedFuncRate (Id func, Id pool)
void	installAndUnschedFuncReac (Id func, Id reac)
unsigned int	getSpecies (unsigned int poolIndex) const
void	setSpecies (unsigned int poolIndex, unsigned int s)
void	setReacKf (const Eref &e, double v) const
void	setReacKb (const Eref &e, double v) const
void	setMMenzKm (const Eref &e, double v) const
double	getMMenzNumKm (const Eref &e) const
void	setMMenzKcat (const Eref &e, double v) const
double	getMMenzKcat (const Eref &e) const
void	setEnzK1 (const Eref &e, double v) const
	Later handle all the volumes when this conversion is done.
double	getEnzNumK1 (const Eref &e) const
void	setEnzK2 (const Eref &e, double v) const
	Set rate k2 (1/sec) for enzyme.
double	getEnzK2 (const Eref &e) const
	Get rate k2 (1/sec) for enzyme.
void	setEnzK3 (const Eref &e, double v) const
	Set rate k3 (1/sec) for enzyme.
double	getEnzK3 (const Eref &e) const
	Get rate k3, aka kcat, for enzyme.
double	getR1 (const Eref &e) const
double	getR1offset1 (const Eref &e) const
double	getR1offset2 (const Eref &e) const
double	getR2 (const Eref &e) const
void	setFunctionExpr (const Eref &e, string expr)
void	updateRatesAfterRemesh ()
void	print () const
	Utility function, prints out N_, used for debugging.
void	printRates () const
	Another utility function, prints out all Kf, kf, Kb, kb.
void	updateReacVelocities (const double *s, vector< double > &vel, unsigned int volIndex) const
void	updateFuncs (double *s, double t) const
	Updates the function values, within s.
const KinSparseMatrix &	getStoichiometryMatrix () const
	Updates the rates for cross-compartment reactions.
const vector< Id > &	getOffSolverPools () const
vector< Id >	getOffSolverCompts () const
const vector< Id > &	offSolverPoolMap (Id compt) const
Static Public Member Functions
static const Cinfo *	initCinfo ()
Static Public Attributes
static const unsigned int	PoolIsNotOnSolver
Protected Attributes
bool	useOneWay_
string	path_
Id	ksolve_
	This contains the Id of the Kinetic solver.
Id	dsolve_
	This contains the Id of the Diffusion solver. Optional.
Id	compartment_
	Contains Id of compartment holding reac system. Optional.
ZombiePoolInterface *	kinterface_
	Pointer for ksolve.
ZombiePoolInterface *	dinterface_
	Pointer for dsolve.
vector< unsigned int >	species_
vector< RateTerm * >	rates_
unsigned int	numVoxels_
	Number of voxels in reac system.
vector< FuncTerm * >	funcs_
	The FuncTerms handle mathematical ops on mol levels.
KinSparseMatrix	N_
	N_ is the stoichiometry matrix.
vector< unsigned int >	objMap_
unsigned int	objMapStart_
vector< Id >	idMap_
vector< Id >	reacMap_
vector< Id >	enzMap_
vector< Id >	mmEnzMap_
vector< Id >	funcMap_
unsigned int	numVarPools_
unsigned int	numBufPools_
unsigned int	numFunctions_
unsigned int	numReac_
int	status_
vector< Id >	offSolverPools_
map< Id, vector< Id > >	offSolverPoolMap_
vector< Id >	offSolverReacs_
vector< pair< Id, Id > >	offSolverReacCompts_
vector< vector< Id > >	subComptVec_
vector< vector< Id > >	prdComptVec_

Detailed Description

Stoich is the class that handles the stoichiometry matrix for a reaction system, and also setting up the computations for reaction rates. It has to coordinate the operation of a number of model definition classes, most importantly: Pools, Reacs and Enz(yme)s. It also coordinates the setup of a large number of numerical solution engines, or solvers: Ksolve, Gsolve, Dsolve, and SteadyState. The setup process has to follow a tight order, most of which is internally manged by the Stoich. The Stoich itself does not do any 'process' functions. It just sets up data structures for the other objects that do the crunching.

1. Compartment is set up to a cell (neuroMesh) or volume (other meshes) 2. Compartment assigned to Stoich. Here it assigns unique vols. 3. Dsolve and Ksolve assigned to Stoich using setKsolve and setDsolve. 3.1 At this point the Stoich::useOneWay_ flag is set if it is a Gsolve. 4. Call Stoich::setPath. All the rest happens internally, done by Stoich: 4.1 assign compartment to Dsolve and Ksolve. 4.2 assign numPools and compts to Dsolve and Ksolve. 4.3 During Zombification, zeroth vector< RateTerm* > is built. 4.4 afterZombification, stoich builds rateTerm vector for all vols. 4.5 Stoich assigns itself to Dsolve and Ksolve.

Ksolve sets up volIndex on each VoxelPool
Dsolve gets vector of pools, extracts DiffConst and MotorConst 4.6 Dsolve assigned to Ksolve::dsolve_ field by the Stoich. 5. Reinit, 5.1 Dsolve builds matrix, provided dt has changed. It needs dt. 5.2 Ksolve builds solvers if not done already, assigning initDt

As seen by the user, this reduces to just 4 stages:

Make the objects.
Assign compartment, Ksolve and Dsolve to stoich.
Set the stoich path.
Reinit.

Constructor & Destructor Documentation

Stoich::Stoich ( )

Stoich::~Stoich ( )

References funcs_, rates_, and unZombifyModel().

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Member Function Documentation

void Stoich::allocateModel ( const vector< Id > & elist )

Calculate sizes of all arrays, and allocate them.

void Stoich::allocateModelObject	(	Id	id,
		vector< Id > &	bufPools
	)

Identifies and allocates objects in the Stoich.

void Stoich::allocateObjMap ( const vector< Id > & elist )

Builds the objMap vector, which maps all Ids to the internal indices for pools and reacs that are used in the solver. In addition to the elist, it also scans through the offSolverPools and offSolverReacs to build the map.

void Stoich::buildXreacs	(	const Eref &	e,
		Id	otherStoich
	)

Builds cross-reaction terms between current stoich and otherStoich. The function scans the voxels at which there are jucntions between different compartments, and orchestrates setup of interfaces between the Ksolves that implement the cross-reactions at these junctions.

References kinterface_, offSolverPoolMap_, and ZombiePoolInterface::setupCrossSolverReacs().

Referenced by initCinfo().

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void Stoich::comptsOnCrossReacTerms ( vector< pair< Id, Id > > & xr ) const

Expands out list of compartment mappings of proxy reactions to the appropriate entries on the rates_vector.

unsigned int Stoich::convertIdToFuncIndex ( Id id ) const

References funcMap_, objMap_, and objMapStart_.

Referenced by installAndUnschedFunc().

unsigned int Stoich::convertIdToPoolIndex ( Id id ) const

References idMap_, objMap_, and objMapStart_.

Referenced by Ksolve::getPoolIndex(), Gsolve::getPoolIndex(), installAndUnschedFunc(), installAndUnschedFuncRate(), and installAndUnschedFuncReac().

unsigned int Stoich::convertIdToReacIndex ( Id id ) const

References objMap_, objMapStart_, and rates_.

Referenced by getNumCoreRates(), getR1(), getR1offset1(), getR1offset2(), getR2(), installAndUnschedFuncRate(), installAndUnschedFuncReac(), installDummyEnzyme(), setEnzK1(), setEnzK2(), setEnzK3(), setMMenzKcat(), setMMenzKm(), setReacKb(), and setReacKf().

void Stoich::convertRatesToStochasticForm ( )

This function is used when the stoich class is employed by a Gsolver for doing stochastic calculations. Here we fix the issue of having a single substrate at more than first order. As the first molecule of the substrate is consumed, the number is depleted by one and so its forward rate is reduced. And so on. This also protects against going negative in mol number or concentration.

References RateTerm::getR1(), and rates_.

Referenced by Gsolve::rebuildGssaSystem().

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void Stoich::filterXreacs ( )

References ZombiePoolInterface::filterCrossRateTerms(), kinterface_, offSolverReacCompts_, and offSolverReacs_.

Referenced by initCinfo().

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const FuncTerm * Stoich::funcs ( unsigned int i ) const

References funcs_.

Referenced by Gsolve::fillMathDep(), and GssaVoxelPools::updateDependentMathExpn().

vector< unsigned int > Stoich::getColIndex ( ) const

References KinSparseMatrix::colIndex(), and N_.

Referenced by initCinfo().

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Id Stoich::getCompartment ( ) const

References compartment_.

Referenced by initCinfo(), and SteadyState::setStoich().

Id Stoich::getDsolve ( ) const

References dsolve_.

Referenced by initCinfo().

double Stoich::getEnzK2 ( const Eref & e ) const

Get rate k2 (1/sec) for enzyme.

References getR1offset1(), getR2(), and useOneWay_.

Referenced by ZombieEnz::vGetK2().

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double Stoich::getEnzK3 ( const Eref & e ) const

Get rate k3, aka kcat, for enzyme.

References getR1offset1(), getR1offset2(), and useOneWay_.

Referenced by ZombieEnz::vGetKcat().

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double Stoich::getEnzNumK1 ( const Eref & e ) const

References getR1().

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Id Stoich::getKsolve ( ) const

References ksolve_.

Referenced by SteadyState::classifyState(), initCinfo(), and Ksolve::print().

vector< int > Stoich::getMatrixEntry ( ) const

References KinSparseMatrix::matrixEntry(), and N_.

Referenced by initCinfo().

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double Stoich::getMMenzKcat ( const Eref & e ) const

References getR2().

Referenced by ZombieMMenz::vGetKcat().

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double Stoich::getMMenzNumKm ( const Eref & e ) const

References getR1().

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unsigned int Stoich::getNumAllPools ( ) const

Returns total number of local pools. Leaves out the pools whose actual calculations happen on another solver, but are given a proxy here in order to handle cross-compartment reactions.

References numBufPools_, and numVarPools_.

Referenced by Gsolve::fillMathDep(), Ksolve::getEstimatedDt(), initCinfo(), Ksolve::setStoich(), and VoxelPools::updateRates().

unsigned int Stoich::getNumBufPools ( ) const

Returns number of local buffered pools.

References numBufPools_.

Referenced by Gsolve::fillMathDep(), and VoxelPools::updateRates().

unsigned int Stoich::getNumCoreRates ( ) const

Utility function to return # of core rates for reacs which are entirely located on current compartment, including all reactants

References convertIdToReacIndex(), offSolverReacs_, and rates_.

Referenced by VoxelPools::print(), Gsolve::rebuildGssaSystem(), VoxelPoolsBase::scaleVolsBufsRates(), SteadyState::setStoich(), VoxelPools::setVolumeAndDependencies(), GssaVoxelPools::setVolumeAndDependencies(), Ksolve::updateRateTerms(), and Gsolve::updateRateTerms().

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unsigned int Stoich::getNumFuncs ( ) const

References funcs_.

Referenced by Gsolve::fillMathDep().

unsigned int Stoich::getNumProxyPools ( ) const

Returns number of proxy pools here for cross-compartment reactions

References offSolverPools_.

Referenced by Gsolve::fillMathDep(), Ksolve::getEstimatedDt(), initCinfo(), Gsolve::rebuildGssaSystem(), Ksolve::reinit(), Gsolve::reinit(), Ksolve::setStoich(), and VoxelPools::updateRates().

unsigned int Stoich::getNumRates ( ) const

Utility function to return # of rates_ entries. This includes the cross-solver reactions.

References rates_.

Referenced by GssaVoxelPools::advance(), Gsolve::fillMathDep(), Gsolve::fillMmEnzDep(), Ksolve::getEstimatedDt(), initCinfo(), Gsolve::makeReacDepsUnique(), and Gsolve::rebuildGssaSystem().

unsigned int Stoich::getNumVarPools ( ) const

Returns number of local pools that are updated by solver.

References numVarPools_.

Referenced by Gsolve::fillMathDep(), initCinfo(), Ksolve::process(), Gsolve::process(), Gsolve::rebuildGssaSystem(), GssaVoxelPools::reinit(), and VoxelPools::updateRates().

vector< Id > Stoich::getOffSolverCompts ( ) const

List all the compartments to which the current compt is coupled, by cross-compartment reactions. Self not included.

References offSolverPoolMap_.

const vector< Id > & Stoich::getOffSolverPools ( ) const

References offSolverPools_.

bool Stoich::getOneWay ( ) const

References useOneWay_.

string Stoich::getPath ( const Eref & e ) const

References path_.

Referenced by initCinfo().

vector< unsigned int > Stoich::getPoolIdMap ( ) const

Map to look up the index of the pool from its Id. poolIndex = poolIdMap[ Id::value() - poolOffset ] where the poolOffset is the smallest Id::value. poolOffset is passed back as the last entry of this vector. Any Ids that are not pools return EMPTY=~0.

References objMap_, and objMapStart_.

Referenced by initCinfo().

vector< Id > Stoich::getProxyPools ( Id i ) const

References Element::cinfo(), dummy(), Id::element(), Cinfo::isA(), and offSolverPoolMap_.

Referenced by initCinfo().

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double Stoich::getR1 ( const Eref & e ) const

Returns the internal rate in #/voxel, for R1, for the specified Eref.

Looks up the matching rate for R1. Later we may have additional scaling terms for the specified voxel.

References convertIdToReacIndex(), Eref::id(), and rates_.

Referenced by getEnzNumK1(), getMMenzNumKm(), getR1offset1(), and getR1offset2().

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double Stoich::getR1offset1 ( const Eref & e ) const

Returns internal rate R1 in #/voxel, for the rate term following the one directly referred to by the Eref e. Enzymes define multiple successive rate terms, so we look up the first, and then select one after it.

References convertIdToReacIndex(), getR1(), Eref::id(), and rates_.

Referenced by getEnzK2(), and getEnzK3().

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double Stoich::getR1offset2 ( const Eref & e ) const

Returns internal rate R1 in #/voxel, for the rate term two after the one directly referred to by the Eref e. Enzymes define multiple successive rate terms, so we look up the first, and then select the second one after it.

References convertIdToReacIndex(), getR1(), Eref::id(), and rates_.

Referenced by getEnzK3().

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double Stoich::getR2 ( const Eref & e ) const

Returns the internal rate in #/voxel, for R2, for the specified reacIndex and voxel index. In some cases R2 is undefined, and it then returns 0.

Looks up the matching rate for R2. Later we may have additional scaling terms for the specified voxel.

References convertIdToReacIndex(), Eref::id(), and rates_.

Referenced by getEnzK2(), and getMMenzKcat().

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const vector< RateTerm * > & Stoich::getRateTerms ( ) const

Returns a reference to the entire rates_ vector.

References rates_.

Referenced by Gsolve::rebuildGssaSystem(), VoxelPoolsBase::scaleVolsBufsRates(), SteadyState::setStoich(), VoxelPools::setVolumeAndDependencies(), GssaVoxelPools::setVolumeAndDependencies(), Ksolve::updateRateTerms(), and Gsolve::updateRateTerms().

vector< unsigned int > Stoich::getRowStart ( ) const

References N_, and KinSparseMatrix::rowStart().

Referenced by initCinfo().

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SpeciesId Stoich::getSpecies ( unsigned int poolIndex ) const

Returns SpeciesId of specified pool

References species_.

int Stoich::getStatus ( ) const

getStatus(): Flag to track status of Stoich object. -1: No path yet assigned. 0: Success 1: Warning: Missing reactant in Reac or Enz 2: Warning: Missing substrate in MMenz 4: Warning: Compartment not defined 8: Warning: Neither Ksolve nor Dsolve defined 16: Warning: No objects found on path

References status_.

Referenced by initCinfo().

const KinSparseMatrix & Stoich::getStoichiometryMatrix ( ) const

Updates the rates for cross-compartment reactions.

Get the rate for a single reaction specified by r, as per all the mol numbers in s. double getReacVelocity( unsigned int r, const double* s, unsigned int volIndex ) const; Returns the stoich matrix. Used by gsolve.

References N_.

Referenced by Gsolve::fillMathDep(), Gsolve::rebuildGssaSystem(), and VoxelPools::updateRates().

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

References buildXreacs(), filterXreacs(), getColIndex(), getCompartment(), getDsolve(), getKsolve(), getMatrixEntry(), getNumAllPools(), getNumProxyPools(), getNumRates(), getNumVarPools(), getPath(), getPoolIdMap(), getProxyPools(), getRowStart(), getStatus(), Neutral::initCinfo(), scaleBufsAndRates(), setCompartment(), setDsolve(), setKsolve(), setPath(), and unZombifyModel().

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unsigned int Stoich::innerInstallReaction	(	Id	reacId,
		const vector< Id > &	subs,
		const vector< Id > &	prds
	)

void Stoich::installAndUnschedFunc	(	Id	func,
		Id	pool
	)

This installs a FuncTerm, which evaluates a function to specify the conc of the specific pool. The pool is a BufPool.

References convertIdToFuncIndex(), convertIdToPoolIndex(), Id::element(), Cinfo::find(), Cinfo::findFinfo(), funcs_, Element::getNeighbors(), FuncTerm::setExpr(), FuncTerm::setReactantIndex(), FuncTerm::setTarget(), Element::setTick(), and Id::value().

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void Stoich::installAndUnschedFuncRate	(	Id	func,
		Id	pool
	)

This installs a FuncRate, which evaluates a function to specify the rate of change of conc of the specific pool. The pool is a Pool.

References convertIdToPoolIndex(), convertIdToReacIndex(), Id::element(), Cinfo::find(), Cinfo::findFinfo(), SparseMatrix< T >::get(), Element::getNeighbors(), N_, rates_, SparseMatrix< T >::set(), Element::setTick(), and Id::value().

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void Stoich::installAndUnschedFuncReac	(	Id	func,
		Id	reac
	)

This installs a FuncReac, which evaluates a function to specify the rate (Kf) of the specified reaction.

References convertIdToPoolIndex(), convertIdToReacIndex(), Id::element(), Cinfo::find(), Cinfo::findFinfo(), Element::getNeighbors(), rates_, FuncRate::setExpr(), FuncRate::setFuncArgIndex(), Element::setTick(), and Id::value().

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void Stoich::installDummyEnzyme	(	Id	enzId,
		Id	enzMolId
	)

This is used when the enzyme lacks sub or prd.

References convertIdToReacIndex(), rates_, status_, and useOneWay_.

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void Stoich::installEnzyme	(	ZeroOrder *	r1,
		ZeroOrder *	r2,
		ZeroOrder *	r3,
		Id	enzId,
		Id	enzMolId,
		const vector< Id > &	prds
	)

This takes the forward, backward and product formation half-reacs belonging to the specified Enzyme, and builds them into the Stoich. This is the low-level function.

void Stoich::installEnzyme	(	Id	enzId,
		Id	enzMolId,
		Id	cplxId,
		const vector< Id > &	subs,
		const vector< Id > &	prds
	)

Referenced by ZombieEnz::setSolver().

void Stoich::installMMenz	(	MMEnzymeBase *	meb,
		unsigned int	rateIndex,
		const vector< Id > &	subs,
		const vector< Id > &	prds
	)

This is the inner function to do the installation.

void Stoich::installMMenz	(	Id	enzId,
		const vector< Id > &	enzMolId,
		const vector< Id > &	subs,
		const vector< Id > &	prds
	)

This takes the baseclass for an MMEnzyme and builds the MMenz into the Stoich.

void Stoich::installReaction	(	Id	reacId,
		const vector< Id > &	subs,
		const vector< Id > &	prds
	)

Referenced by ZombieReac::setSolver().

void Stoich::locateOffSolverReacs	(	Id	myCompt,
		vector< Id > &	elist
	)

Scans through elist to find any reactions that connect to pools not located on solver. Removes these reactions from the elist and maintains Ids of the affected reactions, and their off-solver pools, in offSolverReacs_ and offSolverPools_.

ZeroOrder* Stoich::makeHalfReaction	(	double	rate,
		const vector< Id > &	reactants
	)

Utility function to make a half reac and return the rate term.

const vector< Id > & Stoich::offSolverPoolMap ( Id compt ) const

Looks up the vector of pool Ids originating from the specified compartment, that are represented on this compartment as proxies.

References offSolverPoolMap_.

void Stoich::print ( ) const

Utility function, prints out N_, used for debugging.

References N_, and SparseMatrix< T >::print().

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void Stoich::printRates ( ) const

Another utility function, prints out all Kf, kf, Kb, kb.

References reacMap_.

const RateTerm * Stoich::rates ( unsigned int i ) const

Utility function to return a rates_ entry.

References rates_.

Referenced by Gsolve::fillMmEnzDep().

void Stoich::resizeArrays ( )

Using the computed array sizes, now allocate space for them.

References dinterface_, funcs_, idMap_, kinterface_, N_, numBufPools_, numFunctions_, numReac_, numVarPools_, offSolverPools_, rates_, ZombiePoolInterface::setNumPools(), SparseMatrix< T >::setSize(), and species_.

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void Stoich::scaleBufsAndRates	(	unsigned int	index,
		double	volScale
	)

Used to handle run-time size updates for spines.

References kinterface_, ZombiePoolInterface::pools(), and VoxelPoolsBase::scaleVolsBufsRates().

Referenced by initCinfo().

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void Stoich::setCompartment ( Id v )

assigns compartment occupied by Stoich.

References Element::cinfo(), compartment_, doubleEq(), Id::element(), Cinfo::isA(), and numVoxels_.

Referenced by initCinfo().

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void Stoich::setDsolve ( Id v )

assigns diffusion solver: Dsovle or a Gillespie voxel stepper

References Element::cinfo(), Eref::data(), dinterface_, dsolve_, Id::element(), Id::eref(), and Cinfo::isA().

Referenced by initCinfo().

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void Stoich::setElist	(	const Eref &	e,
		const vector< ObjId > &	elist
	)

Internal function which sets up the model based on the provided elist of all elements managed by this solver.

void Stoich::setEnzK1	(	const Eref &	e,
		double	v
	)			const

Later handle all the volumes when this conversion is done.

Sets the rate v (given in millimoloar concentration units) for the forward enzyme reaction of binding substrate to enzyme. Does this throughout the compartment in which the enzyme lives. Internally the stoich uses #/voxel units so this involves querying the volume subsystem about volumes for each voxel, and scaling accordingly.

References convertIdToReacIndex(), Cinfo::find(), Cinfo::findFinfo(), Eref::id(), kinterface_, rates_, and ZombiePoolInterface::updateRateTerms().

Referenced by updateRatesAfterRemesh(), ZombieEnz::vSetConcK1(), ZombieEnz::vSetK1(), ZombieEnz::vSetKm(), and ZombieEnz::vSetNumKm().

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void Stoich::setEnzK2	(	const Eref &	e,
		double	v
	)			const

Set rate k2 (1/sec) for enzyme.

References convertIdToReacIndex(), Eref::id(), kinterface_, rates_, ZombiePoolInterface::updateRateTerms(), and useOneWay_.

Referenced by updateRatesAfterRemesh(), ZombieEnz::vSetK2(), and ZombieEnz::vSetRatio().

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void Stoich::setEnzK3	(	const Eref &	e,
		double	v
	)			const

Set rate k3 (1/sec) for enzyme.

References convertIdToReacIndex(), Eref::id(), kinterface_, rates_, ZombiePoolInterface::updateRateTerms(), and useOneWay_.

Referenced by updateRatesAfterRemesh(), and ZombieEnz::vSetKcat().

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void Stoich::setFunctionExpr	(	const Eref &	e,
		string	expr
	)

Sets the arithmetic expression used in a FuncRate or FuncReac

void Stoich::setKsolve ( Id v )

assigns kinetic solver: Ksovle or GSSAsolve.

References Element::cinfo(), Eref::data(), Id::element(), Id::eref(), Cinfo::isA(), kinterface_, ksolve_, and setOneWay().

Referenced by initCinfo().

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void Stoich::setMMenzKcat	(	const Eref &	e,
		double	v
	)			const

Sets the kcat for MMenz. No conversions needed.

References convertIdToReacIndex(), Eref::id(), kinterface_, rates_, and ZombiePoolInterface::updateRateTerms().

Referenced by updateRatesAfterRemesh(), and ZombieMMenz::vSetKcat().

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void Stoich::setMMenzKm	(	const Eref &	e,
		double	v
	)			const

Sets the Km for MMenz, using appropriate volume conversion to go from the argument (in millimolar) to #/voxel. This may do the assignment among many voxels containing the enz in case there are different volumes.

References convertIdToReacIndex(), Eref::id(), kinterface_, rates_, and ZombiePoolInterface::updateRateTerms().

Referenced by updateRatesAfterRemesh(), ZombieMMenz::vSetKm(), and ZombieMMenz::vSetNumKm().

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void Stoich::setOneWay ( bool v )

References useOneWay_.

Referenced by setKsolve().

void Stoich::setPath	(	const Eref &	e,
		string	path
	)

Take the provided wildcard path to build the list of elements managed by this solver.

Referenced by initCinfo().

void Stoich::setReacKb	(	const Eref &	e,
		double	v
	)			const

Sets the reverse rate v (given in millimoloar concentration units) for the specified reaction throughout the compartment in which the reaction lives. Internally the stoich uses #/voxel units so this involves querying the volume subsystem about volumes for each voxel, and scaling accordingly.

For now assume a single rate term.

References convertIdToReacIndex(), Cinfo::find(), Cinfo::findFinfo(), Eref::id(), kinterface_, rates_, ZombiePoolInterface::updateRateTerms(), and useOneWay_.

Referenced by updateRatesAfterRemesh(), ZombieReac::vSetConcKb(), and ZombieReac::vSetNumKb().

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void Stoich::setReacKf	(	const Eref &	e,
		double	v
	)			const

Sets the forward rate v (given in millimoloar concentration units) for the specified reaction throughout the compartment in which the reaction lives. Internally the stoich uses #/voxel units so this involves querying the volume subsystem about volumes for each voxel, and scaling accordingly.

Sets the forward rate v (given in millimoloar concentration units) for the specified reaction throughout the compartment in which the reaction lives. Internally the stoich uses #/voxel units so this involves querying the volume subsystem about volumes for each voxel, and scaling accordingly. For now assume a uniform voxel volume and hence just convert on 0 meshIndex.

References convertIdToReacIndex(), Cinfo::find(), Cinfo::findFinfo(), Eref::id(), kinterface_, rates_, and ZombiePoolInterface::updateRateTerms().

Referenced by updateRatesAfterRemesh(), ZombieReac::vSetConcKf(), and ZombieReac::vSetNumKf().

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void Stoich::setSpecies	(	unsigned int	poolIndex,
		unsigned int	s
	)

Assigns SpeciesId of specified pool

References species_.

void Stoich::setupCrossSolverReacVols ( ) const

Used to set up and update all cross solver reac terms and their rates, if there has been a change in volumes. Should also work if there has been a change in voxelization.

References kinterface_, prdComptVec_, ZombiePoolInterface::setupCrossSolverReacVols(), and subComptVec_.

Referenced by VoxelPools::setVolumeAndDependencies(), and GssaVoxelPools::setVolumeAndDependencies().

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void Stoich::unZombifyModel ( )

Converts back to ExpEuler type basic kinetic Elements.

References Element::cinfo(), Eref::element(), enzMap_, Cinfo::find(), funcMap_, Element::getTick(), idMap_, Clock::lookupDefaultTick(), mmEnzMap_, Cinfo::name(), numBufPools_, numVarPools_, offSolverPools_, reacMap_, Element::setTick(), unZombifyPools(), CplxEnzBase::zombify(), EnzBase::zombify(), and ReacBase::zombify().

Referenced by initCinfo(), and ~Stoich().

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void Stoich::unZombifyPools ( )

unZombifies Pools. Helper for unZombifyModel.

References Element::cinfo(), Cinfo::find(), idMap_, Element::isDoomed(), numBufPools_, numVarPools_, offSolverPools_, and PoolBase::zombify().

Referenced by unZombifyModel().

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void Stoich::updateFuncs	(	double *	s,
		double	t
	)			const

Updates the function values, within s.

References funcs_.

Referenced by GssaVoxelPools::advance(), VoxelPools::gslFunc(), and GssaVoxelPools::reinit().

void Stoich::updateRatesAfterRemesh ( )

This function scans all reacs and enzymes and recalculates the internal rate terms depending on the reference terms stored in the original chemical object.

updateJunctionRates: Updates the rates for cross-compartment reactions. These are located at the end of the rates_ vector, and are directly indexed by the reacTerms. void Stoich::updateJunctionRates( const double* s, const vector< unsigned int >& reacTerms, double* yprime ) { for ( vector< unsigned int >::const_iterator i = reacTerms.begin(); i != reacTerms.end(); ++i ) { assert( *i < rates_[0].size() ); yprime++ += (*rates_[0][*i])( s ); } }

References offSolverReacs_, reacMap_, setEnzK1(), setEnzK2(), setEnzK3(), setMMenzKcat(), setMMenzKm(), setReacKb(), and setReacKf().

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void Stoich::updateReacVelocities	(	const double *	s,
		vector< double > &	vel,
		unsigned int	volIndex
	)			const

Updates the yprime array, rate of change of each molecule The volIndex specifies which set of rates to use, since the rates are volume dependent. Moved to VoxelPools void updateRates( const double* s, double* yprime, unsigned int volIndex ) const; Computes the velocity of each reaction, vel. The volIndex specifies which set of rates to use, since the rates are volume dependent.

void Stoich::zombifyChemCompt ( Id compt )

void Stoich::zombifyModel	(	const Eref &	e,
		const vector< Id > &	elist
	)

zombifyModel marches through the specified id list and converts all entries into zombies. The first arg e is the Eref of the Stoich itself.

Member Data Documentation

Id Stoich::compartment_ [protected]

Contains Id of compartment holding reac system. Optional.

Referenced by getCompartment(), and setCompartment().

ZombiePoolInterface* Stoich::dinterface_ [protected]

Pointer for dsolve.

Referenced by resizeArrays(), and setDsolve().

Id Stoich::dsolve_ [protected]

This contains the Id of the Diffusion solver. Optional.

Referenced by getDsolve(), and setDsolve().

vector< Id > Stoich::enzMap_ [protected]

Map back from enz index to Id. Needed to unzombify

Referenced by unZombifyModel().

vector< Id > Stoich::funcMap_ [protected]

Vector of all funcs. Needed to unzombify

Referenced by convertIdToFuncIndex(), and unZombifyModel().

vector< FuncTerm* > Stoich::funcs_ [protected]

The FuncTerms handle mathematical ops on mol levels.

Referenced by funcs(), getNumFuncs(), installAndUnschedFunc(), resizeArrays(), updateFuncs(), and ~Stoich().

vector< Id > Stoich::idMap_ [protected]

Map back from mol index to Id. Primarily for debugging.

Referenced by convertIdToPoolIndex(), resizeArrays(), unZombifyModel(), and unZombifyPools().

ZombiePoolInterface* Stoich::kinterface_ [protected]

Pointer for ksolve.

Referenced by buildXreacs(), filterXreacs(), resizeArrays(), scaleBufsAndRates(), setEnzK1(), setEnzK2(), setEnzK3(), setKsolve(), setMMenzKcat(), setMMenzKm(), setReacKb(), setReacKf(), and setupCrossSolverReacVols().

Id Stoich::ksolve_ [protected]

This contains the Id of the Kinetic solver.

Referenced by getKsolve(), and setKsolve().

vector< Id > Stoich::mmEnzMap_ [protected]

Map back from enz index to Id. Needed to unzombify

Referenced by unZombifyModel().

KinSparseMatrix Stoich::N_ [protected]

N_ is the stoichiometry matrix.

Referenced by getColIndex(), getMatrixEntry(), getRowStart(), getStoichiometryMatrix(), installAndUnschedFuncRate(), print(), and resizeArrays().

unsigned int Stoich::numBufPools_ [protected]

Number of variable molecules that the solver deals with, including the proxy molecules which belong in other compartments.

unsigned int totVarPools_; Number of buffered molecules

Referenced by getNumAllPools(), getNumBufPools(), resizeArrays(), unZombifyModel(), and unZombifyPools().

unsigned int Stoich::numFunctions_ [protected]

Number functions, currently only the ones controlling molecule numbers, like sumtotals.

Referenced by resizeArrays().

unsigned int Stoich::numReac_ [protected]

Number of reactions in the solver model. This includes conversion reactions A + B <---> C enzyme reactions E + S <---> E.S ---> E + P and MM enzyme reactions rate = E.S.kcat / ( Km + S ) The enzyme reactions count as two reaction steps.

Referenced by resizeArrays().

unsigned int Stoich::numVarPools_ [protected]

Number of variable molecules that the solver deals with, that are local to the solver.

Referenced by getNumAllPools(), getNumVarPools(), resizeArrays(), unZombifyModel(), and unZombifyPools().

unsigned int Stoich::numVoxels_ [protected]

Number of voxels in reac system.

This tracks the unique volumes handled by the reac system. Maps one-to-one with the vector of vector of RateTerms. vector< double > uniqueVols_;

Referenced by setCompartment().

vector< unsigned int > Stoich::objMap_ [protected]

Maps Ids to objects in the S_, RateTerm, and FuncTerm vectors. There will be holes in this map, but look up is very fast. The calling Id must know what it wants to find: all it gets back is an integer. The alternative is to have multiple maps, but that is slower. Assume no arrays. Each Pool/reac etc must be a unique Element. Later we'll deal with diffusion.

Referenced by convertIdToFuncIndex(), convertIdToPoolIndex(), convertIdToReacIndex(), and getPoolIdMap().

unsigned int Stoich::objMapStart_ [protected]

Minor efficiency: We will usually have a set of objects that are nearly contiguous in the map. May as well start with the first of them.

Referenced by convertIdToFuncIndex(), convertIdToPoolIndex(), convertIdToReacIndex(), and getPoolIdMap().

map< Id, vector< Id > > Stoich::offSolverPoolMap_ [protected]

Map of vectors of Ids of offSolver pools. Each map entry contains the vector of Ids of proxy pools coming from the specified compartment. In use, the junction will copy the pool indices over for data transfer.

Referenced by buildXreacs(), getOffSolverCompts(), getProxyPools(), and offSolverPoolMap().

vector< Id > Stoich::offSolverPools_ [protected]

These are pools that were not in the original scope of the solver, but have to be brought in because they are reactants of one or more of the offSolverReacs.

Referenced by getNumProxyPools(), getOffSolverPools(), resizeArrays(), unZombifyModel(), and unZombifyPools().

vector< pair< Id, Id > > Stoich::offSolverReacCompts_ [protected]

Which compartment(s) does the off solver reac connect to? Usually it is just one, in which case the second id is Id()

Referenced by filterXreacs().

vector< Id > Stoich::offSolverReacs_ [protected]

Tracks the reactions that go off the current solver.

Referenced by filterXreacs(), getNumCoreRates(), and updateRatesAfterRemesh().

string Stoich::path_ [protected]

Referenced by getPath().

const unsigned int Stoich::PoolIsNotOnSolver [static]

Returns the index of the matching volume, which is also the index into the RateTerm vector. unsigned int indexOfMatchingVolume( double vol ) const;

vector< vector< Id > > Stoich::prdComptVec_ [protected]

prdComptVec_[rateTermIndex][product#]: Identifies compts for each product for each cross-compartment RateTerm in the rates_vector.

Referenced by setupCrossSolverReacVols().

vector< RateTerm* > Stoich::rates_ [protected]

The RateTerms handle the update operations for reaction rate v_. This is the master vector of RateTerms, and it is scaled to a volume such that the 'n' units and the conc units are identical. Duplicates of this vector are made in each voxel with a different volume. The duplicates have rates scaled as per volume. The RateTerms vector also includes reactions that have off-compartment products. These need special volume scaling involving all the interactiong compartments.

Referenced by convertIdToReacIndex(), convertRatesToStochasticForm(), getNumCoreRates(), getNumRates(), getR1(), getR1offset1(), getR1offset2(), getR2(), getRateTerms(), installAndUnschedFuncRate(), installAndUnschedFuncReac(), installDummyEnzyme(), rates(), resizeArrays(), setEnzK1(), setEnzK2(), setEnzK3(), setMMenzKcat(), setMMenzKm(), setReacKb(), setReacKf(), and ~Stoich().

vector< Id > Stoich::reacMap_ [protected]

Map back from reac index to Id. Needed to unzombify

Referenced by printRates(), unZombifyModel(), and updateRatesAfterRemesh().

vector< unsigned int > Stoich::species_ [protected]

Lookup from each molecule to its Species identifer This will eventually be tied into an ontology reference.

Referenced by getSpecies(), resizeArrays(), and setSpecies().

int Stoich::status_ [protected]

Flag to track status of Stoich object. -1: No path yet assigned. 0: Success 1: Warning: Missing reactant in Reac or Enz 2: Warning: Missing substrate in MMenz 4: Warning: Compartment not defined 8: Warning: Neither Ksolve nore Dsolve defined

Referenced by getStatus(), and installDummyEnzyme().

vector< vector< Id > > Stoich::subComptVec_ [protected]

subComptVec_[rateTermIndex][substrate#]: Identifies compts for each substrate for each cross-compartment RateTerm in the rates_vector.

Referenced by setupCrossSolverReacVols().

bool Stoich::useOneWay_ [protected]

True if the stoich matrix is set up to handle only one-way reactions, as is needed in the case of the Gillespie algorithm.

Referenced by getEnzK2(), getEnzK3(), getOneWay(), installDummyEnzyme(), setEnzK2(), setEnzK3(), setOneWay(), and setReacKb().

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

ksolve/Stoich.h
ksolve/Stoich.cpp

Stoich Class Reference

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation