MEDYAN  3.1
Software for simulating active matter dynamics
MotorGhost Class Reference

A container to store a MMotorGhost and CMotorGhost. More...

#include <MotorGhost.h>

Inheritance diagram for MotorGhost:
Collaboration diagram for MotorGhost:

Public Member Functions

 MotorGhost (Cylinder *c1, Cylinder *c2, short motorType, double position1=0.5, double position2=0.5, double onRate=0.0, double offRate=0.0)
 Standard constructor. More...
 
virtual ~MotorGhost () noexcept
 
void updateCoordinate ()
 Helper to get coordinate. More...
 
void setCMotorGhost (CMotorGhost *cMotorGhost)
 Set chem motor ghost. More...
 
CMotorGhostgetCMotorGhost ()
 Get chem motor ghost. More...
 
MMotorGhostgetMMotorGhost ()
 Get mech motor ghost. More...
 
float getBirthTime ()
 Get the birth time. More...
 
virtual void updatePosition ()
 Update the position, inherited from Movable. More...
 
virtual void updateReactionRates ()
 Update the reaction rates, inherited from Reactable. More...
 
void moveMotorHead (Cylinder *c, double oldPosition, double newPosition, short boundType, SubSystem *ps)
 Move a motor head forward. More...
 
void moveMotorHead (Cylinder *oldC, Cylinder *newC, double oldPosition, double newPosition, short boundType, SubSystem *ps)
 Move a motor head to a new cylinder. More...
 
virtual void printSelf ()
 Prints information about this node. Useful for debugging. More...
 
virtual bool apply (Visitor &v)
 When this function is applied to a ConditionalVisitor v, the corresponding v.visit(this) is called, and v is further applied to all children of this node recursively. More...
 
virtual bool apply (SpeciesVisitor &v)
 Implements the apply_if() method of the Component class by recursively applying it to itself and all its children that contain Species. More...
 
virtual bool apply (ReactionVisitor &v)
 Implements the apply_if() method of the Component class by recursively applying it to itself and all its children that contain ReactionBase. More...
 
virtual bool apply_impl (SpeciesVisitor &v)
 Applies SpeciesVisitor v to every Species* object directly owned by this node. More...
 
virtual bool apply_impl (ReactionVisitor &v)
 Applies ReactionBaseVisitor v to every ReactionBase* object directly owned by this node. More...
 
CompositegetParent ()
 Returns the pointer to the parent node. More...
 
void setParent (Composite *other)
 Sets the parent of this node to other. More...
 
bool isRoot () const
 Returns true if this node is the root node. More...
 
CompositegetRoot ()
 Returns the root node of the hieararchy to which this node belongs to. More...
 
virtual size_t numberOfChildren () const
 Returns the number of children of this node. More...
 
virtual bool isComposite () const
 Returns true if this node is a Composite node. More...
 
virtual bool isSpeciesContainer () const
 Returns true if this node contains non-zero number of Species. More...
 
virtual bool isReactionsContainer () const
 Returns true if this node contains non-zero number of reactions (i.e. More...
 
virtual size_t numberOfSpecies () const
 Returns the number of Species being immediately managed by this node (i.e. More...
 
virtual size_t numberOfReactions () const
 Returns the number of ReactionBase objets being immediately managed by this node (i.e. More...
 
virtual string getFullName () const
 Return a string indicating the full name of this node (presumably used mainly for debugging) More...
 
virtual size_t countDescendents () const
 Return the total number of nodes contained under this node's hieararchy. More...
 
virtual size_t countSpecies () const
 Return the number of Species contained under this node's hieararchy. More...
 
virtual size_t countReactions () const
 Return the number of ReactionBase objects contained under this node's hieararchy. More...
 
CylindergetFirstCylinder ()
 Get cylinder. More...
 
CylindergetSecondCylinder ()
 Get cylinder. More...
 
void setFirstCylinder (Cylinder *cylinder)
 Set cylinder. More...
 
void setSecondCylinder (Cylinder *cylinder)
 Set cylinder. More...
 
double getFirstPosition ()
 Position management function. More...
 
void setFirstPosition (double position1)
 Position management function. More...
 
double getSecondPosition ()
 Position management function. More...
 
void setSecondPosition (double position2)
 Position management function. More...
 
virtual int getType ()
 Parameter management. More...
 
int getID ()
 Parameter management. More...
 
void setID (int ID)
 Parameter management. More...
 
virtual void addToSubSystem ()
 SubSystem management, inherited from Trackable. More...
 
virtual void removeFromSubSystem ()
 SubSystem management, inherited from Trackable. More...
 

Static Public Member Functions

static const vector< MotorGhost * > & getMotorGhosts ()
 Get all instances of this class from the SubSystem. More...
 
static int numMotorGhosts ()
 Get the number of motors in this system. More...
 
static HistogramgetLifetimes ()
 Get the lifetimes. More...
 
static HistogramgetWalkLengths ()
 Get walk lengths. More...
 
static species_copy_t countSpecies (const string &name)
 Count the number of motor species with a given name in the system. More...
 

Public Attributes

vector< double > coordinate
 coordinate of midpoint, updated with updatePosition() More...
 

Protected Attributes

bool _movable
 Object type. More...
 
bool _reactable
 Object type. More...
 
bool _dneighbor
 Object type. More...
 
bool _neighbor
 Object type. More...
 

Static Protected Attributes

static SubSystem_subSystem = 0
 A subsystem pointer for every trackable. More...
 

Private Attributes

unique_ptr< MMotorGhost_mMotorGhost
 Pointer to mech motor ghost. More...
 
unique_ptr< CMotorGhost_cMotorGhost
 Pointer to chem motor ghost. More...
 
Cylinder_c1
 First cylinder the motor is bound to. More...
 
Cylinder_c2
 Second cylinder the motor is bound to. More...
 
double _position1
 Position on first cylinder. More...
 
double _position2
 Position on second cylinder. More...
 
short _motorType
 Integer specifying the type of linker. More...
 
int _motorID
 Integer ID of this motor, managed by Database. More...
 
float _birthTime
 Birth time. More...
 
float _walkLength = 0
 Walk length of ensemble. More...
 
Compartment_compartment
 Where this motorghost is. More...
 
int _numHeads = 1
 Number of heads that this motor contains. More...
 
double _numBoundHeads = 1
 Number of bound heads in the ensemble, which is force-dependent. More...
 
double _onRate = 0.0
 Kinetic rates of individual motor heads. More...
 
double _offRate = 0.0
 Kinetic rates of individual motor heads. More...
 

Static Private Attributes

static Database< MotorGhost * > _motorGhosts
 Collection in SubSystem. More...
 
static vector< MotorRateChanger * > _unbindingChangers
 For dynamic rate unbinding. More...
 
static vector< MotorRateChanger * > _walkingChangers
 For dynamic rate walking. More...
 
static Histogram_lifetimes
 Histogram data. More...
 
static Histogram_walkLengths
 Histogram data. More...
 

Friends

class Controller
 
class DRController
 
class MotorBindingManager
 
struct UpdateMotorIDCallback
 
struct MotorBindingCallback
 
struct MotorUnbindingCallback
 

Detailed Description

A container to store a MMotorGhost and CMotorGhost.

MotorGhost class is used to manage and store a MMotorGhost and CMotorGhost. Upon intialization, both of these components are created.

Extending the Movable class, the positions of all instances can be updated by the SubSystem.

Extending the Reactable class, the reactions associated with all instances can be updated by the SubSystem.

Definition at line 47 of file MotorGhost.h.

Constructor & Destructor Documentation

§ MotorGhost()

MotorGhost::MotorGhost ( Cylinder c1,
Cylinder c2,
short  motorType,
double  position1 = 0.5,
double  position2 = 0.5,
double  onRate = 0.0,
double  offRate = 0.0 
)

§ ~MotorGhost()

MotorGhost::~MotorGhost ( )
virtualnoexcept
Note
- record lifetime data here

Definition at line 99 of file MotorGhost.cpp.

References _birthTime, _lifetimes, _walkLength, _walkLengths, Histogram::addValue(), Histogram::getMax(), Histogram::getMin(), and tau().

Member Function Documentation

§ addToSubSystem()

virtual void MotorGhost::addToSubSystem ( )
inlinevirtual

SubSystem management, inherited from Trackable.

Implements Trackable.

Definition at line 157 of file MotorGhost.h.

Referenced by getBirthTime().

§ apply() [1/3]

bool Component::apply ( Visitor v)
virtualinherited

When this function is applied to a ConditionalVisitor v, the corresponding v.visit(this) is called, and v is further applied to all children of this node recursively.

However, the ConditionalVisitor allows the visit() function to be applied only selectively to nodes that conform to specific criteria.

Reimplemented in Composite.

Definition at line 26 of file Component.cpp.

References Visitor::visit().

Referenced by Component::~Component().

§ apply() [2/3]

virtual bool Component::apply ( SpeciesVisitor v)
inlinevirtualinherited

Implements the apply_if() method of the Component class by recursively applying it to itself and all its children that contain Species.

Reimplemented in Composite.

Definition at line 61 of file Component.h.

References Component::apply_impl().

§ apply() [3/3]

virtual bool Component::apply ( ReactionVisitor v)
inlinevirtualinherited

Implements the apply_if() method of the Component class by recursively applying it to itself and all its children that contain ReactionBase.

Reimplemented in Composite.

Definition at line 69 of file Component.h.

References Component::apply_impl().

§ apply_impl() [1/2]

virtual bool Component::apply_impl ( SpeciesVisitor v)
inlinevirtualinherited

Applies SpeciesVisitor v to every Species* object directly owned by this node.

This method needs to be overriden by descendent classes that contain Species.

Reimplemented in Compartment.

Definition at line 65 of file Component.h.

Referenced by Component::apply(), and Composite::apply().

§ apply_impl() [2/2]

virtual bool Component::apply_impl ( ReactionVisitor v)
inlinevirtualinherited

Applies ReactionBaseVisitor v to every ReactionBase* object directly owned by this node.

This method needs to be overriden by descendent classes that contain ReactionBase.

Reimplemented in Compartment.

Definition at line 74 of file Component.h.

§ countDescendents()

virtual size_t Component::countDescendents ( ) const
inlinevirtualinherited

Return the total number of nodes contained under this node's hieararchy.

Note
This is a recursive call, and all nodes under this node are visited.

Reimplemented in Composite.

Definition at line 118 of file Component.h.

§ countReactions()

virtual size_t Component::countReactions ( ) const
inlinevirtualinherited

Return the number of ReactionBase objects contained under this node's hieararchy.

Note
This is a recursive call, and all nodes under this node are visited.

Reimplemented in Composite.

Definition at line 126 of file Component.h.

References Component::getType(), and Component::printSelf().

§ countSpecies() [1/2]

virtual size_t Component::countSpecies ( ) const
inlinevirtualinherited

Return the number of Species contained under this node's hieararchy.

Note
This is a recursive call, and all nodes under this node are visited.

Reimplemented in Composite.

Definition at line 122 of file Component.h.

Referenced by Linker::getLifetimes(), getWalkLengths(), BranchingPoint::numBranchingPoints(), and Chemistry::print().

§ countSpecies() [2/2]

species_copy_t MotorGhost::countSpecies ( const string &  name)
static

Count the number of motor species with a given name in the system.

Definition at line 390 of file MotorGhost.cpp.

References _lifetimes, _motorGhosts, _unbindingChangers, _walkingChangers, _walkLengths, Database< T >::getElements(), and SpeciesNamesDB::removeUniqueFilName().

§ getBirthTime()

float MotorGhost::getBirthTime ( )
inline

Get the birth time.

Definition at line 153 of file MotorGhost.h.

References _birthTime, Database< T >::addElement(), and addToSubSystem().

§ getCMotorGhost()

CMotorGhost* MotorGhost::getCMotorGhost ( )
inline

Get chem motor ghost.

Definition at line 130 of file MotorGhost.h.

§ getFirstCylinder()

Cylinder* MotorGhost::getFirstCylinder ( )
inline

Get cylinder.

Definition at line 115 of file MotorGhost.h.

§ getFirstPosition()

double MotorGhost::getFirstPosition ( )
inline

Position management function.

Definition at line 137 of file MotorGhost.h.

Referenced by getMMotorGhost().

§ getFullName()

virtual string Component::getFullName ( ) const
inlinevirtualinherited

Return a string indicating the full name of this node (presumably used mainly for debugging)

Reimplemented in Compartment, CompartmentGrid, and Composite.

Definition at line 114 of file Component.h.

§ getID()

int MotorGhost::getID ( )
inline

Parameter management.

Definition at line 147 of file MotorGhost.h.

References _motorID.

§ getLifetimes()

static Histogram* MotorGhost::getLifetimes ( )
inlinestatic

Get the lifetimes.

Definition at line 171 of file MotorGhost.h.

References _lifetimes.

Referenced by MotorLifetimes::print().

§ getMMotorGhost()

MMotorGhost* MotorGhost::getMMotorGhost ( )
inline

Get mech motor ghost.

Definition at line 133 of file MotorGhost.h.

References _position1, and getFirstPosition().

§ getMotorGhosts()

§ getParent()

§ getRoot()

Composite * Component::getRoot ( )
inherited

Returns the root node of the hieararchy to which this node belongs to.

Definition at line 19 of file Component.cpp.

References Component::getParent(), Component::getRoot(), and Component::isRoot().

Referenced by Component::getRoot(), ReactionBase::getRoot(), Species::getRoot(), and Component::isRoot().

§ getSecondCylinder()

Cylinder* MotorGhost::getSecondCylinder ( )
inline

Get cylinder.

Definition at line 116 of file MotorGhost.h.

References _c2, and setFirstCylinder().

§ getSecondPosition()

double MotorGhost::getSecondPosition ( )
inline

Position management function.

Definition at line 140 of file MotorGhost.h.

References _position2.

§ getType()

virtual int MotorGhost::getType ( )
inlinevirtual

Parameter management.

Implements Component.

Definition at line 146 of file MotorGhost.h.

Referenced by setSecondPosition().

§ getWalkLengths()

static Histogram* MotorGhost::getWalkLengths ( )
inlinestatic

§ isComposite()

virtual bool Component::isComposite ( ) const
inlinevirtualinherited

Returns true if this node is a Composite node.

Reimplemented in Composite.

Definition at line 95 of file Component.h.

§ isReactionsContainer()

virtual bool Component::isReactionsContainer ( ) const
inlinevirtualinherited

Returns true if this node contains non-zero number of reactions (i.e.

ReactionBase pointers)

Reimplemented in Compartment.

Definition at line 102 of file Component.h.

Referenced by Composite::countReactions().

§ isRoot()

bool Component::isRoot ( ) const
inlineinherited

Returns true if this node is the root node.

A root node has no parent, and the corresponding getParent() call would return a nullptr.

Definition at line 85 of file Component.h.

References Component::getRoot().

Referenced by Component::getRoot().

§ isSpeciesContainer()

virtual bool Component::isSpeciesContainer ( ) const
inlinevirtualinherited

Returns true if this node contains non-zero number of Species.

Reimplemented in Compartment.

Definition at line 98 of file Component.h.

Referenced by Composite::countSpecies().

§ moveMotorHead() [1/2]

void MotorGhost::moveMotorHead ( Cylinder c,
double  oldPosition,
double  newPosition,
short  boundType,
SubSystem ps 
)

Move a motor head forward.

Note
- Updates chemical binding and mechanical parameters accordingly

Definition at line 298 of file MotorGhost.cpp.

References _c1, _cMotorGhost, _motorType, _position1, _position2, _walkLength, GeoParams::cylinderSize, SysParams::Geometry(), Cylinder::getCCylinder(), and Cylinder::getType().

Referenced by getWalkLengths().

§ moveMotorHead() [2/2]

void MotorGhost::moveMotorHead ( Cylinder oldC,
Cylinder newC,
double  oldPosition,
double  newPosition,
short  boundType,
SubSystem ps 
)

Move a motor head to a new cylinder.

Note
- Updates chemical binding and mechanical parameters accordingly

Definition at line 327 of file MotorGhost.cpp.

References _c1, _c2, _cMotorGhost, _motorType, _position1, _position2, _walkLength, GeoParams::cylinderSize, SysParams::Geometry(), Cylinder::getCCylinder(), and Cylinder::getType().

§ numberOfChildren()

virtual size_t Component::numberOfChildren ( ) const
inlinevirtualinherited

Returns the number of children of this node.

Note
Species and ReactionBase objects are not counted.

Reimplemented in Composite.

Definition at line 92 of file Component.h.

§ numberOfReactions()

virtual size_t Component::numberOfReactions ( ) const
inlinevirtualinherited

Returns the number of ReactionBase objets being immediately managed by this node (i.e.

not counting reactions belonging to children nodes, etc.

Reimplemented in Compartment, and Composite.

Definition at line 110 of file Component.h.

§ numberOfSpecies()

virtual size_t Component::numberOfSpecies ( ) const
inlinevirtualinherited

Returns the number of Species being immediately managed by this node (i.e.

not counting Species belonging to children nodes, etc.

Reimplemented in Compartment, and Composite.

Definition at line 106 of file Component.h.

§ numMotorGhosts()

static int MotorGhost::numMotorGhosts ( )
inlinestatic

Get the number of motors in this system.

Definition at line 166 of file MotorGhost.h.

References Database< T >::countElements().

Referenced by BasicSnapshot::print(), BirthTimes::print(), Forces::print(), Tensions::print(), WallTensions::print(), and Types::print().

§ printSelf()

void MotorGhost::printSelf ( )
virtual

Prints information about this node. Useful for debugging.

Implements Component.

Definition at line 355 of file MotorGhost.cpp.

References _birthTime, _c1, _c2, _cMotorGhost, _motorID, _motorType, _numHeads, _position1, _position2, coordinate, and Cylinder::printSelf().

Referenced by getWalkLengths(), MotorGhost(), updatePosition(), and MotorGhostFF::whoIsCulprit().

§ removeFromSubSystem()

virtual void MotorGhost::removeFromSubSystem ( )
inlinevirtual

SubSystem management, inherited from Trackable.

Implements Trackable.

Definition at line 158 of file MotorGhost.h.

References Database< T >::removeElement().

§ setCMotorGhost()

void MotorGhost::setCMotorGhost ( CMotorGhost cMotorGhost)
inline

Set chem motor ghost.

Definition at line 126 of file MotorGhost.h.

Referenced by updatePosition().

§ setFirstCylinder()

void MotorGhost::setFirstCylinder ( Cylinder cylinder)
inline

Set cylinder.

Definition at line 121 of file MotorGhost.h.

Referenced by getSecondCylinder().

§ setFirstPosition()

void MotorGhost::setFirstPosition ( double  position1)
inline

Position management function.

Definition at line 138 of file MotorGhost.h.

§ setID()

void MotorGhost::setID ( int  ID)
inline

Parameter management.

Definition at line 149 of file MotorGhost.h.

§ setParent()

void Component::setParent ( Composite other)
inlineinherited

Sets the parent of this node to other.

Definition at line 81 of file Component.h.

§ setSecondCylinder()

void MotorGhost::setSecondCylinder ( Cylinder cylinder)
inline

Set cylinder.

Definition at line 122 of file MotorGhost.h.

§ setSecondPosition()

void MotorGhost::setSecondPosition ( double  position2)
inline

Position management function.

Definition at line 141 of file MotorGhost.h.

References _motorType, and getType().

§ updateCoordinate()

void MotorGhost::updateCoordinate ( )

Helper to get coordinate.

Definition at line 30 of file MotorGhost.cpp.

References mathfunc::midPointCoordinate().

Referenced by MotorGhost(), and updatePosition().

§ updatePosition()

§ updateReactionRates()

void MotorGhost::updateReactionRates ( )
virtual

Update the reaction rates, inherited from Reactable.

Updates unbinding rates based on the stretch force.

Note
- This function updates forward walking rates using the stetching force in the opposite direction of the motor walk. Does not consider negative forces in this direction. Does not consider compression forces, only stretching.

Implements Reactable.

Definition at line 185 of file MotorGhost.cpp.

References _c1, _c2, _cMotorGhost, _mMotorGhost, _motorType, _numBoundHeads, _numHeads, _offRate, _onRate, _position1, _position2, _unbindingChangers, _walkingChangers, ReactionBase::activateReaction(), Bead::coordinate, mathfunc::dotProduct(), Cylinder::getFirstBead(), Species::getRSpecies(), Cylinder::getSecondBead(), mathfunc::midPointCoordinate(), MOTORWALKINGBACKWARD, MOTORWALKINGFORWARD, RSpecies::reactantReactions(), SysParams::RUNSTATE, ReactionBase::setRate(), and mathfunc::twoPointDirection().

Referenced by getWalkLengths().

Friends And Related Function Documentation

§ Controller

friend class Controller
friend

Definition at line 49 of file MotorGhost.h.

§ DRController

friend class DRController
friend

Definition at line 50 of file MotorGhost.h.

§ MotorBindingCallback

friend struct MotorBindingCallback
friend

Definition at line 55 of file MotorGhost.h.

§ MotorBindingManager

friend class MotorBindingManager
friend

Definition at line 52 of file MotorGhost.h.

§ MotorUnbindingCallback

friend struct MotorUnbindingCallback
friend

Definition at line 56 of file MotorGhost.h.

§ UpdateMotorIDCallback

friend struct UpdateMotorIDCallback
friend

Definition at line 54 of file MotorGhost.h.

Member Data Documentation

§ _birthTime

float MotorGhost::_birthTime
private

Birth time.

Definition at line 71 of file MotorGhost.h.

Referenced by getBirthTime(), printSelf(), and ~MotorGhost().

§ _c1

Cylinder* MotorGhost::_c1
private

First cylinder the motor is bound to.

Definition at line 62 of file MotorGhost.h.

Referenced by MotorGhost(), moveMotorHead(), printSelf(), updatePosition(), and updateReactionRates().

§ _c2

Cylinder* MotorGhost::_c2
private

Second cylinder the motor is bound to.

Definition at line 63 of file MotorGhost.h.

Referenced by getSecondCylinder(), MotorGhost(), moveMotorHead(), printSelf(), updatePosition(), and updateReactionRates().

§ _cMotorGhost

unique_ptr<CMotorGhost> MotorGhost::_cMotorGhost
private

Pointer to chem motor ghost.

Definition at line 60 of file MotorGhost.h.

Referenced by MotorGhost(), moveMotorHead(), printSelf(), updatePosition(), and updateReactionRates().

§ _compartment

Compartment* MotorGhost::_compartment
private

Where this motorghost is.

Definition at line 74 of file MotorGhost.h.

Referenced by MotorGhost(), and updatePosition().

§ _dneighbor

bool Trackable::_dneighbor
protectedinherited

Object type.

Definition at line 54 of file Trackable.h.

§ _lifetimes

Histogram * MotorGhost::_lifetimes
staticprivate

Histogram data.

Definition at line 90 of file MotorGhost.h.

Referenced by countSpecies(), getLifetimes(), and ~MotorGhost().

§ _mMotorGhost

unique_ptr<MMotorGhost> MotorGhost::_mMotorGhost
private

Pointer to mech motor ghost.

Definition at line 59 of file MotorGhost.h.

Referenced by MotorGhost(), updatePosition(), and updateReactionRates().

§ _motorGhosts

Database< MotorGhost * > MotorGhost::_motorGhosts
staticprivate

Collection in SubSystem.

Definition at line 86 of file MotorGhost.h.

Referenced by countSpecies().

§ _motorID

int MotorGhost::_motorID
private

Integer ID of this motor, managed by Database.

Definition at line 69 of file MotorGhost.h.

Referenced by getID(), and printSelf().

§ _motorType

short MotorGhost::_motorType
private

Integer specifying the type of linker.

Definition at line 68 of file MotorGhost.h.

Referenced by MotorGhost(), moveMotorHead(), printSelf(), setSecondPosition(), updatePosition(), and updateReactionRates().

§ _movable

bool Trackable::_movable
protectedinherited

Object type.

Definition at line 52 of file Trackable.h.

§ _neighbor

bool Trackable::_neighbor
protectedinherited

Object type.

Definition at line 55 of file Trackable.h.

§ _numBoundHeads

double MotorGhost::_numBoundHeads = 1
private

Number of bound heads in the ensemble, which is force-dependent.

Definition at line 77 of file MotorGhost.h.

Referenced by MotorGhost(), updatePosition(), and updateReactionRates().

§ _numHeads

int MotorGhost::_numHeads = 1
private

Number of heads that this motor contains.

Definition at line 76 of file MotorGhost.h.

Referenced by MotorGhost(), printSelf(), updatePosition(), and updateReactionRates().

§ _offRate

double MotorGhost::_offRate = 0.0
private

Kinetic rates of individual motor heads.

Definition at line 83 of file MotorGhost.h.

Referenced by MotorGhost(), updatePosition(), and updateReactionRates().

§ _onRate

double MotorGhost::_onRate = 0.0
private

Kinetic rates of individual motor heads.

Definition at line 82 of file MotorGhost.h.

Referenced by MotorGhost(), updatePosition(), and updateReactionRates().

§ _position1

double MotorGhost::_position1
private

Position on first cylinder.

Definition at line 65 of file MotorGhost.h.

Referenced by getMMotorGhost(), moveMotorHead(), printSelf(), updatePosition(), and updateReactionRates().

§ _position2

double MotorGhost::_position2
private

Position on second cylinder.

Definition at line 66 of file MotorGhost.h.

Referenced by getSecondPosition(), moveMotorHead(), printSelf(), updatePosition(), and updateReactionRates().

§ _reactable

bool Trackable::_reactable
protectedinherited

Object type.

Definition at line 53 of file Trackable.h.

§ _subSystem

SubSystem * Trackable::_subSystem = 0
staticprotectedinherited

A subsystem pointer for every trackable.

Definition at line 46 of file Trackable.h.

Referenced by Controller::Controller(), and BranchingPoint::~BranchingPoint().

§ _unbindingChangers

vector< MotorRateChanger * > MotorGhost::_unbindingChangers
staticprivate

For dynamic rate unbinding.

Definition at line 95 of file MotorGhost.h.

Referenced by countSpecies(), DRController::initialize(), MotorGhost(), updatePosition(), and updateReactionRates().

§ _walkingChangers

vector< MotorRateChanger * > MotorGhost::_walkingChangers
staticprivate

For dynamic rate walking.

Definition at line 97 of file MotorGhost.h.

Referenced by countSpecies(), DRController::initialize(), and updateReactionRates().

§ _walkLength

float MotorGhost::_walkLength = 0
private

Walk length of ensemble.

Definition at line 72 of file MotorGhost.h.

Referenced by moveMotorHead(), and ~MotorGhost().

§ _walkLengths

Histogram * MotorGhost::_walkLengths
staticprivate

Histogram data.

Definition at line 91 of file MotorGhost.h.

Referenced by countSpecies(), getWalkLengths(), and ~MotorGhost().

§ coordinate

vector<double> MotorGhost::coordinate

coordinate of midpoint, updated with updatePosition()

Definition at line 100 of file MotorGhost.h.

Referenced by MotorGhost(), printSelf(), and updatePosition().


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