Stoich.cpp File Reference

#include "header.h"
#include "ElementValueFinfo.h"
#include "PoolBase.h"
#include "ReacBase.h"
#include "EnzBase.h"
#include "CplxEnzBase.h"
#include "FuncTerm.h"
#include "RateTerm.h"
#include "FuncRateTerm.h"
#include "SparseMatrix.h"
#include "KinSparseMatrix.h"
#include "VoxelPoolsBase.h"
#include "../mesh/VoxelJunction.h"
#include "XferInfo.h"
#include "ZombiePoolInterface.h"
#include "../builtins/Variable.h"
#include "../builtins/Function.h"
#include "ZombieFunction.h"
#include "Stoich.h"
#include "lookupVolumeFromMesh.h"
#include "../scheduling/Clock.h"
#include "../shell/Shell.h"
#include "../shell/Wildcard.h"

Include dependency graph for Stoich.cpp:

Go to the source code of this file.

Functions
void	convWildcards (vector< Id > &ret, const vector< ObjId > &elist)
pair< Id, Id >	extractCompts (const vector< Id > &compts)
void	filterWildcards (vector< Id > &ret, const vector< ObjId > &elist)
static Id	findFuncMsgSrc (Id pa, const string &msg)
	Returns Function, if any, acting as src of specified msg into pa. More...
void	installDummy (RateTerm **entry, Id enzId, const string &s)
static bool	isOffSolverReac (const Element *e, Id myCompt, vector< Id > &poolCompts, map< Id, Id > &poolComptMap)
void	myUnique (vector< Id > &v)

Variables
static const Cinfo *	stoichCinfo = Stoich::initCinfo()

Function Documentation

void convWildcards	(	vector< Id > &	ret,
		const vector< ObjId > &	elist
	)

Definition at line 341 of file Stoich.cpp.

{
    ret.resize( elist.size() );
    for ( unsigned int i = 0; i < elist.size(); ++i )
        ret[i] = elist[i].id;
}

pair< Id, Id > extractCompts

(

const vector< Id > &

compts

)

Extracts and orders the compartments associated with a given reac.

Definition at line 694 of file Stoich.cpp.

Referenced by Stoich::locateOffSolverReacs().

{
    pair< Id, Id > ret;
    for ( vector< Id >::const_iterator i = compts.begin();
            i != compts.end(); ++i )
    {
        if ( ret.first == Id() )
        {
            ret.first = *i;
        }
        else if ( ret.first != *i )
        {
            if ( ret.second == Id() )
                ret.second = *i;
            else
            {
                cout << "Error: Stoich::extractCompts: more than 2 compartments\n";
                assert( 0 );
            }
        }
    }
    if ( ( ret.second != Id() ) && ret.second < ret.first )
    {
        Id temp = ret.first;
        ret.first = ret.second;
        ret.second = ret.first;
    }

    return ret;
}

Here is the caller graph for this function:

void filterWildcards	(	vector< Id > &	ret,
		const vector< ObjId > &	elist
	)

Definition at line 348 of file Stoich.cpp.

Referenced by Stoich::setElist().

{
    ret.clear();
    ret.reserve( elist.size() );
    for ( vector< ObjId >::const_iterator
            i = elist.begin(); i != elist.end(); ++i )
    {
        if ( i->element()->cinfo()->isA( "PoolBase" ) ||
                i->element()->cinfo()->isA( "ReacBase" ) ||
                i->element()->cinfo()->isA( "EnzBase" ) ||
                i->element()->cinfo()->isA( "Function" ) )
            ret.push_back( i->id );
    }
}

Here is the caller graph for this function:

static Id findFuncMsgSrc ( Id  pa, const string &  msg  )

static

Returns Function, if any, acting as src of specified msg into pa.

Definition at line 1231 of file Stoich.cpp.

References Element::cinfo(), Id::element(), Cinfo::findFinfo(), and Element::getNeighbors().

Referenced by Stoich::zombifyModel(), and Stoich::zombifyPoolFuncWithScaling().

{
    const Finfo *finfo = pa.element()->cinfo()->findFinfo( msg );
    if ( !finfo ) return Id();
    vector< Id > ret;
    if ( pa.element()->getNeighbors( ret, finfo ) > 0 )
    {
        if ( ret[0].element()->cinfo()->isA( "Function" ) )
            return ret[0];
    }
    return Id(); // failure
}

Here is the call graph for this function:

Here is the caller graph for this function:

void installDummy	(	RateTerm **	entry,
		Id	enzId,
		const string &	s
	)

Definition at line 1625 of file Stoich.cpp.

References Id::path().

Referenced by Stoich::installMMenz().

{
    cout << "Warning: Stoich::installMMenz: No " << s << " for: "  <<
         enzId.path() << endl;
    *entry = new ZeroOrder( 0.0 );
}

Here is the call graph for this function:

Here is the caller graph for this function:

static bool isOffSolverReac ( const Element *  e, Id  myCompt, vector< Id > &  poolCompts, map< Id, Id > &  poolComptMap  )

static

Checks if specified reac is off solver. As side-effect it compiles a vector of the pools that are off-solver, and the corresponding compartments for those pools

Definition at line 658 of file Stoich.cpp.

References Element::cinfo(), Id::element(), Cinfo::findFinfo(), getCompt(), Element::getNeighbors(), Cinfo::isA(), and Id::path().

Referenced by Stoich::locateOffSolverReacs().

{
    assert( myCompt != Id() );
    assert( myCompt.element()->cinfo()->isA( "ChemCompt" ) );
    bool ret = false;
    vector< Id > neighbors;
    e->getNeighbors( neighbors, e->cinfo()->findFinfo( "subOut" ));
    vector< Id > n2;
    e->getNeighbors( n2, e->cinfo()->findFinfo( "prdOut" ));
    neighbors.insert( neighbors.end(), n2.begin(), n2.end() );
    for ( vector< Id >::const_iterator
            j = neighbors.begin(); j != neighbors.end(); ++j )
    {
        Id otherCompt = getCompt( *j );
        if ( myCompt != otherCompt )
        {
            // offSolverPools.push_back( *j );
            poolCompts.push_back( otherCompt );
            poolComptMap[ *j ] = otherCompt; // Avoids duplication of pools
            ret = true;
            if ( j->element()->cinfo()->isA( "BufPool" ) )
            {
                cout << "Warning: Avoid BufPool: " << j->path() <<
                     "\n as reactant in cross-compartment reactions\n";
            }
        }
    }
    return ret;
}

Here is the call graph for this function:

Here is the caller graph for this function:

void myUnique

(

vector< Id > &

v

)

Definition at line 924 of file Stoich.cpp.

Referenced by Stoich::resizeArrays().

{
    sort( v.begin(), v.end() );
    vector< Id >::iterator last = unique( v.begin(), v.end() );
    v.erase( last, v.end() );
}

Here is the caller graph for this function:

Variable Documentation

const Cinfo* stoichCinfo = Stoich::initCinfo()

static

Definition at line 251 of file Stoich.cpp.

Referenced by Stoich::initCinfo().