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ZombieEnz Class Reference

#include <ZombieEnz.h>

+ Inheritance diagram for ZombieEnz:
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Public Member Functions

void setSolver (Id solver, Id orig)
 Assign solver info. More...
 
double vGetConcK1 (const Eref &e) const
 
double vGetK1 (const Eref &e) const
 
double vGetK2 (const Eref &e) const
 
double vGetKcat (const Eref &e) const
 
double vGetKm (const Eref &e) const
 
double vGetNumKm (const Eref &e) const
 
double vGetRatio (const Eref &e) const
 
void vSetConcK1 (const Eref &e, double v)
 
void vSetK1 (const Eref &e, double v)
 
void vSetK2 (const Eref &e, double v)
 
void vSetKcat (const Eref &e, double v)
 
void vSetKm (const Eref &e, double v)
 
void vSetNumKm (const Eref &e, double v)
 
void vSetRatio (const Eref &e, double v)
 
 ZombieEnz ()
 
 ~ZombieEnz ()
 
- Public Member Functions inherited from CplxEnzBase
void cplx (double n)
 
 CplxEnzBase ()
 
double getConcK1 (const Eref &e) const
 
double getK1 (const Eref &e) const
 
double getK2 (const Eref &e) const
 
double getRatio (const Eref &e) const
 
void setConcK1 (const Eref &e, double v)
 
void setK1 (const Eref &e, double v)
 
void setK2 (const Eref &e, double v)
 
void setRatio (const Eref &e, double v)
 
virtual void vCplx (double n)
 
virtual ~CplxEnzBase ()
 
- Public Member Functions inherited from EnzBase
void enz (double n)
 
 EnzBase ()
 
double getKcat (const Eref &e) const
 
double getKm (const Eref &e) const
 
double getNumKm (const Eref &e) const
 
unsigned int getNumPrd (const Eref &e) const
 
unsigned int getNumSub (const Eref &e) const
 
void prd (double n)
 
void process (const Eref &e, ProcPtr p)
 
void reinit (const Eref &e, ProcPtr p)
 
void remesh (const Eref &e)
 
void setKcat (const Eref &e, double v)
 
void setKm (const Eref &e, double v)
 
void setNumKm (const Eref &e, double v)
 
void sub (double n)
 
virtual void vEnz (double n)
 
virtual void vProcess (const Eref &e, ProcPtr p)
 
virtual void vReinit (const Eref &e, ProcPtr p)
 
virtual void vRemesh (const Eref &e)
 
virtual void vSub (double n)
 
virtual ~EnzBase ()
 

Static Public Member Functions

static const Cinfo * initCinfo ()
 
- Static Public Member Functions inherited from CplxEnzBase
static const Cinfo * initCinfo ()
 
static void zombify (Element *original, const Cinfo *zClass, Id solver)
 
- Static Public Member Functions inherited from EnzBase
static const Cinfo * initCinfo ()
 
static void zombify (Element *original, const Cinfo *zClass, Id solver)
 

Private Attributes

double concK1_
 
Stoich * stoich_
 

Detailed Description

Definition at line 13 of file ZombieEnz.h.

Constructor & Destructor Documentation

ZombieEnz::ZombieEnz ( )

Definition at line 63 of file ZombieEnz.cpp.

64  :
65  stoich_( 0 ),
66  concK1_( 1.0 )
67 { ; }
ZombieEnz::stoich_
Stoich * stoich_
Definition: ZombieEnz.h:64
ZombieEnz::concK1_
double concK1_
Definition: ZombieEnz.h:65
ZombieEnz::~ZombieEnz ( )

Definition at line 69 of file ZombieEnz.cpp.

70 { ; }

Member Function Documentation

const Cinfo * ZombieEnz::initCinfo ( )
static

Definition at line 28 of file ZombieEnz.cpp.

References CplxEnzBase::initCinfo(), and zombieEnzCinfo.

29 {
31  // Field Definitions
34  // MsgDest Definitions
37  // Shared Msg Definitions
39 
40  static Dinfo< ZombieEnz > dinfo;
41  static Cinfo zombieEnzCinfo (
42  "ZombieEnz",
43  CplxEnzBase::initCinfo(),
44  0,
45  0,
46  &dinfo
47  );
48 
49  return &zombieEnzCinfo;
50 }
Dinfo
Definition: Dinfo.h:60
zombieEnzCinfo
static const Cinfo * zombieEnzCinfo
Definition: ZombieEnz.cpp:53
Cinfo
Definition: Cinfo.h:18
CplxEnzBase::initCinfo
static const Cinfo * initCinfo()
Definition: CplxEnzBase.cpp:49

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void ZombieEnz::setSolver ( Id  solver,
Id  orig 
)
virtual

Assign solver info.

Reimplemented from EnzBase.

Definition at line 216 of file ZombieEnz.cpp.

References Element::cinfo(), Eref::data(), Id::element(), Id::eref(), Cinfo::find(), Cinfo::findFinfo(), Element::getNeighbors(), Stoich::installEnzyme(), Cinfo::isA(), Id::path(), and stoich_.

217 {
218  static const Finfo* subFinfo = Cinfo::find("Enz")->findFinfo( "subOut");
219  static const Finfo* prdFinfo = Cinfo::find("Enz")->findFinfo( "prdOut");
220  static const Finfo* enzFinfo = Cinfo::find("Enz")->findFinfo( "enzOut");
221  static const Finfo* cplxFinfo= Cinfo::find("Enz")->findFinfo("cplxOut");
222 
223  assert( subFinfo );
224  assert( prdFinfo );
225  assert( enzFinfo );
226  assert( cplxFinfo );
227  vector< Id > enzMols;
228  vector< Id > cplxMols;
229  bool isOK = true;
230  unsigned int numReactants;
231  numReactants = enz.element()->getNeighbors( enzMols, enzFinfo );
232  bool hasEnz = ( numReactants == 1 );
233  vector< Id > subs;
234  numReactants = enz.element()->getNeighbors( subs, subFinfo );
235  bool hasSubs = ( numReactants > 0 );
236  numReactants = enz.element()->getNeighbors( cplxMols, cplxFinfo );
237  bool hasCplx = ( numReactants == 1 );
238  vector< Id > prds;
239  numReactants = enz.element()->getNeighbors( prds, prdFinfo );
240  bool hasPrds = ( numReactants > 0 );
241  assert( stoich.element()->cinfo()->isA( "Stoich" ) );
242  stoich_ = reinterpret_cast< Stoich* >( stoich.eref().data() );
243 
244  if ( hasEnz && hasSubs && hasCplx && hasPrds ) {
245  stoich_->installEnzyme( enz, enzMols[0], cplxMols[0], subs, prds );
246  } else {
247  stoich_->installDummyEnzyme( enz, Id() );
248  string msg = "";
249  if ( !hasEnz ) msg = msg + " enzyme";
250  if ( !hasCplx ) msg = msg + " enzyme-substrate complex";
251  if ( !hasSubs ) msg = msg + " substrates";
252  if ( !hasPrds ) msg = msg + " products";
253  cout << "Warning: ZombieEnz:setSolver: Dangling Enz '" <<
254  enz.path() << "':\nMissing " << msg << endl;
255  }
256 }
Cinfo::find
static const Cinfo * find(const std::string &name)
Definition: Cinfo.cpp:200
Stoich::installEnzyme
void installEnzyme(Id enzId, Id enzMolId, Id cplxId, const vector< Id > &subs, const vector< Id > &prds)
Definition: Stoich.cpp:1732
Stoich
Definition: Stoich.h:49
EnzBase::enz
void enz(double n)
Definition: EnzBase.cpp:187
Id
Definition: Id.h:17
ZombieEnz::stoich_
Stoich * stoich_
Definition: ZombieEnz.h:64
Cinfo::findFinfo
const Finfo * findFinfo(const string &name) const
Definition: Cinfo.cpp:224
Finfo
Definition: Finfo.h:12

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double ZombieEnz::vGetConcK1 ( const Eref &  e) const
virtual

Implements CplxEnzBase.

Definition at line 206 of file ZombieEnz.cpp.

References concK1_.

207 {
208  return concK1_;
209 }
ZombieEnz::concK1_
double concK1_
Definition: ZombieEnz.h:65
double ZombieEnz::vGetK1 ( const Eref &  e) const
virtual

Implements CplxEnzBase.

Definition at line 99 of file ZombieEnz.cpp.

References concK1_, and convertConcToNumRateUsingMesh().

100 {
101  // return stoich_->getEnzNumK1( e );
102  double volScale =
103  convertConcToNumRateUsingMesh( e, subOut, true );
104 
105  return concK1_ / volScale;
106 }
subOut
static const SrcFinfo2< double, double > * subOut
Definition: ZombieEnz.cpp:55
convertConcToNumRateUsingMesh
double convertConcToNumRateUsingMesh(const Eref &e, const SrcFinfo *pools, bool doPartialConversion)
Definition: lookupVolumeFromMesh.cpp:114
ZombieEnz::concK1_
double concK1_
Definition: ZombieEnz.h:65

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double ZombieEnz::vGetK2 ( const Eref &  e) const
virtual

Implements CplxEnzBase.

Definition at line 113 of file ZombieEnz.cpp.

References Stoich::getEnzK2(), and stoich_.

Referenced by vGetNumKm().

114 {
115  return stoich_->getEnzK2( e );
116 }
Stoich::getEnzK2
double getEnzK2(const Eref &e) const
Get rate k2 (1/sec) for enzyme.
Definition: Stoich.cpp:1986
ZombieEnz::stoich_
Stoich * stoich_
Definition: ZombieEnz.h:64

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double ZombieEnz::vGetKcat ( const Eref &  e) const
virtual

Implements EnzBase.

Definition at line 136 of file ZombieEnz.cpp.

References Stoich::getEnzK3(), and stoich_.

Referenced by vGetNumKm().

137 {
138  return stoich_->getEnzK3( e );
139 }
Stoich::getEnzK3
double getEnzK3(const Eref &e) const
Get rate k3, aka kcat, for enzyme.
Definition: Stoich.cpp:1994
ZombieEnz::stoich_
Stoich * stoich_
Definition: ZombieEnz.h:64

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double ZombieEnz::vGetKm ( const Eref &  e) const
virtual

Implements EnzBase.

Definition at line 150 of file ZombieEnz.cpp.

References concK1_, CplxEnzBase::getK2(), and EnzBase::getKcat().

151 {
152  double k2 = getK2( e );
153  double k3 = getKcat( e );
154 
155  return ( k2 + k3 ) / concK1_;
156 }
CplxEnzBase::getK2
double getK2(const Eref &e) const
Definition: CplxEnzBase.cpp:211
EnzBase::getKcat
double getKcat(const Eref &e) const
Definition: EnzBase.cpp:256
ZombieEnz::concK1_
double concK1_
Definition: ZombieEnz.h:65

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double ZombieEnz::vGetNumKm ( const Eref &  e) const
virtual

Implements EnzBase.

Definition at line 169 of file ZombieEnz.cpp.

References concK1_, convertConcToNumRateUsingMesh(), vGetK2(), and vGetKcat().

170 {
171  double k2 = vGetK2( e );
172  double k3 = vGetKcat( e );
173  double volScale =
174  convertConcToNumRateUsingMesh( e, subOut, 1 );
175 
176  return volScale * ( k2 + k3 ) / concK1_;
177 }
ZombieEnz::vGetKcat
double vGetKcat(const Eref &e) const
Definition: ZombieEnz.cpp:136
subOut
static const SrcFinfo2< double, double > * subOut
Definition: ZombieEnz.cpp:55
convertConcToNumRateUsingMesh
double convertConcToNumRateUsingMesh(const Eref &e, const SrcFinfo *pools, bool doPartialConversion)
Definition: lookupVolumeFromMesh.cpp:114
ZombieEnz::concK1_
double concK1_
Definition: ZombieEnz.h:65
ZombieEnz::vGetK2
double vGetK2(const Eref &e) const
Definition: ZombieEnz.cpp:113

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double ZombieEnz::vGetRatio ( const Eref &  e) const
virtual

Implements CplxEnzBase.

Definition at line 193 of file ZombieEnz.cpp.

References CplxEnzBase::getK2(), and EnzBase::getKcat().

194 {
195  double k2 = getK2( e );
196  double k3 = getKcat( e );
197  return k2 / k3;
198 }
CplxEnzBase::getK2
double getK2(const Eref &e) const
Definition: CplxEnzBase.cpp:211
EnzBase::getKcat
double getKcat(const Eref &e) const
Definition: EnzBase.cpp:256

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void ZombieEnz::vSetConcK1 ( const Eref &  e,
double  v 
)
virtual

Implements CplxEnzBase.

Definition at line 200 of file ZombieEnz.cpp.

References concK1_, Stoich::setEnzK1(), and stoich_.

201 {
202  concK1_ = v;
203  stoich_->setEnzK1( e, v );
204 }
Stoich::setEnzK1
void setEnzK1(const Eref &e, double v) const
Later handle all the volumes when this conversion is done.
Definition: Stoich.cpp:1943
ZombieEnz::stoich_
Stoich * stoich_
Definition: ZombieEnz.h:64
ZombieEnz::concK1_
double concK1_
Definition: ZombieEnz.h:65

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void ZombieEnz::vSetK1 ( const Eref &  e,
double  v 
)
virtual

Implements CplxEnzBase.

Definition at line 89 of file ZombieEnz.cpp.

References concK1_, convertConcToNumRateUsingMesh(), Stoich::setEnzK1(), and stoich_.

90 {
91  double volScale =
92  convertConcToNumRateUsingMesh( e, subOut, true );
93 
94  concK1_ = v * volScale;
95  stoich_->setEnzK1( e, concK1_ );
96 }
Stoich::setEnzK1
void setEnzK1(const Eref &e, double v) const
Later handle all the volumes when this conversion is done.
Definition: Stoich.cpp:1943
subOut
static const SrcFinfo2< double, double > * subOut
Definition: ZombieEnz.cpp:55
convertConcToNumRateUsingMesh
double convertConcToNumRateUsingMesh(const Eref &e, const SrcFinfo *pools, bool doPartialConversion)
Definition: lookupVolumeFromMesh.cpp:114
ZombieEnz::stoich_
Stoich * stoich_
Definition: ZombieEnz.h:64
ZombieEnz::concK1_
double concK1_
Definition: ZombieEnz.h:65

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void ZombieEnz::vSetK2 ( const Eref &  e,
double  v 
)
virtual

Implements CplxEnzBase.

Definition at line 108 of file ZombieEnz.cpp.

References Stoich::setEnzK2(), and stoich_.

109 {
110  stoich_->setEnzK2( e, v );
111 }
Stoich::setEnzK2
void setEnzK2(const Eref &e, double v) const
Set rate k2 (1/sec) for enzyme.
Definition: Stoich.cpp:1951
ZombieEnz::stoich_
Stoich * stoich_
Definition: ZombieEnz.h:64

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void ZombieEnz::vSetKcat ( const Eref &  e,
double  v 
)
virtual

Implements EnzBase.

Definition at line 118 of file ZombieEnz.cpp.

References concK1_, EPSILON, CplxEnzBase::getK2(), EnzBase::getKcat(), Stoich::setEnzK1(), Stoich::setEnzK2(), Stoich::setEnzK3(), and stoich_.

119 {
120  double k2 = getK2( e );
121  double k3 = getKcat( e );
122  double ratio = 4.0;
123  if ( v < EPSILON )
124  v = EPSILON;
125  if ( k3 > EPSILON ) {
126  ratio = k2/k3;
127  }
128  double Km = (k2 + k3) / concK1_;
129  concK1_ = v * (1.0 + ratio) / Km;
130 
131  stoich_->setEnzK1( e, concK1_ );
132  stoich_->setEnzK3( e, v );
133  stoich_->setEnzK2( e, v * ratio );
134 }
Stoich::setEnzK3
void setEnzK3(const Eref &e, double v) const
Set rate k3 (1/sec) for enzyme.
Definition: Stoich.cpp:1966
CplxEnzBase::getK2
double getK2(const Eref &e) const
Definition: CplxEnzBase.cpp:211
Stoich::setEnzK1
void setEnzK1(const Eref &e, double v) const
Later handle all the volumes when this conversion is done.
Definition: Stoich.cpp:1943
Stoich::setEnzK2
void setEnzK2(const Eref &e, double v) const
Set rate k2 (1/sec) for enzyme.
Definition: Stoich.cpp:1951
EPSILON
#define EPSILON
Definition: ZombieEnz.cpp:26
EnzBase::getKcat
double getKcat(const Eref &e) const
Definition: EnzBase.cpp:256
ZombieEnz::stoich_
Stoich * stoich_
Definition: ZombieEnz.h:64
ZombieEnz::concK1_
double concK1_
Definition: ZombieEnz.h:65

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void ZombieEnz::vSetKm ( const Eref &  e,
double  v 
)
virtual

Implements EnzBase.

Definition at line 142 of file ZombieEnz.cpp.

References concK1_, CplxEnzBase::getK2(), EnzBase::getKcat(), Stoich::setEnzK1(), and stoich_.

143 {
144  double k2 = getK2( e );
145  double k3 = getKcat( e );
146  concK1_ = ( k2 + k3 ) / v;
147  stoich_->setEnzK1( e, concK1_ );
148 }
CplxEnzBase::getK2
double getK2(const Eref &e) const
Definition: CplxEnzBase.cpp:211
Stoich::setEnzK1
void setEnzK1(const Eref &e, double v) const
Later handle all the volumes when this conversion is done.
Definition: Stoich.cpp:1943
EnzBase::getKcat
double getKcat(const Eref &e) const
Definition: EnzBase.cpp:256
ZombieEnz::stoich_
Stoich * stoich_
Definition: ZombieEnz.h:64
ZombieEnz::concK1_
double concK1_
Definition: ZombieEnz.h:65

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void ZombieEnz::vSetNumKm ( const Eref &  e,
double  v 
)
virtual

Implements EnzBase.

Definition at line 158 of file ZombieEnz.cpp.

References concK1_, convertConcToNumRateUsingMesh(), CplxEnzBase::getK2(), EnzBase::getKcat(), Stoich::setEnzK1(), and stoich_.

159 {
160  double k2 = getK2( e );
161  double k3 = getKcat( e );
162  double volScale =
163  convertConcToNumRateUsingMesh( e, subOut, 1 );
164  concK1_ = ( k2 + k3 ) / ( v * volScale );
165 
166  stoich_->setEnzK1( e, concK1_ );
167 }
CplxEnzBase::getK2
double getK2(const Eref &e) const
Definition: CplxEnzBase.cpp:211
Stoich::setEnzK1
void setEnzK1(const Eref &e, double v) const
Later handle all the volumes when this conversion is done.
Definition: Stoich.cpp:1943
subOut
static const SrcFinfo2< double, double > * subOut
Definition: ZombieEnz.cpp:55
convertConcToNumRateUsingMesh
double convertConcToNumRateUsingMesh(const Eref &e, const SrcFinfo *pools, bool doPartialConversion)
Definition: lookupVolumeFromMesh.cpp:114
EnzBase::getKcat
double getKcat(const Eref &e) const
Definition: EnzBase.cpp:256
ZombieEnz::stoich_
Stoich * stoich_
Definition: ZombieEnz.h:64
ZombieEnz::concK1_
double concK1_
Definition: ZombieEnz.h:65

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void ZombieEnz::vSetRatio ( const Eref &  e,
double  v 
)
virtual

Implements CplxEnzBase.

Definition at line 179 of file ZombieEnz.cpp.

References CplxEnzBase::getK2(), EnzBase::getKcat(), EnzBase::getKm(), CplxEnzBase::setConcK1(), Stoich::setEnzK2(), and stoich_.

180 {
181  double Km = getKm( e );
182  double k2 = getK2( e );
183  double k3 = getKcat( e );
184 
185  k2 = v * k3;
186 
187  stoich_->setEnzK2( e, k2 );
188  double k1 = ( k2 + k3 ) / Km;
189 
190  setConcK1( e, k1 );
191 }
CplxEnzBase::getK2
double getK2(const Eref &e) const
Definition: CplxEnzBase.cpp:211
EnzBase::getKm
double getKm(const Eref &e) const
Definition: EnzBase.cpp:235
CplxEnzBase::setConcK1
void setConcK1(const Eref &e, double v)
Definition: CplxEnzBase.cpp:233
Stoich::setEnzK2
void setEnzK2(const Eref &e, double v) const
Set rate k2 (1/sec) for enzyme.
Definition: Stoich.cpp:1951
EnzBase::getKcat
double getKcat(const Eref &e) const
Definition: EnzBase.cpp:256
ZombieEnz::stoich_
Stoich * stoich_
Definition: ZombieEnz.h:64

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Member Data Documentation

double ZombieEnz::concK1_
private

Definition at line 65 of file ZombieEnz.h.

Referenced by vGetConcK1(), vGetK1(), vGetKm(), vGetNumKm(), vSetConcK1(), vSetK1(), vSetKcat(), vSetKm(), and vSetNumKm().

Stoich* ZombieEnz::stoich_
private

Definition at line 64 of file ZombieEnz.h.

Referenced by setSolver(), vGetK2(), vGetKcat(), vSetConcK1(), vSetK1(), vSetK2(), vSetKcat(), vSetKm(), vSetNumKm(), and vSetRatio().

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