ReadCspace Class Reference

#include <ReadCspace.h>

Collaboration diagram for ReadCspace:

Public Member Functions
void	build (const char *name)
void	deployParameters ()
void	expandEnzyme (const char *name, int e, int s, int p, int p2=0)
void	expandReaction (const char *name, int nm1)
void	makeMolecule (char name)
void	makePlots (double plotdt)
void	printEnz (Id id, Id cplx, double k1, double k2, double k3)
void	printFooter ()
void	printHeader ()
void	printMol (Id id, double conc, double concinit, double vol)
void	printReac (Id id, double kf, double kb)
	ReadCspace ()
Id	readModelString (const string &model, const string &modelname, Id pa, const string &solverClass)
void	testReadModel ()

Private Attributes
Id	base_
Id	compt_
ostream *	fout_
Id	mesh_
vector< Id >	mol_
vector< CspaceMolInfo >	mollist_
vector< double >	molparms_
vector< unsigned int >	molseq_
vector< double >	parms_
vector< Id >	reac_
vector< CspaceReacInfo >	reaclist_

Static Private Attributes
static const double	DEFAULT_CONC = 1.0
static const double	DEFAULT_KM = 1.0
static const double	DEFAULT_RATE = 0.1
static const double	SCALE = 1.0
static const bool	USE_PIPE = 1

Detailed Description

Definition at line 74 of file ReadCspace.h.

Constructor & Destructor Documentation

ReadCspace::ReadCspace

(

)

Definition at line 24 of file ReadCspace.cpp.

    :
        base_(),
        compt_(),
        mesh_(),
        fout_( &cout )
{;}

Member Function Documentation

void ReadCspace::build

(

const char *

name

)

Definition at line 253 of file ReadCspace.cpp.

References expandEnzyme(), expandReaction(), and makeMolecule().

Referenced by readModelString().

{
    makeMolecule( name[1] );
    makeMolecule( name[2] );
    makeMolecule( name[3] );
    char tname[6];
    strncpy( tname, name, 4 );
    tname[4] = '\0';

    switch ( tname[0] ) {
        case 'A':
        case 'E':
            expandReaction( tname, 1 );
            break;
        case 'B':
        case 'F':
        case 'G':
        case 'H':
            expandReaction( tname, 2 );
            break;
        case 'I':
            expandReaction( tname, 4 );
            break;
        case 'C':
            expandEnzyme( tname, 1, 1, 2 );
            break;
        case 'D':
            expandEnzyme( tname, 2, 1, 2 );
            break;
        case 'J':
            expandEnzyme( tname, 2, 1, 3 );
            break;
        case 'K':
            expandEnzyme( tname, 1, 1, 2, 3 );
            break;
        case 'L':
            expandEnzyme( tname, 2, 1, 2, 3 );
            break;
        default:
            break;
    }
}

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void ReadCspace::deployParameters

(

)

Definition at line 329 of file ReadCspace.cpp.

References Neutral::children(), mol_, parms_, reac_, and Field< A >::set().

Referenced by readModelString().

{
    // static Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
    unsigned long i, j;
    if ( parms_.size() != mol_.size() + 2 * reac_.size() ) {
        cerr << "ReadCspace::deployParameters: Error: # of parms mismatch\n";
        return;
    }
    for ( i = 0; i < mol_.size(); i++ ) {
        // SetField(mol_[ i ], "volscale", volscale );
        // SetField(mol_[ molseq_[i] ], "ninit", parms_[ i ] );

        // Parameters are in micromolar, but the conc units are millimolar.
        Field< double >::set( mol_[i], "concInit", parms_[i] *  1e-3 );
    }
    for ( j = 0; j < reac_.size(); j++ ) {
        if ( reac_[ j ].element()->cinfo()->isA( "Reac" ) ) {
            Field< double >::set( reac_[j], "Kf", parms_[i++] );
            Field< double >::set( reac_[j], "Kb", parms_[i++] );
        } else {
            Field< double >::set( reac_[j], "k3", parms_[i] );
            Field< double >::set( reac_[j], "k2", 4.0 * parms_[i++] );
            // Again, note that conc units in MOOSE are millimolar, so we
            // need to convert from the CSPACE micromolar units.
            Field< double >::set( reac_[j], "Km", parms_[i++] * 1e-3 );
            vector< Id > cplx( 0 );
            Neutral::children( reac_[j].eref(), cplx );
            assert( cplx.size() == 1 );
        }
    }
}

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void ReadCspace::expandEnzyme	(	const char *	name,
		int	e,
		int	s,
		int	p,
		int	p2 = 0
	)

Definition at line 184 of file ReadCspace.cpp.

References Eref::data(), DEFAULT_KM, DEFAULT_RATE, Shell::doAddMsg(), Shell::doCreate(), Id::eref(), mol_, name, parms_, and reac_.

Referenced by build().

{
    static Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );

    Id enzMolId = mol_[ name[e] - 'a' ];

    Id enzId = shell->doCreate( "Enz", enzMolId, name, 1 );
    assert( enzId != Id() );
    string cplxName = name;
    cplxName += "_cplx";
    Id cplxId = shell->doCreate( "Pool", enzId, cplxName, 1 );
    assert( cplxId != Id() );
    ObjId ret = shell->doAddMsg( "OneToOne",
        enzId, "cplx", cplxId, "reac" );

    ret = shell->doAddMsg( "OneToOne",
        enzMolId, "reac", enzId, "enz" );

    ret = shell->doAddMsg( "OneToOne",
        mol_[ name[ s ] - 'a' ], "reac", enzId, "sub" );

    ret = shell->doAddMsg( "OneToOne",
        mol_[ name[ p ] - 'a' ], "reac", enzId, "prd" );

    if ( p2 != 0 )
        ret = shell->doAddMsg( "OneToOne",
            mol_[ name[ p2 ] - 'a' ], "reac", enzId, "prd" );

    assert( ret != ObjId() );

    reac_.push_back( enzId );
    parms_.push_back( DEFAULT_RATE );
    parms_.push_back( DEFAULT_KM );
}

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void ReadCspace::expandReaction	(	const char *	name,
		int	nm1
	)

Definition at line 220 of file ReadCspace.cpp.

References compt_, Eref::data(), DEFAULT_RATE, Shell::doAddMsg(), Shell::doCreate(), Id::eref(), mol_, parms_, and reac_.

Referenced by build().

{
    static Shell* s = reinterpret_cast< Shell* >( Id().eref().data() );

    if ( name[0] == 'C' || name[0] == 'D' || name[0] >= 'J' ) // enzymes
        return;
    int i;

    Id reacId = s->doCreate( "Reac", compt_, name, 1 );

    // A is always a substrate
    for (i = 0; i < nm1; i++ ) {
        s->doAddMsg( "OneToOne", reacId, "sub", mol_[ name[1] - 'a' ], "reac" );
    }

    if ( name[0] < 'G' ) { // B is a product
        s->doAddMsg( "OneToOne", reacId, "prd", mol_[ name[2] - 'a' ], "reac" );
    } else { // B is a substrate
        s->doAddMsg( "OneToOne", reacId, "sub", mol_[ name[2] - 'a' ], "reac" );
    }

    if ( name[0] > 'D' ) { // C is a product
        s->doAddMsg( "OneToOne", reacId, "prd", mol_[ name[3] - 'a' ], "reac" );
    }

    if ( name[0] == 'H' ) { // C is a dual product
        s->doAddMsg( "OneToOne", reacId, "prd", mol_[ name[3] - 'a' ], "reac" );
    }
    reac_.push_back( reacId );
    parms_.push_back( DEFAULT_RATE );
    parms_.push_back( DEFAULT_RATE );
}

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void ReadCspace::makeMolecule

(

char

name

)

Definition at line 296 of file ReadCspace.cpp.

References compt_, Eref::data(), DEFAULT_CONC, Shell::doCreate(), Id::eref(), mol_, molparms_, and molseq_.

Referenced by build().

{
    static Shell* s = reinterpret_cast< Shell* >( Id().eref().data() );

    if ( name == 'X' ) // silently ignore it, as it is a legal state
        return;
    if ( name < 'a' || name > 'z' ) {
        cerr << "ReadCspace::makeMolecule Error: name '" << name <<
            "' out of range 'a' to 'z'\n";
        return;
    }

    unsigned int index = 1 + name - 'a';

    // Put in molecule if it is a new one.
    if ( find( molseq_.begin(), molseq_.end(), index - 1 ) ==
                    molseq_.end() )
            molseq_.push_back( index - 1 );

    for ( unsigned int i = mol_.size(); i < index; i++ ) {
        string molname("");
        molname += 'a' + i;
        /*
        stringstream ss( "a" );
        ss << i ;
        string molname = ss.str();
        */
        Id temp = s->doCreate( "Pool", compt_, molname, 1 );
        mol_.push_back( temp );
        molparms_.push_back( DEFAULT_CONC );
    }
}

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void ReadCspace::makePlots

(

double

plotdt

)

Definition at line 139 of file ReadCspace.cpp.

References base_, Neutral::children(), compt_, Eref::data(), Shell::doAddMsg(), Shell::doCreate(), Id::eref(), Cinfo::isA(), and Id::path().

Referenced by Shell::doLoadModel().

{
    Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
    vector< Id > children;
    Neutral::children( compt_.eref(), children );
    string basepath = base_.path();
    Id graphs( basepath + "/graphs" );
    assert( graphs != Id () );
    for ( unsigned int i = 0; i < children.size(); ++i ) {
        const Cinfo* kidCinfo = children[i].element()->cinfo();
        if ( kidCinfo->isA( "PoolBase" ) ) {
            string plotname = "plot" + children[i].element()->getName();
            Id tab = shell->doCreate( "Table2", graphs, plotname, 1 );
            assert( tab != Id() );
            // cout << "ReadCspace made plot " << plotname << endl;
            ObjId mid = shell->doAddMsg( "Single",
                tab, "requestOut", children[i], "getConc" );
            assert( mid != ObjId() );
        }
    }
    /* Clocks are now assigned automatically
    shell->doSetClock( 8, plotdt );

    string plotpath = basepath + "/graphs/##[TYPE=Table2]";
    shell->doUseClock( plotpath, "process", 8 );
    */
}

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void ReadCspace::printEnz	(	Id	id,
		Id	cplx,
		double	k1,
		double	k2,
		double	k3
	)

Definition at line 78 of file ReadCspace.cpp.

References reaclist_.

{
    CspaceReacInfo r( id.element()->getName(), k3, (k3 + k2) / k1 );
    reaclist_.push_back( r );
}

void ReadCspace::printFooter

(

)

Definition at line 38 of file ReadCspace.cpp.

References fout_, mollist_, name, reaclist_, and USE_PIPE.

{
    string separator = ( USE_PIPE ) ? "|" : "" ;
    // We do this in all cases, regardless of the doOrdering flag.
    sort( mollist_.begin(), mollist_.end() );
    sort( reaclist_.begin(), reaclist_.end() );
    unsigned int i;
    *fout_ << separator;
    for ( i = 0; i < reaclist_.size(); i++ )
        *fout_ << reaclist_[ i ].name() << separator;

    for ( i = 0; i < mollist_.size(); i++ )
        *fout_ << " " << mollist_[i].conc();
    for ( i = 0; i < reaclist_.size(); i++ )
        *fout_ << " " << reaclist_[i].r1() << " " << reaclist_[i].r2();
    *fout_ << "\n";
}

void ReadCspace::printHeader

(

)

Definition at line 32 of file ReadCspace.cpp.

References mollist_, and reaclist_.

{
    reaclist_.resize( 0 );
    mollist_.resize( 0 );
}

void ReadCspace::printMol	(	Id	id,
		double	conc,
		double	concinit,
		double	vol
	)

Definition at line 56 of file ReadCspace.cpp.

References Element::cinfo(), ObjId::element(), Element::getName(), Cinfo::isA(), mollist_, and Neutral::parent().

{

    // Skip explicit enzyme complexes.
    ObjId parent = Neutral::parent( id.eref() );
    if ( parent.element()->cinfo()->isA( "Enzyme" ) &&
        id.element()->getName() == ( parent.element()->getName() + "_cplx" )
    )
        return;

    CspaceMolInfo m( id.element()->getName()[ 0 ], concinit );
    mollist_.push_back( m );
    // Need to look up concs in a final step so that the sorted order
    // is maintained.
}

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void ReadCspace::printReac	(	Id	id,
		double	kf,
		double	kb
	)

Definition at line 72 of file ReadCspace.cpp.

References reaclist_.

{
    CspaceReacInfo r( id.element()->getName(), kf, kb );
    reaclist_.push_back( r );
}

Id ReadCspace::readModelString	(	const string &	model,
		const string &	modelname,
		Id	pa,
		const string &	solverClass
	)

Definition at line 86 of file ReadCspace.cpp.

References base_, build(), compt_, deployParameters(), makeStandardElements(), mol_, molparms_, molseq_, parms_, Id::path(), reac_, and Field< A >::set().

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

{
    // Defined in ReadKkit.cpp
    extern Id makeStandardElements( Id pa, const string& modelname );
    unsigned long pos = model.find_first_of( "|" );
    if ( pos == string::npos ) {
        cerr << "ReadCspace::readModelString: Error: model undefined in\n";
        cerr << model << "\n";
        return Id();
    }
    mol_.resize( 0 );
    molseq_.resize( 0 );
    reac_.resize( 0 );
    molparms_.resize( 0 );
    parms_.resize( 0 );
    // Shell* s = reinterpret_cast< Shell* >( Id().eref().data() );
    base_ = makeStandardElements( pa, modelname );
    assert( base_ != Id() );
    string modelpath = base_.path();
    compt_ = Id( modelpath + "/kinetics");
    assert( compt_ != Id() );
    Field< double >::set( compt_, "volume", 1e-18 );
    // SetGet2< double, unsigned int >::set( compt_, "buildDefaultMesh",     1e-18, 1 );
    string temp = model.substr( pos + 1 );
    pos = temp.find_first_of( "     \n" );

    for (unsigned long i = 0 ; i < temp.length() && i < pos; i += 5 ) {
        build( temp.c_str() + i );
        if ( temp[ i + 4 ] != '|' )
            break;
    }

    parms_.insert( parms_.begin(), molparms_.begin(), molparms_.end() );

    pos = model.find_last_of( "|" ) + 1;
    double val = 0;
    unsigned int i = 0;
    while ( pos < model.length() ) {
        if ( model[ pos ] == ' ' ) {
            val = atof( model.c_str() + pos + 1 );
            assert( i < parms_.size() );
            parms_[ i++ ] = val;
        }
        pos++;
    }

    deployParameters();

    // SetGet1< string >::set( base_, "build", solverClass );
    return base_;
}

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void ReadCspace::testReadModel

(

)

Definition at line 361 of file ReadCspace.cpp.

References base_, Eref::data(), Shell::doDelete(), doubleEq(), Id::eref(), Field< A >::get(), mol_, Id::path(), path, reac_, and readModelString().

Referenced by testReadCspace().

{
    const double CONCSCALE = 1e-3;
    Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
    // cout << "Testing ReadCspace::readModelString()\n";
    Id modelId = readModelString( "|Habc|Lbca|", "mod1", Id(), "Neutral" );
    assert( mol_.size() == 3 );
    assert( reac_.size() == 2 );

    shell->doDelete( modelId );

    modelId = readModelString( "|AabX|BbcX|CcdX|DdeX|Eefg|Ffgh|Gghi|Hhij|Iijk|Jjkl|Kklm|Llmn| 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 10.0 11.0 12.0 13.0 14.0 101 102 201 202 301 302 401 402 501 502 601 602 701 702 801 802 901 902 1001 1002 1101 1102 1201 1202",
        "model", Id(), "Neutral" );
    assert( mol_.size() == 14 );
    assert( reac_.size() == 12 );
    double concInit;
    int i;
    // cout << "\nTesting ReadCspace:: conc assignment\n";
    for ( i = 0; i < 14; i++ ) {
        string path( base_.path() + "/kinetics/" );
        path += 'a' + i;
        /*
        stringstream ss( "/kinetics/" );
        // const char* molname = ss.str();
        ss << 'a' + i;
        Id temp( ss.str() );
        */
        Id temp( path );
        concInit = Field< double >::get( temp, "concInit" );

        // The 0.001 is for converting to millimolar, which is the internal
        // unit used in MOOSE.
        assert( doubleEq( concInit, 0.001 * ( i + 1 ) ) );
    }

    // cout << "\nTesting ReadCspace:: reac construction\n";
    assert( reac_[ 0 ].path() == "/model/kinetics/AabX" );
    assert( reac_[ 1 ].path() == "/model/kinetics/BbcX" );
    assert( reac_[ 2 ].path() == "/model/kinetics/c/CcdX" );
    assert( reac_[ 3 ].path() == "/model/kinetics/e/DdeX" );
    assert( reac_[ 4 ].path() == "/model/kinetics/Eefg" );
    assert( reac_[ 5 ].path() == "/model/kinetics/Ffgh" );
    assert( reac_[ 6 ].path() == "/model/kinetics/Gghi" );
    assert( reac_[ 7 ].path() == "/model/kinetics/Hhij" );
    assert( reac_[ 8 ].path() == "/model/kinetics/Iijk" );
    assert( reac_[ 9 ].path() == "/model/kinetics/k/Jjkl" );
    assert( reac_[ 10 ].path() == "/model/kinetics/k/Kklm" );
    assert( reac_[ 11 ].path() == "/model/kinetics/m/Llmn" );

    // cout << "\nTesting ReadCspace:: reac rate assignment\n";
    Id tempA( "/model/kinetics/AabX" );
    double r1 = Field< double >::get( tempA, "Kf");
    double r2 = Field< double >::get( tempA, "Kb");
    assert( doubleEq( r1, 101 ) && doubleEq( r2, 102 ) );

    Id tempB( "/model/kinetics/BbcX" );
    r1 = Field< double >::get( tempB, "Kf");
    r2 = Field< double >::get( tempB, "Kb");
    assert( doubleEq( r1, 201 ) && doubleEq( r2, 202 ) );

    Id tempC( "/model/kinetics/c/CcdX" );
    r1 = Field< double >::get( tempC, "k3");
    r2 = Field< double >::get( tempC, "Km");
    assert( doubleEq( r1, 301 ) && doubleEq( r2, 302 * CONCSCALE ) );

    Id tempD( "/model/kinetics/e/DdeX" );
    r1 = Field< double >::get( tempD, "k3");
    r2 = Field< double >::get( tempD, "Km");
    assert( doubleEq( r1, 401 ) && doubleEq( r2, 402 * CONCSCALE ) );

    for ( i = 4; i < 9; i++ ) {
        /*
        stringstream ss( "/kinetics/A" );
        ss << i << 'a' + i << 'b' + i << 'c' + i;
        // sprintf( ename, "/kinetics/%c%c%c%c", 'A' + i, 'a' + i, 'b' + i, 'c' + i );
        Id temp( ss.str() );
        */

        string path( "/model/kinetics/" );
        path += 'A' + i;
        path += 'a' + i;
        path += 'b' + i;
        path += 'c' + i;
        Id temp( path );
        r1 = Field< double >::get( temp, "Kf");
        r2 = Field< double >::get( temp, "Kb");
        assert( doubleEq( r1, i* 100 + 101 ) &&
            doubleEq( r2, i * 100 + 102 ) );
    }

    Id tempJ( "/model/kinetics/k/Jjkl" );
    r1 = Field< double >::get( tempJ, "k3");
    r2 = Field< double >::get( tempJ, "Km");
    assert( doubleEq( r1, 1001 ) && doubleEq( r2, 1002 * CONCSCALE ) );

    Id tempK( "/model/kinetics/k/Kklm" );
    r1 = Field< double >::get( tempK, "k3");
    r2 = Field< double >::get( tempK, "Km");
    assert( doubleEq( r1, 1101 ) && doubleEq( r2, 1102 * CONCSCALE ) );

    Id tempL( "/model/kinetics/m/Llmn" );
    r1 = Field< double >::get( tempL, "k3");
    r2 = Field< double >::get( tempL, "Km");
    assert( doubleEq( r1, 1201 ) && doubleEq( r2, 1202 * CONCSCALE ) );
    shell->doDelete( modelId );
}

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Member Data Documentation

Id ReadCspace::base_

private

Definition at line 111 of file ReadCspace.h.

Referenced by makePlots(), readModelString(), and testReadModel().

Id ReadCspace::compt_

private

Definition at line 112 of file ReadCspace.h.

Referenced by expandReaction(), makeMolecule(), makePlots(), and readModelString().

const double ReadCspace::DEFAULT_CONC = 1.0

staticprivate

Definition at line 106 of file ReadCspace.h.

Referenced by makeMolecule().

const double ReadCspace::DEFAULT_KM = 1.0

staticprivate

Definition at line 108 of file ReadCspace.h.

Referenced by expandEnzyme().

const double ReadCspace::DEFAULT_RATE = 0.1

staticprivate

Definition at line 107 of file ReadCspace.h.

Referenced by expandEnzyme(), and expandReaction().

ostream* ReadCspace::fout_

private

Definition at line 114 of file ReadCspace.h.

Referenced by printFooter().

Id ReadCspace::mesh_

private

Definition at line 113 of file ReadCspace.h.

vector< Id > ReadCspace::mol_

private

Definition at line 117 of file ReadCspace.h.

Referenced by deployParameters(), expandEnzyme(), expandReaction(), makeMolecule(), readModelString(), and testReadModel().

vector< CspaceMolInfo > ReadCspace::mollist_

private

Definition at line 126 of file ReadCspace.h.

Referenced by printFooter(), printHeader(), and printMol().

vector< double > ReadCspace::molparms_

private

Definition at line 124 of file ReadCspace.h.

Referenced by makeMolecule(), and readModelString().

vector< unsigned int > ReadCspace::molseq_

private

Definition at line 118 of file ReadCspace.h.

Referenced by makeMolecule(), and readModelString().

vector< double > ReadCspace::parms_

private

Definition at line 122 of file ReadCspace.h.

Referenced by deployParameters(), expandEnzyme(), expandReaction(), and readModelString().

vector< Id > ReadCspace::reac_

private

Definition at line 120 of file ReadCspace.h.

Referenced by deployParameters(), expandEnzyme(), expandReaction(), readModelString(), and testReadModel().

vector< CspaceReacInfo > ReadCspace::reaclist_

private

Definition at line 127 of file ReadCspace.h.

Referenced by printEnz(), printFooter(), printHeader(), and printReac().

const double ReadCspace::SCALE = 1.0

staticprivate

Definition at line 105 of file ReadCspace.h.

const bool ReadCspace::USE_PIPE = 1

staticprivate

Definition at line 109 of file ReadCspace.h.

Referenced by printFooter().

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

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