ReadKkit Class Reference

#include <ReadKkit.h>

Collaboration diagram for ReadKkit:

Public Types
enum	ParseMode { DATA, INIT, COMMENT, LINE_CONTINUE }

Public Member Functions
void	addmsg (const vector< string > &args)
void	assignEnzCompartments ()
void	assignMMenzCompartments ()
void	assignPoolCompartments ()
void	assignReacCompartments ()
Id	buildChan (const vector< string > &args)
Id	buildCompartment (const vector< string > &args)
Id	buildEnz (const vector< string > &args)
Id	buildGeometry (const vector< string > &args)
Id	buildGraph (const vector< string > &args)
Id	buildGroup (const vector< string > &args)
Id	buildInfo (Id parent, map< string, int > &m, const vector< string > &args)
Id	buildPlot (const vector< string > &args)
Id	buildPool (const vector< string > &args)
Id	buildReac (const vector< string > &args)
Id	buildStim (const vector< string > &args)
void	buildSumTotal (const string &src, const string &dest)
Id	buildTable (const vector< string > &args)
Id	buildText (const vector< string > &args)
void	call (const vector< string > &args)
string	cleanPath (const string &path) const
void	convertEnzRatesToConcUnits ()
void	convertMMenzRatesToConcUnits ()
void	convertParametersToConcUnits ()
void	convertPoolAmountToConcUnits ()
	Convert pool amounts. Initially given in n, but scaling issue. More...
void	convertReacRatesToConcUnits ()
	Convert Reac rates, initially in n units. More...
void	dumpPlots (const string &filename)
Id	findSumTotSrc (const string &src)
string	getBasePath () const
double	getDefaultVol () const
double	getMaxTime () const
bool	getMoveOntoCompartment () const
double	getPlotDt () const
unsigned int	getVersion () const
void	innerAddMsg (const string &src, const map< string, Id > &m1, const string &srcMsg, const string &dest, const map< string, Id > &m2, const string &destMsg, bool isBackward=0)
void	innerRead (ifstream &fin)
unsigned int	loadTab (const vector< string > &args)
void	objdump (const vector< string > &args)
string	pathTail (const string &path, string &head) const
Id	read (const string &filename, const string &cellname, Id parent, const string &solverClass="Stoich")
void	readData (const string &line)
ParseMode	readInit (const string &line)
	ReadKkit ()
void	run ()
void	separateVols (Id pool, double vol)
void	setMoveOntoCompartment (bool v)
void	setupSlaveMsg (const string &src, const string &dest)
void	textload (const vector< string > &args)
void	undump (const vector< string > &args)

Private Attributes
Id	baseId_
	Base path into which entire kkit model will go. More...
string	basePath_
map< string, Id >	chanIds_
map< string, int >	chanMap_
vector< Id >	compartments_
double	controldt_
	regular numerical timestep from kkit. More...
double	defaultVol_
	Use both fast and sim dts. More...
vector< pair< Id, Id > >	enzCplxMols_
map< string, Id >	enzIds_
map< string, int >	enzMap_
double	fastdt_
	Base Id onto which entire kkit model will go. More...
map< string, int >	groupMap_
unsigned int	initdumpVersion_
	KKit version. More...
Id	lastTab_
	This keeps track of the last Table used in loadtab. More...
unsigned int	lineNum_
double	maxtime_
	Timestep for updating plots. More...
map< string, Id >	mmEnzIds_
bool	moveOntoCompartment_
	Initdump too has a version. More...
unsigned int	numCompartments_
unsigned int	numEnz_
unsigned int	numMMenz_
unsigned int	numOthers_
unsigned int	numPlot_
unsigned int	numPools_
unsigned int	numReacs_
unsigned int	numStim_
double	plotdt_
	Timestep for updating control graphics. More...
map< string, Id >	plotIds_
map< Id, int >	poolFlags_
map< string, Id >	poolIds_
map< string, int >	poolMap_
map< Id, double >	poolVols_
map< string, Id >	reacIds_
map< string, int >	reacMap_
Shell *	shell_
double	simdt_
	fast numerical timestep from kkit. More...
map< string, Id >	stimIds_
map< string, int >	stimMap_
vector< double >	tabEntries_
	This holds the vector of array entries for loadtab. More...
map< string, Id >	tabIds_
map< string, int >	tableMap_
double	transientTime_
	Simulation run time. More...
bool	useVariableDt_
	Time to run model at fastdt. More...
unsigned int	version_
	Default volume for new compartments. More...
vector< vector< Id > >	volCategories_
	List of Ids in each unique volume. More...
vector< double >	vols_
	This keeps track of unique volumes. More...

Static Private Attributes
static const double	EPSILON = 1.0e-15

Detailed Description

Loads in a kkit.g model. It makes a separate compartment for each distinct volume it finds in the system. The largest volume gets set to /model/kinetics. The next volume is in /model/compartment_1. The next volume is in /model/compartment_2. And so on. Has two options for handling compartments and solvers. By default, it puts the entire reaction system on /kinetics and makes just one solver. If the moveOntoCompartments_ flag is set it will put each model entity onto the appropriate compartment. It will create separate solvers for each compartment.

Definition at line 28 of file ReadKkit.h.

Member Enumeration Documentation

enum ReadKkit::ParseMode

Enumerator
DATA
INIT
COMMENT
LINE_CONTINUE

Definition at line 31 of file ReadKkit.h.

                       {
            DATA,
            INIT,
            COMMENT,
            LINE_CONTINUE
        };

Constructor & Destructor Documentation

ReadKkit::ReadKkit

(

)

Definition at line 52 of file ReadKkit.cpp.

    :
    basePath_( "" ),
    baseId_(),
    fastdt_( 0.001 ),
    simdt_( 0.01 ),
    controldt_( 0.1 ),
    plotdt_( 1 ),
    maxtime_( 1.0 ),
    transientTime_( 1.0 ),
    useVariableDt_( 0 ),
    defaultVol_( 1 ),
    version_( 11 ),
    initdumpVersion_( 3 ),
    moveOntoCompartment_( true ),
    numCompartments_( 0 ),
    numPools_( 0 ),
    numReacs_( 0 ),
    numEnz_( 0 ),
    numMMenz_( 0 ),
    numPlot_( 0 ),
    numStim_( 0 ),
    numOthers_( 0 ),
    lineNum_( 0 ),
    shell_( reinterpret_cast< Shell* >( Id().eref().data() ) )
{
    ;
}

Member Function Documentation

void ReadKkit::addmsg

(

const vector< string > &

args

)

Definition at line 1346 of file ReadKkit.cpp.

References buildSumTotal(), chanIds_, cleanPath(), Shell::doAddMsg(), enzIds_, innerAddMsg(), mmEnzIds_, pathTail(), plotIds_, poolIds_, reacIds_, setupSlaveMsg(), and shell_.

Referenced by readData().

{
    string src = cleanPath( args[1] ).substr( 10 );
    string dest = cleanPath( args[2] ).substr( 10 );

    if ( args[3] == "REAC" ) {
        if ( args[4] == "A" && args[5] == "B" ) {
            if ( chanIds_.find( src ) != chanIds_.end() )
                innerAddMsg( src, chanIds_, "in", dest, poolIds_, "reac");
            else
                innerAddMsg( src, reacIds_, "sub", dest, poolIds_, "reac");
        }
        else if ( args[4] == "B" && args[5] == "A" ) {
            if ( chanIds_.find( src ) != chanIds_.end() )
                innerAddMsg( src, chanIds_, "out", dest, poolIds_, "reac");
            else
                // dest pool is product of src reac
                innerAddMsg( src, reacIds_, "prd", dest, poolIds_, "reac");
        }
        else if ( args[4] == "sA" && args[5] == "B" ) {
            // Msg from enzyme to substrate.
            if ( mmEnzIds_.find( src ) == mmEnzIds_.end() )
                innerAddMsg( src, enzIds_, "sub", dest, poolIds_, "reac" );
            else
                innerAddMsg( src, mmEnzIds_, "sub", dest, poolIds_, "reac" );
        }
    }
    else if ( args[3] == "ENZYME" ) { // Msg from enz pool to enz site
        if ( mmEnzIds_.find( dest ) == mmEnzIds_.end() )
            innerAddMsg( dest, enzIds_, "enz", src, poolIds_, "reac" );
        else
            innerAddMsg( src, poolIds_, "nOut", dest, mmEnzIds_, "enzDest", 1);
            // innerAddMsg( dest, mmEnzIds_, "enz", src, poolIds_, "nOut", 1);
        /*
        if ( mmEnzIds_.find( dest ) == mmEnzIds_.end() )
            innerAddMsg( src, poolIds_, "reac", dest, enzIds_, "enz" );
        else
            innerAddMsg( src, poolIds_, "nOut", dest, mmEnzIds_, "enz" );
            */
    }
    else if ( args[3] == "MM_PRD" ) { // Msg from enz to Prd pool
        if ( mmEnzIds_.find( src ) == mmEnzIds_.end() )
            innerAddMsg( src, enzIds_, "prd", dest, poolIds_, "reac" );
        else
            innerAddMsg( src, mmEnzIds_, "prd", dest, poolIds_, "reac" );
    }
    else if ( args[3] == "NUMCHAN" ) { // Msg from chan pool to concchan 
        if ( chanIds_.find( dest ) != chanIds_.end() )
            innerAddMsg( src, poolIds_, "nOut", dest, chanIds_, "setNumChan");
    }
    else if ( args[3] == "PLOT" ) { // Time-course output for pool
        string head;
        string temp;
        dest = pathTail( cleanPath( args[2] ), head );
        string graph = pathTail( head, temp );
        temp = graph + "/" + dest;
        map< string, Id >::const_iterator i = plotIds_.find( temp );
        assert( i != plotIds_.end() );
        Id plot = i->second;

        i = poolIds_.find( src );
        Id pool;
        if ( i == poolIds_.end() ) {
            i = enzIds_.find( src ); // might be plotting an enzCplx.
            if ( i == enzIds_.end() ) {
                cout << "Error: ReadKkit: Unable to find src for plot: " <<
                    src << ", " << dest << endl;
                assert( 0 );
                return;
            }
            vector< Id > enzcplx;
            i->second.element()->getNeighbors( enzcplx,
                i->second.element()->cinfo()->findFinfo( "cplxOut" ) );
            assert( enzcplx.size() == 1 );
            pool = enzcplx[0];
        }  else {
            pool = i->second;
        }

        if ( args[4] == "Co" || args[4] == "CoComplex" ) {
            ObjId ret = shell_->doAddMsg( "Single",
                plot, "requestOut", pool, "getConc" );
            assert( ret != ObjId() );
        } else if ( args[4] == "n" || args[4] == "nComplex") {
            ObjId ret = shell_->doAddMsg( "Single",
                plot, "requestOut", pool, "getN" );
            assert( ret != ObjId() );
        } else {
            cout << "Unknown PLOT msg field '" << args[4] << "'\n";
        }
    }
    else if ( args[3] == "SUMTOTAL" ) { // Summation function.
        buildSumTotal( src, dest );
    }
    else if ( args[3] == "SLAVE" ) { // Summation function.
        if ( args[4] == "output" ) {
            setupSlaveMsg( src, dest );
        }
    }
}

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void ReadKkit::assignEnzCompartments

(

)

Goes through all Enzs and connects them up to each of the compartments in which one or more of their reactants resides. Thus, if any of these compartments changes volume, the Enz will be informed.

Definition at line 847 of file ReadKkit.cpp.

Referenced by read().

{
        /*
        Should not be needed, because the parent pool will move.
    for ( map< string, Id >::iterator i = enzIds_.begin();
        i != enzIds_.end(); ++i ) {
        Id compt = getCompt( Neutral::parent( i->second ).id );
        if ( moveOntoCompartment_ ) {
            if ( ! (getCompt( i->second ).id == compt ) )
                shell_->doMove( i->second, compt );
        }
    }
    */
}

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void ReadKkit::assignMMenzCompartments

(

)

Goes through all MMenzs and connects them up to each of the compartments in which one or more of their reactants resides. Thus, if any of these compartments changes volume, the MMenz will be informed.

Definition at line 868 of file ReadKkit.cpp.

Referenced by read().

{
        /*
        Should not be needed, because the parent pool will move.
    for ( map< string, Id >::iterator i = mmEnzIds_.begin();
        i != mmEnzIds_.end(); ++i ) {
        Id compt = getCompt( Neutral::parent( i->second ).id );
        if ( moveOntoCompartment_ ) {
            if ( ! (getCompt( i->second ).id == compt ) )
                shell_->doMove( i->second, compt );
        }
    }
    */
}

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void ReadKkit::assignPoolCompartments

(

)

Definition at line 740 of file ReadKkit.cpp.

References baseId_, Neutral::child(), Shell::doCreate(), Shell::doMove(), Id::eref(), findVolOrder(), getCompt(), ObjId::id, name, SetGet1< A >::set(), shell_, volCategories_, and vols_.

Referenced by read().

{
    Id kinetics = Neutral::child( baseId_.eref(), "kinetics" );
    assert( kinetics != Id() );
    vector< unsigned int > volOrder = findVolOrder( vols_ );
    assert( volCategories_.size() == vols_.size() );
    assert( volCategories_.size() == volOrder.size() );

    for ( unsigned int j = 0 ; j < volOrder.size(); ++j ) {
        unsigned int i = volOrder[j];
        if ( vols_[i] < 0 ) // Special case for enz complexes: vol == -1.
            continue;
        string name;
        Id kinId = Neutral::child( baseId_.eref(), "kinetics" );
        assert( kinId != Id() );
        Id comptId;
        // if ( i == maxi )
        if ( j == 0 ) {
            comptId = kinId;
        } else {
            stringstream ss;
            ss << "compartment_" << j;
            name = ss.str();
            comptId = Neutral::child( baseId_.eref(), name );
            if ( comptId == Id() )
                comptId = shell_->doCreate( "CubeMesh", baseId_, name, 1 );
        }
        SetGet1< double >::set( comptId, "setVolumeNotRates",vols_[i]);
        /*
        if ( comptId.element()->cinfo()->isA( "CubeMesh" ) ) {
            double side = pow( vols_[i], 1.0 / 3.0 );
            vector< double > coords( 9, side );
            coords[0] = coords[1] = coords[2] = 0;
            // Field< double >::set( comptId, "volume", vols_[i] );
            Field< vector< double > >::set( comptId, "coords", coords );
        } else {
        }
        */
        // compartments_.push_back( comptId );
        for ( vector< Id >::iterator k = volCategories_[i].begin();
            k != volCategories_[i].end(); ++k ) {
            // if ( moveOntoCompartment_ ) {
                if ( ! (getCompt( *k ).id == comptId ) )
                    shell_->doMove( *k, comptId );
            // }
        }
    }
}

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void ReadKkit::assignReacCompartments

(

)

Goes through all Reacs and connects them up to each of the compartments in which one or more of their reactants resides. Thus, if any of these compartments changes volume, the Reac will be informed.

Definition at line 810 of file ReadKkit.cpp.

References Shell::doMove(), findParentComptOfReac(), getCompt(), ObjId::id, reacIds_, and shell_.

Referenced by read().

{
    for ( map< string, Id >::iterator i = reacIds_.begin();
        i != reacIds_.end(); ++i ) {
        Id compt = findParentComptOfReac( i->second );
        if ( compt != Id() ) {
            if ( ! (getCompt( i->second ).id == compt ) )
                shell_->doMove( i->second, compt );
        }
    }
}

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Id ReadKkit::buildChan

(

const vector< string > &

args

)

Build a Kchan entry in simulation. For now a dummy Neutral.

Definition at line 1182 of file ReadKkit.cpp.

References chanIds_, chanMap_, cleanPath(), Shell::doCreate(), Shell::doFind(), ObjId::id, pathTail(), Field< A >::set(), and shell_.

Referenced by undump().

{
    string head;
    string clean = cleanPath( args[2] );
    string tail = pathTail( clean, head );
    Id pa = shell_->doFind( head ).id;
    assert( pa != Id() );

    // cout << "Warning: Kchan not yet supported in MOOSE, creating dummy:\n" << "  " << clean << "\n";
    //
    double permeability = atof( args[ chanMap_["perm"] ].c_str() );
    Id chan = shell_->doCreate( "ConcChan", pa, tail, 1 );
    Field< double >::set( chan, "permeability", permeability );
    assert( chan != Id() );
    string chanPath = clean.substr( 10 );
    chanIds_[ chanPath ] = chan;
    return chan;
}

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Id ReadKkit::buildCompartment

(

const vector< string > &

args

)

Definition at line 661 of file ReadKkit.cpp.

References numCompartments_.

{
    Id compt;
    numCompartments_++;
    return compt;
}

Id ReadKkit::buildEnz

(

const vector< string > &

args

)

vsf is vol scale factor, which is what GENESIS stores in 'vol' field n = vsf * conc( uM ) Also, n = ( conc (uM) / 1e6 ) * NA * vol so, vol = 1e6 * vsf / NA

Definition at line 883 of file ReadKkit.cpp.

References buildInfo(), cleanPath(), Shell::doAddMsg(), Shell::doCreate(), Shell::doFind(), enzCplxMols_, enzIds_, enzMap_, EPSILON, Id::eref(), ObjId::id, moose::info, KKIT_NA, lookupVolumeFromMesh(), mmEnzIds_, numEnz_, numMMenz_, pathTail(), poolIds_, poolVols_, separateVols(), Field< A >::set(), SetGet2< A1, A2 >::set(), and shell_.

Referenced by undump().

{
    string head;
    string clean = cleanPath( args[2] );
    string tail = pathTail( clean, head );
    Id pa = shell_->doFind( head ).id;
    assert ( pa != Id() );

    double k1 = atof( args[ enzMap_[ "k1" ] ].c_str() );
    double k2 = atof( args[ enzMap_[ "k2" ] ].c_str() );
    double k3 = atof( args[ enzMap_[ "k3" ] ].c_str() );
    // double volscale = atof( args[ enzMap_[ "vol" ] ].c_str() );
    double nComplexInit =
        atof( args[ enzMap_[ "nComplexInit" ] ].c_str() );
    // double vol = atof( args[ enzMap_[ "vol" ] ].c_str());
    bool isMM = atoi( args[ enzMap_[ "usecomplex" ] ].c_str());
    assert( poolVols_.find( pa ) != poolVols_.end() );
    double vol = poolVols_[ pa ];

    if ( isMM ) {
        Id enz = shell_->doCreate( "MMenz", pa, tail, 1 );
        assert( enz != Id () );
        string mmEnzPath = clean.substr( 10 );
        mmEnzIds_[ mmEnzPath ] = enz;

        assert( k1 > EPSILON );
        double Km = ( k2 + k3 ) / k1;

        Field< double >::set( enz, "Km", Km );
        Field< double >::set( enz, "kcat", k3 );
        Id info = buildInfo( enz, enzMap_, args );
        numMMenz_++;
        return enz;
    } else {
        Id enz = shell_->doCreate( "Enz", pa, tail, 1 );
        // double parentVol = Field< double >::get( pa, "volume" );
        assert( enz != Id () );
        string enzPath = clean.substr( 10 );
        enzIds_[ enzPath ] = enz;

        // Need to figure out what to do about these. Perhaps it is OK
        // to do this assignments in raw #/cell units.
        Field< double >::set( enz, "k3", k3 );
        Field< double >::set( enz, "k2", k2 );
        // Here we explicitly calculate Km because the substrates are
        // not set up till later, and without them the volume calculations
        // are confused.
        double volScale = lookupVolumeFromMesh(pa.eref());
        double Km = (k2+k3)/(k1 * KKIT_NA * vol ); // Scaling for uM to mM.
        SetGet2< double, double >::set( enz, "setKmK1", Km, k1 );

        string cplxName = tail + "_cplx";
        string cplxPath = enzPath + "/" + cplxName;
        Id cplx = shell_->doCreate( "Pool", enz, cplxName, 1 );
        assert( cplx != Id () );
        poolIds_[ cplxPath ] = cplx;
        // Field< double >::set( cplx, "nInit", nComplexInit );
        Field< double >::set( cplx, "nInit", nComplexInit );

        // Use this later to assign mesh entries to enz cplx.
        enzCplxMols_.push_back( pair< Id, Id >(  pa, cplx ) );
        separateVols( cplx, -1 ); // -1 vol is a flag to defer mesh assignment for the cplx pool.

        ObjId ret = shell_->doAddMsg( "OneToAll",
            ObjId( enz, 0 ), "cplx",
            ObjId( cplx, 0 ), "reac" );
        assert( ret != ObjId() );


        // cplx()->showFields();
        // enz()->showFields();
        // pa()->showFields();
        Id info = buildInfo( enz, enzMap_, args );
        numEnz_++;
        return enz;
    }
}

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Id ReadKkit::buildGeometry

(

const vector< string > &

args

)

Definition at line 1202 of file ReadKkit.cpp.

References numOthers_.

Referenced by undump().

{
    Id geometry;
    numOthers_++;
    return geometry;
}

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Id ReadKkit::buildGraph

(

const vector< string > &

args

)

Definition at line 1209 of file ReadKkit.cpp.

References cleanPath(), Shell::doCreate(), Shell::doFind(), ObjId::id, numOthers_, pathTail(), and shell_.

Referenced by undump().

{
    string head;
    string tail = pathTail( cleanPath( args[2] ), head );

    Id pa = shell_->doFind( head ).id;
    assert( pa != Id() );
    Id graph = shell_->doCreate( "Neutral", pa, tail, 1 );
    assert( graph != Id() );
    numOthers_++;
    return graph;
}

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Id ReadKkit::buildGroup

(

const vector< string > &

args

)

Definition at line 992 of file ReadKkit.cpp.

References buildInfo(), cleanPath(), Shell::doCreate(), Shell::doFind(), group(), groupMap_, ObjId::id, moose::info, numOthers_, pathTail(), and shell_.

Referenced by undump().

{
    string head;
    string tail = pathTail( cleanPath( args[2] ), head );
    Id pa = shell_->doFind( head ).id;
    assert( pa != Id() );
    Id group = shell_->doCreate( "Neutral", pa, tail, 1 );
    assert( group != Id() );
    Id info = buildInfo( group, groupMap_, args );

    numOthers_++;
    return group;
}

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Id ReadKkit::buildInfo	(	Id	parent,
		map< string, int > &	m,
		const vector< string > &	args
	)

Definition at line 975 of file ReadKkit.cpp.

References Shell::doCreate(), moose::info, Field< A >::set(), and shell_.

Referenced by buildEnz(), buildGroup(), buildPool(), buildReac(), and buildTable().

{
    Id info = shell_->doCreate( "Annotator", parent, "info", 1 );
    assert( info != Id() );

    double x = atof( args[ m[ "x" ] ].c_str() );
    double y = atof( args[ m[ "y" ] ].c_str() );

    Field< double >::set( info, "x", x );
    Field< double >::set( info, "y", y );
    Field< string >::set( info, "color", args[ m[ "xtree_fg_req" ] ] );
    Field< string >::set( info, "textColor",
        args[ m[ "xtree_textfg_req" ] ] );
    return info;
}

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Id ReadKkit::buildPlot

(

const vector< string > &

args

)

Definition at line 1222 of file ReadKkit.cpp.

References cleanPath(), Shell::doCreate(), Shell::doFind(), ObjId::id, numPlot_, pathTail(), plotIds_, and shell_.

Referenced by undump().

{
    string head;
    string tail = pathTail( cleanPath( args[2] ), head ); // Name of plot
    string temp;
    string graph = pathTail( head, temp ); // Name of graph

    Id pa = shell_->doFind( head ).id;
    assert( pa != Id() );

    Id plot = shell_->doCreate( "Table2", pa, tail, 1 );
    assert( plot != Id() );

    temp = graph + "/" + tail;
    plotIds_[ temp ] = plot;

    numPlot_++;
    return plot;
}

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Id ReadKkit::buildPool

(

const vector< string > &

args

)

There is a problem with this conversion, because of the discrepancy of the correct NA and the version (6e23) used in kkit. I take the concentration as authoritative, not the # of molecules. This is because I use conc units for the rates as well, and to use n for pools and conc for reactions will always introduce errors. This is still not a great solution, because, for example, simulations involving receptor traffic are originally framed in terms of number of receptors, not conc.

vsf is vol scale factor, which is what GENESIS stores in 'vol' field n = vsf * conc( uM ) Also, n = ( conc (uM) / 1e6 ) * NA * vol so, vol = 1e6 * vsf / NA

Definition at line 1015 of file ReadKkit.cpp.

References buildInfo(), cleanPath(), Shell::doCreate(), Shell::doFind(), ObjId::id, moose::info, KKIT_NA, numPools_, pathTail(), poolFlags_, poolIds_, poolMap_, poolVols_, separateVols(), Field< A >::set(), and shell_.

Referenced by undump().

{   
    string head;
    string clean = cleanPath( args[2] );
    string tail = pathTail( clean, head );
    Id pa = shell_->doFind( head ).id;
    assert( pa != Id() );

    double nInit = atof( args[ poolMap_[ "nInit" ] ].c_str() );
    double vsf = atof( args[ poolMap_[ "vol" ] ].c_str() );
    double vol = 1.0e3 * vsf / KKIT_NA; // Converts volscale to actual vol in m^3
    int slaveEnable = atoi( args[ poolMap_[ "slave_enable" ] ].c_str() );
    double diffConst = atof( args[ poolMap_[ "DiffConst" ] ].c_str() );

    // I used -ve D as a flag to replace pool-specific D
    // with the global value of D. Here we just ignore it.
    if ( diffConst < 0 )
        diffConst = 0;

    Id pool;
    if ( slaveEnable == 0 ) {
        pool = shell_->doCreate( "Pool", pa, tail, 1 );
    } else if ( slaveEnable & 4 ) {
        pool = shell_->doCreate( "BufPool", pa, tail, 1 );
    } else {
        pool = shell_->doCreate( "Pool", pa, tail, 1 );
        /*
        cout << "ReadKkit::buildPool: Unknown slave_enable flag '" <<
            slaveEnable << "' on " << clean << "\n";
            */
        poolFlags_[pool] = slaveEnable;
    }
    assert( pool != Id() );
    // skip the 10 chars of "/kinetics/"
    poolIds_[ clean.substr( 10 ) ] = pool;

    Field< double >::set( pool, "nInit", nInit );
    Field< double >::set( pool, "diffConst", diffConst );
    // SetGet1< double >::set( pool, "setVolume", vol );
    separateVols( pool, vol );
    poolVols_[pool] = vol;

    Id info = buildInfo( pool, poolMap_, args );
    /*
    cout << setw( 20 ) << head << setw( 15 ) << tail << "   " <<
        setw( 12 ) << nInit << "    " <<
        vol << "    " << diffConst << " " <<
        slaveEnable << endl;
        */
    numPools_++;
    return pool;
}

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Id ReadKkit::buildReac

(

const vector< string > &

args

)

Definition at line 668 of file ReadKkit.cpp.

References buildInfo(), cleanPath(), Shell::doCreate(), Shell::doFind(), ObjId::id, moose::info, numReacs_, pathTail(), reacIds_, reacMap_, Field< A >::set(), and shell_.

Referenced by undump().

{
    string head;
    string clean = cleanPath( args[2] );
    string tail = pathTail( clean, head );
    Id pa = shell_->doFind( head ).id;
    assert( pa != Id() );

    double kf = atof( args[ reacMap_[ "kf" ] ].c_str() );
    double kb = atof( args[ reacMap_[ "kb" ] ].c_str() );

    // We have a slight problem because MOOSE has a more precise value for
    // NA than does kkit. Here we assume that the conc units from Kkit are
    // meant to be OK, so they override the #/cell (lower case k) units.
    // So we convert all the Kfs and Kbs in the entire system after
    // the model has been created, once we know the order of each reac.

    Id reac = shell_->doCreate( "Reac", pa, tail, 1 );
    reacIds_[ clean.substr( 10 ) ] = reac;
    // Here is another hack: The native values stored in the reac are
    // Kf and Kb, in conc units. However the 'clean' values from kkit
    // are the number values numKf and numKb. In the
    // function convertReacRatesToNumUnits we take the numKf and numKb and
    // do proper conc scaling.
    Field< double >::set( reac, "Kf", kf );
    Field< double >::set( reac, "Kb", kb );

    Id info = buildInfo( reac, reacMap_, args );
    numReacs_++;
    return reac;
}

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Id ReadKkit::buildStim

(

const vector< string > &

args

)

Build a Stim entry in simulation, i.e., a PulseGen

Definition at line 1147 of file ReadKkit.cpp.

References cleanPath(), Shell::doCreate(), Shell::doFind(), ObjId::id, numStim_, pathTail(), Field< A >::set(), shell_, stimIds_, and stimMap_.

Referenced by undump().

{
    string head;
    string clean = cleanPath( args[2] );
    string tail = pathTail( clean, head );
    Id pa = shell_->doFind( head ).id;
    assert( pa != Id() );

    double level1 = atof( args[ stimMap_[ "firstLevel" ] ].c_str() );
    double width1 = atof( args[ stimMap_[ "firstWidth" ] ].c_str() );
    double delay1 = atof( args[ stimMap_[ "firstDelay" ] ].c_str() );
    double level2 = atof( args[ stimMap_[ "secondLevel" ] ].c_str() );
    double width2 = atof( args[ stimMap_[ "secondWidth" ] ].c_str() );
    double delay2 = atof( args[ stimMap_[ "secondLevel" ] ].c_str() );
    double baselevel = atof( args[ stimMap_[ "baseLevel" ] ].c_str() );

    Id stim = shell_->doCreate( "PulseGen", pa, tail, 1 );
    assert( stim != Id() );
    string stimPath = clean.substr( 10 );
    stimIds_[ stimPath ] = stim;
    Field< double >::set( stim, "firstLevel", level1 );
    Field< double >::set( stim, "firstWidth", width1 );
    Field< double >::set( stim, "firstDelay", delay1 );
    Field< double >::set( stim, "secondLevel", level2 );
    Field< double >::set( stim, "secondWidth", width2 );
    Field< double >::set( stim, "secondDelay", delay2 );
    Field< double >::set( stim, "baseLevel", baselevel );

    numStim_++;
    return stim;
}

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void ReadKkit::buildSumTotal	(	const string &	src,
		const string &	dest
	)

Definition at line 1098 of file ReadKkit.cpp.

References Neutral::child(), Shell::doAddMsg(), Shell::doCreate(), Id::element(), findSumTotSrc(), Field< A >::get(), BufPool::initCinfo(), poolIds_, Field< A >::set(), shell_, Id::value(), and Element::zombieSwap().

Referenced by addmsg().

{
    map< string, Id >::iterator i = poolIds_.find( dest );
    assert( i != poolIds_.end() );
    Id destId = i->second;

    Id sumId;
    // Check if the pool has not yet been converted to handle SumTots.
    if ( destId.element()->cinfo()->name() == "Pool" ) {
        sumId = shell_->doCreate( "Function", destId, "func", 1 );
        // Turn dest into a FuncPool.
        destId.element()->zombieSwap( BufPool::initCinfo() );

        ObjId ret = shell_->doAddMsg( "single",
            ObjId( sumId, 0 ), "valueOut",
            ObjId( destId, 0 ), "setN" );
        assert( ret != ObjId() );
    } else {
        sumId = Neutral::child( destId.eref(), "func" );
    }

    if ( sumId == Id() ) {
        cout << "Error: ReadKkit::buildSumTotal: could not make Function on '"
        << dest << "'\n";
        return;
    }

    Id srcId = findSumTotSrc( src );
    unsigned int numVars = Field< unsigned int >::get( sumId, "numVars" );
    ObjId xi( sumId.value() + 1, 0, numVars );
    Field< unsigned int >::set( sumId, "numVars", numVars + 1 );

    ObjId ret = shell_->doAddMsg( "single",
        ObjId( srcId, 0 ), "nOut",
        xi, "input" );
    assert( ret != ObjId() );


    stringstream ss;
    for ( unsigned int i = 0; i < numVars; ++i ) {
        ss << "x" << i << "+";
    }
    ss << "x" << numVars;
    Field< string >::set( sumId, "expr", ss.str() );
}

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Id ReadKkit::buildTable

(

const vector< string > &

args

)

Definition at line 1245 of file ReadKkit.cpp.

References buildInfo(), cleanPath(), Shell::doCreate(), Shell::doFind(), ObjId::id, moose::info, pathTail(), Field< A >::set(), shell_, TAB_IO, TAB_LOOP, TAB_ONCE, tabIds_, and tableMap_.

Referenced by undump().

{
    string head;
    string clean = cleanPath( args[2] );
    string tail = pathTail( clean, head ); // Name of xtab

    Id pa = shell_->doFind( head ).id;
    assert( pa != Id() );
    Id tab;

    int mode = atoi( args[ tableMap_[ "step_mode" ] ].c_str() );
    if ( mode == TAB_IO ) {
    } else if ( mode == TAB_LOOP || mode == TAB_ONCE ) {
        tab = shell_->doCreate( "StimulusTable", pa, tail, 1 );
        assert( tab != Id() );
        double stepSize = atof( args[ tableMap_[ "stepsize" ] ].c_str() );
        Field< double >::set( tab, "stepSize", stepSize );
        if ( mode == TAB_LOOP )
            Field< bool >::set( tab, "doLoop", 1 );
        double input = atof( args[ tableMap_[ "input" ] ].c_str() );
        Field< double >::set( tab, "startTime", -input );
        // The other StimulusTable parameters will have to wait till the
        // loadTab is invoked.
    }


    string temp = clean.substr( 10 );
    tabIds_[ temp ] = tab;

    Id info = buildInfo( tab, tableMap_, args );

    return tab;
}

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Id ReadKkit::buildText

(

const vector< string > &

args

)

Definition at line 968 of file ReadKkit.cpp.

References numOthers_.

Referenced by undump().

{
    Id text;
    numOthers_++;
    return text;
}

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void ReadKkit::call

(

const vector< string > &

args

)

call /kinetics/foo/notes LOAD notes_string_here

Definition at line 585 of file ReadKkit.cpp.

References basePath_, cleanPath(), and Field< A >::set().

Referenced by readData().

{
    if ( args.size() > 3 ) {
        unsigned int len = args[1].length();
        if ( ( args[1].substr( len - 5 ) ==  "notes" ) &&
            args[2] == "LOAD" ) {
            if ( args[3].length() == 0 )
                return;
            //HARSHA: Added CleanPath.
            string objName = cleanPath(args[1].substr( 0, len - 5 ));
                Id test(basePath_+objName);
            Id obj( basePath_ + objName + "info" );
            if ( obj != Id() ) {
                string notes = "";
                string space = "";
                for ( unsigned int i = 3; i < args.size(); ++i ) {
                    unsigned int innerLength = args[i].length();
                    if ( innerLength == 0 )
                        continue;
                    unsigned int start = 0;
                    unsigned int end = innerLength;
                    if ( args[i][0] == '\"' )
                        start = 1;
                    if ( args[i][innerLength - 1] == '\"' )
                        end = innerLength - 1 - start;

                    notes += space + args[i].substr( start, end );
                    space = " ";
                }
                Field< string >::set( obj, "notes", notes );
            }
        }
    }
}

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string ReadKkit::cleanPath

(

const string &

path

)

const

Utility function. Cleans up path strings. In most cases, it replaces things with underscores. Replaces square braces with underscores. Replaces '*' with 'p' as it is usually there to indicate phosphorylation Replaces '-' with underscore Replaces '@' with underscore Replaces ' ' with underscore

Definition at line 519 of file ReadKkit.cpp.

Referenced by addmsg(), buildChan(), buildEnz(), buildGraph(), buildGroup(), buildPlot(), buildPool(), buildReac(), buildStim(), buildTable(), and call().

{
    // Could surely do this better with STL. But harder to understand.
    // Harsha: Cleaned up this function
    // minus was getting replaced with underscore, but in some genesis model
    // pool and reaction/Enzyme has same string name with
    // difference of minus and underscore like eIF4G_A-clx and eIF4G_A_clx,
    // which later created a problem as the same name exist in moose when minus
    // was replaced with underscore.
    //So replacing minus with _minus_ like I do in SBML
    size_t Iindex = 0;
    string cleanDigit="/";
    while(true)
    { 
        size_t sindex = path.find('/',Iindex+1);
        if (sindex == string::npos) 
        {   if (isdigit((path.substr(Iindex+1,sindex-Iindex-1))[0]) )
                cleanDigit += '_' ;
            cleanDigit += path.substr(Iindex+1,sindex-Iindex-1);
            break;
        }
        if (isdigit((path.substr(Iindex+1,sindex-Iindex-1))[0]))
            cleanDigit+='_';
        cleanDigit += path.substr(Iindex+1,sindex-Iindex);
        Iindex = sindex; 
    }
    string ret = cleanDigit;
    //string ret = path;
    string cleanString;
    for ( unsigned int i = 0; i < cleanDigit.length(); ++i ) {
        char c = ret[i];
        if ( c == '*' )
            cleanString += "_p";
        else if ( c == '[' || c == ']' || c == '@' || c == ' ')
            cleanString += '_';
        else if (c == '-')
            cleanString += "_";
        else
            cleanString += c;
    }
    return cleanString;
}

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void ReadKkit::convertEnzRatesToConcUnits

(

)

Convert regular Enz rates. Binding step k1 has similar issues as reac rates. k2 and k3 are both in units of 1/time, so OK.

Definition at line 1588 of file ReadKkit.cpp.

References enzIds_, Field< A >::get(), KKIT_NA, NA, and Field< A >::set().

Referenced by convertParametersToConcUnits().

{
    const double NA_RATIO = KKIT_NA / NA;
    for ( map< string, Id >::iterator i = enzIds_.begin();
        i != enzIds_.end(); ++i ) {
        Id enz = i->second;
        double k1 = Field< double >::get( enz, "k1" );
        // At this point the k1 is inaaccurate because the
        // NA for kkit is not accurate. So we correct for this.
        double numSub =
            Field< unsigned int >::get( enz, "numSubstrates" );
        // Note that we always have the enz itself as a substrate term.
        if ( numSub > 0 )
            k1 *= pow( NA_RATIO, numSub );
        Field< double >::set( enz, "k1", k1 );
    }
}

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void ReadKkit::convertMMenzRatesToConcUnits

(

)

Convert MMEnz rates. Km should be in conc units. Actually rates stored as k1, k2, k3 in num units, so this has to be computed and then converted.

Definition at line 1562 of file ReadKkit.cpp.

References Field< A >::get(), KKIT_NA, mmEnzIds_, NA, and Field< A >::set().

Referenced by convertParametersToConcUnits().

{
    const double NA_RATIO = KKIT_NA / NA;
    for ( map< string, Id >::iterator i = mmEnzIds_.begin();
        i != mmEnzIds_.end(); ++i ) {
        Id enz = i->second;
        // This was set in the original # units.
        double numKm = Field< double >::get( enz, "Km" );
        // At this point the numKm is inaaccurate because the
        // NA for kkit is not accurate. So we correct for this.
        double numSub =
            Field< unsigned int >::get( enz, "numSubstrates" );
        // Note that we always have the enz itself as a substrate term.
        if ( numSub > 0 )
            numKm *= pow( NA_RATIO, -numSub );

        // Now we have the correct numKm, plug it into the MMenz, and
        // let it internally fix up the Km
        Field< double >::set( enz, "numKm", numKm );
    }
}

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void ReadKkit::convertParametersToConcUnits

(

)

We have a slight problem because MOOSE has a more precise value for NA than does kkit. Also, at the time the model is loaded, the volume relationships are unknown. So we need to fix up conc units of all pools reacs post-facto. Here we assume that the conc units from Kkit are meant to be OK, so they override the #/cell (lower case k) units. So we convert all the Kfs and Kbs in the entire system after the model has been created, once we know the order of each reac.

Definition at line 1506 of file ReadKkit.cpp.

References convertEnzRatesToConcUnits(), convertMMenzRatesToConcUnits(), convertPoolAmountToConcUnits(), and convertReacRatesToConcUnits().

Referenced by read().

{
    convertPoolAmountToConcUnits();
    convertReacRatesToConcUnits();
    convertMMenzRatesToConcUnits();
    convertEnzRatesToConcUnits();
}

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void ReadKkit::convertPoolAmountToConcUnits

(

)

Convert pool amounts. Initially given in n, but scaling issue.

Definition at line 1514 of file ReadKkit.cpp.

References Field< A >::get(), KKIT_NA, NA, poolIds_, and Field< A >::set().

Referenced by convertParametersToConcUnits().

{
    const double NA_RATIO = KKIT_NA / NA;
    for ( map< string, Id >::iterator i = poolIds_.begin();
        i != poolIds_.end(); ++i ) {
        Id pool = i->second;
        double nInit = Field< double >::get( pool, "nInit" );
        double n = Field< double >::get( pool, "n" );

        nInit /= NA_RATIO;
        n /= NA_RATIO;
        Field< double >::set( pool, "nInit", nInit );
        Field< double >::set( pool, "n", n );
    }
}

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void ReadKkit::convertReacRatesToConcUnits

(

)

Convert Reac rates, initially in n units.

Definition at line 1530 of file ReadKkit.cpp.

References Field< A >::get(), KKIT_NA, NA, reacIds_, and Field< A >::set().

Referenced by convertParametersToConcUnits().

{
    const double NA_RATIO = KKIT_NA / NA;
    for ( map< string, Id >::iterator i = reacIds_.begin();
        i != reacIds_.end(); ++i ) {
        Id reac = i->second;
        double kf = Field< double >::get( reac, "Kf" );
        double kb = Field< double >::get( reac, "Kb" );
        // Note funny access here, using the Conc unit term (Kf) to get the
        // num unit term (kf). When reading, there are no volumes so the
        // Kf gets assigned to what was the kf value from kkit.

        // At this point the kf and kb are off because the
        // NA for kkit is not accurate. So we correct for this.
        unsigned int numSub =
            Field< unsigned int >::get( reac, "numSubstrates" );
        unsigned int numPrd =
            Field< unsigned int >::get( reac, "numProducts" );

        if ( numSub > 1 )
            kf *= pow( NA_RATIO, numSub - 1.0 );

        if ( numPrd > 1 )
            kb *= pow( NA_RATIO, numPrd - 1.0 );

        // Now we have the correct numKf and numKb, plug them into the
        // reac, and let it internally fix up the Kf and Kb.
        Field< double >::set( reac, "numKf", kf );
        Field< double >::set( reac, "numKb", kb );
    }
}

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void ReadKkit::dumpPlots

(

const string &

filename

)

Definition at line 347 of file ReadKkit.cpp.

References basePath_, and wildcardFind().

Referenced by testReadKkit().

{
    // ofstream fout ( filename.c_str() );
    vector< ObjId > plots;
    string plotpath = basePath_ + "/graphs/##[TYPE=Table2]," +
        basePath_ + "/moregraphs/##[TYPE=Table2]";
    wildcardFind( plotpath, plots );
    for ( vector< ObjId >::iterator
                    i = plots.begin(); i != plots.end(); ++i )
        SetGet2< string, string >::set( *i, "xplot",
            filename, i->element()->getName() );
}

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Id ReadKkit::findSumTotSrc

(

const string &

src

)

Finds the source pool for a SumTot. It also deals with cases where the source is an enz-substrate complex

Definition at line 1078 of file ReadKkit.cpp.

References enzIds_, pathTail(), and poolIds_.

Referenced by buildSumTotal().

{
    map< string, Id >::iterator i = poolIds_.find( src );
    if ( i != poolIds_.end() ) {
        return i->second;
    }
    i = enzIds_.find( src );
    if ( i != enzIds_.end() ) {
        string head;
        string cplx = src + '/' + pathTail( src, head ) + "_cplx";
        i = poolIds_.find( cplx );
        if ( i != poolIds_.end() ) {
            return i->second;
        }
    }
    cout << "Error: ReadKkit::findSumTotSrc: Cannot find source pool '" << src << endl;
    assert( 0 );
    return Id();
}

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string ReadKkit::getBasePath

(

)

const

Definition at line 100 of file ReadKkit.cpp.

References basePath_.

{
    return basePath_;
}

double ReadKkit::getDefaultVol

(

)

const

Definition at line 95 of file ReadKkit.cpp.

References defaultVol_.

{
    return defaultVol_;
}

double ReadKkit::getMaxTime

(

)

const

Definition at line 85 of file ReadKkit.cpp.

References maxtime_.

{
    return maxtime_;
}

bool ReadKkit::getMoveOntoCompartment

(

)

const

Definition at line 110 of file ReadKkit.cpp.

References moveOntoCompartment_.

{
    return moveOntoCompartment_;
}

double ReadKkit::getPlotDt

(

)

const

Definition at line 90 of file ReadKkit.cpp.

References plotdt_.

{
    return plotdt_;
}

unsigned int ReadKkit::getVersion

(

)

const

Definition at line 105 of file ReadKkit.cpp.

References version_.

{
    return version_;
}

void ReadKkit::innerAddMsg	(	const string &	src,
		const map< string, Id > &	m1,
		const string &	srcMsg,
		const string &	dest,
		const map< string, Id > &	m2,
		const string &	destMsg,
		bool	isBackward = 0
	)

Definition at line 1318 of file ReadKkit.cpp.

References Shell::doAddMsg(), and shell_.

Referenced by addmsg(), and setupSlaveMsg().

{
    map< string, Id >::const_iterator i = m1.find( src );
    assert( i != m1.end() );
    Id srcId = i->second;

    i = m2.find( dest );
    assert( i != m2.end() );
    Id destId = i->second;

    // dest pool is substrate of src reac
    if ( isBackward ) {
        ObjId ret = shell_->doAddMsg( "AllToOne",
            ObjId( srcId, 0 ), srcMsg,
            ObjId( destId, 0 ), destMsg );
        assert( ret != ObjId() );
    } else {
        ObjId ret = shell_->doAddMsg( "OneToAll",
            ObjId( srcId, 0 ), srcMsg,
            ObjId( destId, 0 ), destMsg );
        assert( ret != ObjId() );
    }
}

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void ReadKkit::innerRead

(

ifstream &

fin

)

Definition at line 360 of file ReadKkit.cpp.

References COMMENT, DATA, INIT, lineNum_, readData(), readInit(), and moose::trim().

Referenced by read().

{
    string line;
    string temp;
    lineNum_ = 0;
    string::size_type pos;
    bool clearLine = 1;
    ParseMode parseMode = INIT;

    while ( getline( fin, temp ) ) {
        lineNum_++;
        if ( clearLine )
            line = "";
                temp = moose::trim(temp);
        if ( temp.length() == 0 )
                continue;
        pos = temp.find_last_not_of( "\t " );
        if ( pos == string::npos ) {
            // Nothing new in line, go with what was left earlier,
            // and clear out line for the next cycle.
            temp = "";
            clearLine = 1;
        } else {
            if ( temp[pos] == '\\' ) {
                temp[pos] = ' ';
                line.append( temp );
                clearLine = 0;
                continue;
            } else {
                line.append( temp );
                clearLine = 1;
            }
        }

        pos = line.find_first_not_of( "\t " );
        if ( pos == string::npos )
                continue;
        else
            line = line.substr( pos );
        if ( line.substr( 0, 2 ) == "//" )
                continue;
        if ( (pos = line.find("//")) != string::npos )
            line = line.substr( 0, pos );
        if ( line.substr( 0, 2 ) == "/*" ) {
                parseMode = COMMENT;
                line = line.substr( 2 );
        }

        if ( parseMode == COMMENT ) {
            pos = line.find( "*/" );
            if ( pos != string::npos ) {
                parseMode = DATA;
                if ( line.length() > pos + 2 )
                    line = line.substr( pos + 2 );
            }
        }

        if ( parseMode == DATA )
                readData( line );
        else if ( parseMode == INIT ) {
                parseMode = readInit( line );
        }
    }

    /*
    cout << " innerRead: " <<
            lineNum_ << " lines read, " <<
            numCompartments_ << " compartments, " <<
            numPools_ << " molecules, " <<
            numReacs_ << " reacs, " <<
            numEnz_ << " enzs, " <<
            numMMenz_ << " MM enzs, " <<
            numOthers_ << " others," <<
            numPlot_ << " plots," <<
            " PlotDt = " << plotdt_ <<
            endl;
            */
}

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unsigned int ReadKkit::loadTab

(

const vector< string > &

args

)

Definition at line 1279 of file ReadKkit.cpp.

References basePath_, Element::cinfo(), Id::element(), Field< A >::get(), Cinfo::isA(), lastTab_, Field< A >::set(), and tabEntries_.

Referenced by readData().

{
    Id tab;
    unsigned int start = 0;
    if ( args[1].substr( 0, 5 ) == "-cont" || args[1] == "-end" ) {
        start = 2;
        tab = lastTab_;
        assert( tab != Id() );
    } else {
        tabEntries_.resize( 0 );
        start = 7;
        assert( args.size() >= start );
        lastTab_ = tab = Id( basePath_ + args[1] );
        assert( tab != Id() );
        // int calc_mode = atoi( args[3].c_str() );
        // int xdivs = atoi( args[4].c_str() );
        if ( tab.element()->cinfo()->isA( "StimulusTable" ) ) {
            double xmin = atof( args[5].c_str() );
            double xmax = atof( args[6].c_str() );
            double start = Field< double >::get( tab, "startTime" );
            start += xmin;
            Field< double >::set( tab, "startTime", start );
            Field< double >::set( tab, "stopTime", xmax );
        }
    }

    for ( unsigned int i = start; i < args.size(); ++i ) {
        tabEntries_.push_back( atof( args[i].c_str() ) );
    }
    Field< vector< double > >::set( tab, "vector", tabEntries_ );

    // cout << "Loading table for " << args[0] << "," << args[1] << "," << clean << endl;

    if ( args[1] == "-end" )
        lastTab_ = Id();

    return 0;
}

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void ReadKkit::objdump

(

const vector< string > &

args

)

Definition at line 568 of file ReadKkit.cpp.

References assignArgs(), chanMap_, enzMap_, groupMap_, poolMap_, reacMap_, stimMap_, and tableMap_.

Referenced by readData().

{   if ( args[1] == "kpool" )
        assignArgs( poolMap_, args );
    else if ( args[1] == "kreac" )
        assignArgs( reacMap_, args );
    else if ( args[1] == "kenz" )
        assignArgs( enzMap_, args );
    else if ( args[1] == "group" )
        assignArgs( groupMap_, args );
    else if ( args[1] == "xtab" )
        assignArgs( tableMap_, args );
    else if ( args[1] == "stim" )
        assignArgs( stimMap_, args );
    else if ( args[1] == "kchan" )
        assignArgs( chanMap_, args );
}

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string ReadKkit::pathTail	(	const string &	path,
		string &	head
	)		const

Splits up kkit path into head and tail portions, tail is returned. Note that this prepends the basePath to the head.

Definition at line 510 of file ReadKkit.cpp.

References basePath_.

Referenced by addmsg(), buildChan(), buildEnz(), buildGraph(), buildGroup(), buildPlot(), buildPool(), buildReac(), buildStim(), buildTable(), and findSumTotSrc().

{
    string::size_type pos = path.find_last_of( "/" );
    assert( pos != string::npos );

    head = basePath_ + path.substr( 0, pos );
    return path.substr( pos + 1 );
}

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Id ReadKkit::read	(	const string &	filename,
		const string &	cellname,
		Id	parent,
		const string &	solverClass = "Stoich"
	)

The readcell function implements the old GENESIS cellreader functionality. Although it is really a parser operation, I put it here in Kinetics because the cell format is independent of parser and is likely to remain a legacy for a while.

Definition at line 276 of file ReadKkit.cpp.

References assignEnzCompartments(), assignMMenzCompartments(), assignPoolCompartments(), assignReacCompartments(), baseId_, basePath_, convertParametersToConcUnits(), ObjId::data(), Shell::doCreate(), Shell::doReinit(), enzCplxMols_, innerRead(), makeStandardElements(), maxtime_, moveOntoCompartment_, Id::path(), plotdt_, Field< A >::set(), setMethod(), and simdt_.

Referenced by Shell::doLoadModel(), and testReadKkit().

{
    string method = methodArg;
    ifstream fin( filename.c_str() );
    if (!fin){
        cerr << "ReadKkit::read: could not open file " << filename << endl;
        return Id();
    }

    if ( method.substr(0, 4) == "old_" ) {
        moveOntoCompartment_ = false;
        method = method.substr( 4 );
    }

    Shell* s = reinterpret_cast< Shell* >( ObjId().data() );
    Id mgr = makeStandardElements( pa, modelname );
    assert( mgr != Id() );
    baseId_ = mgr;
    basePath_ = mgr.path();
    enzCplxMols_.resize( 0 );

    innerRead( fin );
    assignPoolCompartments();
    assignReacCompartments();
    assignEnzCompartments();
    assignMMenzCompartments();

    convertParametersToConcUnits();

    setMethod( s, mgr, simdt_, plotdt_, method );

    //Harsha: Storing solver and runtime at model level rather than model level
    Id kinetics( basePath_+"/kinetics");
    assert(kinetics != Id());
    Id cInfo = s->doCreate( "Annotator", basePath_, "info", 1 );
    assert( cInfo != Id() );
    Field< string > ::set(cInfo, "solver", "ee");
    Field< double > ::set(cInfo, "runtime", maxtime_);
    s->doReinit();
    return mgr;
}

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void ReadKkit::readData

(

const string &

line

)

Definition at line 491 of file ReadKkit.cpp.

References addmsg(), call(), chopLine(), loadTab(), objdump(), textload(), and undump().

Referenced by innerRead().

{
    vector< string > argv;
    chopLine( line, argv );

    if ( argv[0] == "simundump" )
        undump( argv );
    else if ( argv[0] == "addmsg" )
        addmsg( argv );
    else if ( argv[0] == "call" )
        call( argv );
    else if ( argv[0] == "simobjdump" )
        objdump( argv );
    else if ( argv[0] == "xtextload" )
        textload( argv );
    else if ( argv[0] == "loadtab" )
        loadTab( argv );
}

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ReadKkit::ParseMode ReadKkit::readInit

(

const string &

line

)

Definition at line 439 of file ReadKkit.cpp.

References chopLine(), controldt_, DATA, defaultVol_, fastdt_, INIT, initdumpVersion_, maxtime_, plotdt_, simdt_, transientTime_, useVariableDt_, and version_.

Referenced by innerRead().

{
    vector< string > argv;
    chopLine( line, argv );
    if ( argv.size() < 3 )
        return INIT;

    if ( argv[0] == "FASTDT" ) {
        fastdt_ = atof( argv[2].c_str() );
        return INIT;
    }
    if ( argv[0] == "SIMDT" ) {
        simdt_ = atof( argv[2].c_str() );
        return INIT;
    }
    if ( argv[0] == "CONTROLDT" ) {
        controldt_ = atof( argv[2].c_str() );
        return INIT;
    }
    if ( argv[0] == "PLOTDT" ) {
        plotdt_ = atof( argv[2].c_str() );
        return INIT;
    }
    if ( argv[0] == "MAXTIME" ) {
        maxtime_ = atof( argv[2].c_str() );
        return INIT;
    }
    if ( argv[0] == "TRANSIENT_TIME" ) {
        transientTime_ = atof( argv[2].c_str() );
        return INIT;
    }
    if ( argv[0] == "VARIABLE_DT_FLAG" ) {
        useVariableDt_ = atoi( argv[2].c_str() );
        return INIT;
    }
    if ( argv[0] == "DEFAULT_VOL" ) {
        defaultVol_ = atof( argv[2].c_str() );
        return INIT;
    }
    if ( argv[0] == "VERSION" ) {
        version_ = atoi( argv[2].c_str() );
        return INIT;
    }

    if ( argv[0] == "initdump" ) {
        initdumpVersion_ = atoi( argv[2].c_str() );
        return DATA;
    }
    return INIT;
}

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void ReadKkit::run

(

)

This function sets up the kkit model for a run using the GSL, which means numerical integration using the GSL, all the plots specified by the kkit file, and the timestep for plots as specified by the kkit file.

Definition at line 321 of file ReadKkit.cpp.

References Shell::doReinit(), Shell::doSetClock(), Shell::doStart(), fastdt_, maxtime_, plotdt_, shell_, simdt_, transientTime_, and useVariableDt_.

Referenced by testReadKkit().

{
    shell_->doSetClock( 11, simdt_ );
    shell_->doSetClock( 12, simdt_ );
    shell_->doSetClock( 13, simdt_ );
    shell_->doSetClock( 14, simdt_ );
    shell_->doSetClock( 16, plotdt_ );
    shell_->doSetClock( 17, plotdt_ );
    shell_->doSetClock( 18, plotdt_ );
    shell_->doReinit();
    if ( useVariableDt_ ) {
        shell_->doSetClock( 11, fastdt_ );
        shell_->doSetClock( 12, fastdt_ );
        shell_->doSetClock( 13, fastdt_ );
        shell_->doSetClock( 14, fastdt_ );
        shell_->doStart( transientTime_ );
        shell_->doSetClock( 11, simdt_ );
        shell_->doSetClock( 12, simdt_ );
        shell_->doSetClock( 13, simdt_ );
        shell_->doSetClock( 14, simdt_ );
        shell_->doStart( maxtime_ - transientTime_ );
    } else {
        shell_->doStart( maxtime_ );
    }
}

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void ReadKkit::separateVols	(	Id	pool,
		double	vol
	)

Definition at line 700 of file ReadKkit.cpp.

References volCategories_, and vols_.

Referenced by buildEnz(), and buildPool().

{
    static const double TINY = 1e-3;

    for ( unsigned int i = 0 ; i < vols_.size(); ++i ) {
        if ( fabs( vols_[i] - vol ) / ( fabs( vols_[i] ) + fabs( vol ) ) < TINY ) {
            volCategories_[i].push_back( pool );
            return;
        }
    }
    vols_.push_back( vol );
    vector< Id > temp( 1, pool );
    volCategories_.push_back( temp );
}

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void ReadKkit::setMoveOntoCompartment

(

bool

v

)

Definition at line 115 of file ReadKkit.cpp.

References moveOntoCompartment_.

{
    moveOntoCompartment_ = v;
}

void ReadKkit::setupSlaveMsg	(	const string &	src,
		const string &	dest
	)

Definition at line 1447 of file ReadKkit.cpp.

References basePath_, Element::cinfo(), Id::element(), Field< A >::get(), BufPool::initCinfo(), innerAddMsg(), Cinfo::isA(), output(), poolFlags_, poolIds_, Field< A >::set(), SetGet2< A1, A2 >::set(), stimIds_, tabIds_, and Element::zombieSwap().

Referenced by addmsg().

{
    // Convert the pool to a BufPool, if it isn't one already
    Id destId( basePath_ + "/kinetics/" + dest );
    assert( destId != Id() );

    if( !destId.element()->cinfo()->isA( "BufPool" )) {
        destId.element()->zombieSwap( BufPool::initCinfo() );
    }

    map< string, Id >* nameMap;
    // Check if the src is a table or a stim
    Id srcId( basePath_ + "/kinetics/" + src );
    assert( srcId != Id() );
    string output = "output";
    if ( srcId.element()->cinfo()->isA( "TableBase" ) ) {
        nameMap = &tabIds_;
    } else if ( srcId.element()->cinfo()->isA( "PulseGen" ) ) {
        nameMap = &stimIds_;
        output = "output";
    } else {
        cout << "Error: Unknown source for SLAVE msg: (" << src <<
            ", " << dest << ")\n";
        return;
    }

    // NSLAVE is 1, CONCSLAVE is 2.
    map< Id, int >::iterator i = poolFlags_.find( destId );
    if ( i == poolFlags_.end() || !( i->second & 2 ) ) {
        innerAddMsg( src, *nameMap, output, dest, poolIds_,
            "setNInit" );
    } else {
        innerAddMsg( src, *nameMap, output, dest, poolIds_,
            "setConcInit" );

        double CONCSCALE = 0.001;
        // Rescale from uM to millimolar.
        if ( nameMap == &tabIds_ ) {
            SetGet2< double, double >::set( srcId, "linearTransform",
                CONCSCALE, 0 );
        } else if ( nameMap == &stimIds_ ) {
            double x = Field< double >::get( srcId, "baseLevel" );
            Field< double >::set( srcId, "baseLevel", x * CONCSCALE );
            x = Field< double >::get( srcId, "firstLevel" );
            Field< double >::set( srcId, "firstLevel", x * CONCSCALE );
            x = Field< double >::get( srcId, "secondLevel" );
            Field< double >::set( srcId, "secondLevel", x * CONCSCALE );
        }
    }
    // cout << "Added slave msg from " << src << " to " << dest << endl;
}

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void ReadKkit::textload

(

const vector< string > &

args

)

Definition at line 621 of file ReadKkit.cpp.

Referenced by readData().

{
}

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void ReadKkit::undump

(

const vector< string > &

args

)

Definition at line 625 of file ReadKkit.cpp.

References buildChan(), buildEnz(), buildGeometry(), buildGraph(), buildGroup(), buildPlot(), buildPool(), buildReac(), buildStim(), buildTable(), and buildText().

Referenced by readData().

{   if ( args[1] == "kpool" )
        buildPool( args );
    else if ( args[1] == "kreac" )
        buildReac( args );
    else if ( args[1] == "kenz" )
        buildEnz( args );
    else if ( args[1] == "text" )
        buildText( args );
    else if ( args[1] == "xplot" )
        buildPlot( args );
    else if ( args[1] == "xgraph" )
        buildGraph( args );
    else if ( args[1] == "group" )
        buildGroup( args );
    else if ( args[1] == "geometry" )
        buildGeometry( args );
    else if ( args[1] == "stim" )
        buildStim( args );
    else if ( args[1] == "xcoredraw" )
        ;
    else if ( args[1] == "xtree" )
        ;
    else if ( args[1] == "xtext" )
        ;
    else if ( args[1] == "doqcsinfo" )
        ;
    else if ( args[1] == "kchan" )
        buildChan( args );
    else if ( args[1] == "xtab" )
        buildTable( args );
    else
        cout << "ReadKkit::undump: Do not know how to build '" << args[1] <<
        "'\n";
}

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Member Data Documentation

Id ReadKkit::baseId_

private

Base path into which entire kkit model will go.

Definition at line 181 of file ReadKkit.h.

Referenced by assignPoolCompartments(), and read().

string ReadKkit::basePath_

private

Definition at line 180 of file ReadKkit.h.

Referenced by call(), dumpPlots(), getBasePath(), loadTab(), pathTail(), read(), and setupSlaveMsg().

map< string, Id > ReadKkit::chanIds_

private

Definition at line 228 of file ReadKkit.h.

Referenced by addmsg(), and buildChan().

map< string, int > ReadKkit::chanMap_

private

Definition at line 220 of file ReadKkit.h.

Referenced by buildChan(), and objdump().

vector< Id > ReadKkit::compartments_

private

Definition at line 246 of file ReadKkit.h.

double ReadKkit::controldt_

private

regular numerical timestep from kkit.

Definition at line 185 of file ReadKkit.h.

Referenced by readInit().

double ReadKkit::defaultVol_

private

Use both fast and sim dts.

Definition at line 190 of file ReadKkit.h.

Referenced by getDefaultVol(), and readInit().

vector< pair< Id, Id > > ReadKkit::enzCplxMols_

private

Definition at line 247 of file ReadKkit.h.

Referenced by buildEnz(), and read().

map< string, Id > ReadKkit::enzIds_

private

Definition at line 223 of file ReadKkit.h.

Referenced by addmsg(), buildEnz(), convertEnzRatesToConcUnits(), and findSumTotSrc().

map< string, int > ReadKkit::enzMap_

private

Definition at line 216 of file ReadKkit.h.

Referenced by buildEnz(), and objdump().

const double ReadKkit::EPSILON = 1.0e-15

staticprivate

Definition at line 255 of file ReadKkit.h.

Referenced by buildEnz().

double ReadKkit::fastdt_

private

Base Id onto which entire kkit model will go.

Definition at line 183 of file ReadKkit.h.

Referenced by readInit(), and run().

map< string, int > ReadKkit::groupMap_

private

Definition at line 217 of file ReadKkit.h.

Referenced by buildGroup(), and objdump().

unsigned int ReadKkit::initdumpVersion_

private

KKit version.

Definition at line 192 of file ReadKkit.h.

Referenced by readInit().

Id ReadKkit::lastTab_

private

This keeps track of the last Table used in loadtab.

Definition at line 240 of file ReadKkit.h.

Referenced by loadTab().

unsigned int ReadKkit::lineNum_

private

Definition at line 212 of file ReadKkit.h.

Referenced by innerRead().

double ReadKkit::maxtime_

private

Timestep for updating plots.

Definition at line 187 of file ReadKkit.h.

Referenced by getMaxTime(), read(), readInit(), and run().

map< string, Id > ReadKkit::mmEnzIds_

private

Definition at line 224 of file ReadKkit.h.

Referenced by addmsg(), buildEnz(), and convertMMenzRatesToConcUnits().

bool ReadKkit::moveOntoCompartment_

private

Initdump too has a version.

Normally ReadKkit puts things on the same tree as the kkit tree. This flag tells the system to reorganize the tree so that each pool or reac or enz is on an appropriate compartment. Reacs are a bit arbitrary though, just go onto same compt as substrate. Defaults to false.

Definition at line 201 of file ReadKkit.h.

Referenced by getMoveOntoCompartment(), read(), and setMoveOntoCompartment().

unsigned int ReadKkit::numCompartments_

private

Definition at line 203 of file ReadKkit.h.

Referenced by buildCompartment().

unsigned int ReadKkit::numEnz_

private

Definition at line 206 of file ReadKkit.h.

Referenced by buildEnz().

unsigned int ReadKkit::numMMenz_

private

Definition at line 207 of file ReadKkit.h.

Referenced by buildEnz().

unsigned int ReadKkit::numOthers_

private

Definition at line 210 of file ReadKkit.h.

Referenced by buildGeometry(), buildGraph(), buildGroup(), and buildText().

unsigned int ReadKkit::numPlot_

private

Definition at line 208 of file ReadKkit.h.

Referenced by buildPlot().

unsigned int ReadKkit::numPools_

private

Definition at line 204 of file ReadKkit.h.

Referenced by buildPool().

unsigned int ReadKkit::numReacs_

private

Definition at line 205 of file ReadKkit.h.

Referenced by buildReac().

unsigned int ReadKkit::numStim_

private

Definition at line 209 of file ReadKkit.h.

Referenced by buildStim().

double ReadKkit::plotdt_

private

Timestep for updating control graphics.

Definition at line 186 of file ReadKkit.h.

Referenced by getPlotDt(), read(), readInit(), and run().

map< string, Id > ReadKkit::plotIds_

private

Definition at line 225 of file ReadKkit.h.

Referenced by addmsg(), and buildPlot().

map< Id, int > ReadKkit::poolFlags_

private

Definition at line 249 of file ReadKkit.h.

Referenced by buildPool(), and setupSlaveMsg().

map< string, Id > ReadKkit::poolIds_

private

Definition at line 221 of file ReadKkit.h.

Referenced by addmsg(), buildEnz(), buildPool(), buildSumTotal(), convertPoolAmountToConcUnits(), findSumTotSrc(), and setupSlaveMsg().

map< string, int > ReadKkit::poolMap_

private

Definition at line 214 of file ReadKkit.h.

Referenced by buildPool(), and objdump().

map< Id, double > ReadKkit::poolVols_

private

Definition at line 251 of file ReadKkit.h.

Referenced by buildEnz(), and buildPool().

map< string, Id > ReadKkit::reacIds_

private

Definition at line 222 of file ReadKkit.h.

Referenced by addmsg(), assignReacCompartments(), buildReac(), and convertReacRatesToConcUnits().

map< string, int > ReadKkit::reacMap_

private

Definition at line 215 of file ReadKkit.h.

Referenced by buildReac(), and objdump().

Shell* ReadKkit::shell_

private

Definition at line 253 of file ReadKkit.h.

Referenced by addmsg(), assignPoolCompartments(), assignReacCompartments(), buildChan(), buildEnz(), buildGraph(), buildGroup(), buildInfo(), buildPlot(), buildPool(), buildReac(), buildStim(), buildSumTotal(), buildTable(), innerAddMsg(), and run().

double ReadKkit::simdt_

private

fast numerical timestep from kkit.

Definition at line 184 of file ReadKkit.h.

Referenced by read(), readInit(), and run().

map< string, Id > ReadKkit::stimIds_

private

Definition at line 227 of file ReadKkit.h.

Referenced by buildStim(), and setupSlaveMsg().

map< string, int > ReadKkit::stimMap_

private

Definition at line 219 of file ReadKkit.h.

Referenced by buildStim(), and objdump().

vector< double > ReadKkit::tabEntries_

private

This holds the vector of array entries for loadtab.

Definition at line 242 of file ReadKkit.h.

Referenced by loadTab().

map< string, Id > ReadKkit::tabIds_

private

Definition at line 226 of file ReadKkit.h.

Referenced by buildTable(), and setupSlaveMsg().

map< string, int > ReadKkit::tableMap_

private

Definition at line 218 of file ReadKkit.h.

Referenced by buildTable(), and objdump().

double ReadKkit::transientTime_

private

Simulation run time.

Definition at line 188 of file ReadKkit.h.

Referenced by readInit(), and run().

bool ReadKkit::useVariableDt_

private

Time to run model at fastdt.

Definition at line 189 of file ReadKkit.h.

Referenced by readInit(), and run().

unsigned int ReadKkit::version_

private

Default volume for new compartments.

Definition at line 191 of file ReadKkit.h.

Referenced by getVersion(), and readInit().

vector< vector< Id > > ReadKkit::volCategories_

private

List of Ids in each unique volume.

Definition at line 245 of file ReadKkit.h.

Referenced by assignPoolCompartments(), and separateVols().

vector< double > ReadKkit::vols_

private

This keeps track of unique volumes.

Definition at line 237 of file ReadKkit.h.

Referenced by assignPoolCompartments(), and separateVols().

---

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

• moose-core/kinetics/ReadKkit.h
• moose-core/kinetics/ReadKkit.cpp