kinetics/ReadKkit.cpp File Reference

#include <iomanip>
#include <fstream>
#include "header.h"
#include "../utility/utility.h"
#include "PoolBase.h"
#include "Pool.h"
#include "BufPool.h"
#include "ReacBase.h"
#include "EnzBase.h"
#include "lookupVolumeFromMesh.h"
#include "../shell/Shell.h"
#include "../shell/Wildcard.h"
#include "ReadKkit.h"

Include dependency graph for ReadKkit.cpp:

Enumerations
enum	GenesisTableModes {   TAB_IO, TAB_LOOP, TAB_ONCE, TAB_BUF,   TAB_SPIKE, TAB_FIELDS, TAB_DELAY }
Functions
unsigned int	chopLine (const string &line, vector< string > &ret)
string	lower (const string &input)
Id	makeStandardElements (Id pa, const string &modelname)
void	setMethod (Shell *s, Id mgr, double simdt, double plotdt, const string &method)
void	assignArgs (map< string, int > &argConv, const vector< string > &args)
bool	volCompare (const pair< unsigned int, double > &A, const pair< unsigned int, double > &B)
vector< unsigned int >	findVolOrder (const vector< double > &vols)
Id	findParentComptOfReac (Id reac)
Id	findMeshOfEnz (Id enz)

---

Enumeration Type Documentation

enum GenesisTableModes

Enumerator:

TAB_IO
TAB_LOOP
TAB_ONCE
TAB_BUF
TAB_SPIKE
TAB_FIELDS
TAB_DELAY

---

Function Documentation

void assignArgs	(	map< string, int > &	argConv,
		const vector< string > &	args
	)

unsigned int chopLine	(	const string &	line,
		vector< string > &	ret
	)

References trim().

Here is the call graph for this function:

Id findMeshOfEnz

(

Id

enz

)

Return the MeshEntry into which the enzyme should be placed. This is simple: Just identify the compartment holding the enzyme molecule.

References Id::element(), Cinfo::findFinfo(), getCompt(), Element::getNeighbors(), and EnzBase::initCinfo().

Here is the call graph for this function:

Id findParentComptOfReac

(

Id

reac

)

References Id::element(), Cinfo::findFinfo(), getCompt(), Element::getNeighbors(), and ReacBase::initCinfo().

Referenced by ReadKkit::assignReacCompartments().

Here is the call graph for this function:

vector< unsigned int > findVolOrder

(

const vector< double > &

vols

)

References volCompare().

Referenced by ReadKkit::assignPoolCompartments(), and testVolSort().

Here is the call graph for this function:

string lower

(

const string &

input

)

Referenced by setMethod().

Id makeStandardElements	(	Id	pa,
		const string &	modelname
	)

References Shell::doCreate(), MooseGlobal, Id::path(), and SetGet2< A1, A2 >::set().

Here is the call graph for this function:

void setMethod	(	Shell *	s,
		Id	mgr,
		double	simdt,
		double	plotdt,
		const string &	method
	)

References Shell::doCreate(), Shell::doSetClock(), Shell::doUseClock(), lower(), Id::path(), and Field< A >::set().

Here is the call graph for this function:

bool volCompare	(	const pair< unsigned int, double > &	A,
		const pair< unsigned int, double > &	B
	)

Referenced by findVolOrder().