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Version 1.2 (June 2013)
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Version 1.2 (June 2013)
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Extends Bacterium Param for use by BactEPS species, a bacterium with a permanent hydrolytic activity of its EPS capsule. More...
Public Member Functions | |
| BactEPSParam () | |
| Creates a parameter storage object for the Bacterium EPS species type. More... | |
| void | init (Simulator aSim, XMLParser aSpeciesRoot) |
| Initialises Bacterium EPS Species parameters, calling the relevant superclasses to initialise common parameters and reading in the hydrolysis speed. More... | |
 Public Member Functions inherited from simulator.agent.zoo.BacteriumParam | |
| BacteriumParam () | |
| Constructor to create a BacteriumParam parameter storage object. More... | |
| void | init (Simulator aSim, XMLParser aSpeciesRoot) |
| Initialises Bacterium species parameters, calling the relevant superclasses to initialise common parameters for Bacterium derived species. More... | |
| Public Member Functions inherited from simulator.agent.LocatedParam | |
| LocatedParam () | |
| Create a new LocatedParam parameter storage object, calling the relevant extended class constructors. More... | |
| void | init (Simulator aSim, XMLParser aSpeciesRoot) |
| Assigns values to each of the location and behavioural specific parameters, reading these from the protocol file. More... | |
| double | getCellRunSpeed () |
| Return the cell run speed. Used in agent self-attachment scenarios. More... | |
| double | getStickinessRadius () |
| Return the cell stickiness radius. Used in agent self-attachment scenarios. More... | |
| Public Member Functions inherited from simulator.agent.ActiveParam | |
| void | init (Simulator aSim, XMLParser aSpeciesRoot) |
| Stores the reaction parameters for an active species and calculates the particle density of compounds involved in the reaction. More... | |
| Public Member Functions inherited from simulator.agent.SpeciesParam | |
| void | init (Simulator aSim, XMLParser aSpeciesRoot) |
| Read in specific parameters for this species, changing the default if required. More... | |
Public Attributes | |
| double | kHyd = 0.007 |
| Public Attributes inherited from simulator.agent.zoo.BacteriumParam | |
| double | epsMax = .15 |
| Color | epsColor = Color.lightGray |
| Boolean | distMethod = false |
| Public Attributes inherited from simulator.agent.LocatedParam | |
| double | divRadius = .97 |
| double | divRadiusCV = .1 |
| double | babyMassFrac = .5 |
| double | babyMassFracCV = .1 |
| double | deathRadius = .2 |
| double | deathRadiusCV = .1 |
| double | shoveFactor = 1.15 |
| double | shoveLimit = 0 |
| double | cellRunSpeed |
| double | tumbleInterval |
| double | stickinessAddition |
| Public Attributes inherited from simulator.agent.ActiveParam | |
| double[] | particleDensity |
| double[][] | soluteYield |
| double[][] | particleYield |
| double[][] | reactionKinetic |
| double[] | lysisYield |
| Public Attributes inherited from simulator.agent.SpeciesParam | |
| double | initialMassCV = .1 |
Extends Bacterium Param for use by BactEPS species, a bacterium with a permanent hydrolytic activity of its EPS capsule.
Extends Bacterium Param for use by BactEPS species, a bacterium with a permanent hydrolytic activity of its EPS capsule.
| simulator.agent.zoo.BactEPSParam.BactEPSParam | ( | ) |
Initialises Bacterium EPS Species parameters, calling the relevant superclasses to initialise common parameters and reading in the hydrolysis speed.
Initialises Bacterium EPS Species parameters, calling the relevant superclasses to initialise common parameters and reading in the hydrolysis speed
| aSim | The simulation object used to simulate the conditions specified in the protocol file |
| aSpeciesRoot | A species mark-up within the specified protocol file |
| double simulator.agent.zoo.BactEPSParam.kHyd = 0.007 |
Hydrolysis speed of capsule EPS (h-1)
1.8.3.1
