Deprecated. Was used to create pathways described by a simple Monod kinetic y1 S1 -> y2 S2+X where µ=muMax*S1/(Ks+S1)
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| SingleMonod () |
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void | init (Simulator aSim, XMLParser aReactionRoot) |
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void | initFromAgent (ActiveAgent anAgent, Simulator aSim, XMLParser aReactionRoot) |
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void | computeSpecificGrowthRate (ActiveAgent anAgent) |
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void | computeSpecificGrowthRate (double[] s, ActiveAgent anAgent) |
| Return the specific reaction rate. More...
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void | computeSpecificGrowthRate (double[] s) |
| Compute specific growth rate in function of concentrations sent. Parameters used are those defined for the reaction. More...
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double | computeMassGrowthRate (ActiveAgent anAgent) |
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double | computeMassGrowthRate (ActiveAgent anAgent, double[] reactionKinetic) |
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double | computeSpecGrowthRate (ActiveAgent anAgent) |
| Compute the specific growth rate. More...
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void | computeAllUptakeRate (double[] s, double mass, double[] soluteYield, double[] kineticParam) |
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void | computeUptakeRate (double[] s, double mass, double tdel) |
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void | computeUptakeRate (double[] s, ActiveAgent anAgent) |
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double | kineticValue (double solute, double[] paramTable, int index) |
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double | kineticValue (double solute) |
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double | kineticDiff (double solute, double[] paramTable, int index) |
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double | kineticDiff (double solute) |
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double | kineticMax () |
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double | kineticMax (double[] paramTable, int index) |
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Matrix | calcdMUdS (Matrix S, double biomass) |
| Calculate the rate of change of each uptake rate with respect to each solute. Returned as a matrix. More...
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Matrix | calcdMUdT (Matrix S, double biomass) |
| Calculate the rate of change of each uptake rate with respect to time. More...
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double[] | computeMarginalDiffMu (double[] s) |
| Compute the marginal difference array. More...
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double | computeSpecRate (double[] s) |
| Compute the specific growth rate. More...
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void | updateMarginalMu (double[] s) |
| Update the Marginal Mu data matrix. More...
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void | init (Simulator aSim, XMLParser aReactionRoot) |
| Initialises a reaction object, giving the object the properties stated in the protocol file. More...
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void | initFromAgent (ActiveAgent anAgent, Simulator aSim, XMLParser xmlRoot) |
| Use the reaction class to fill the parameters fields of the agent. Populate only the yield vector, the kinetic vector will be filled by the subdefined method in the child classes. More...
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void | register (String aReactionName, Simulator aSimulator) |
| End of the initialization procedure. Store the name and simulation dictionary index for this reaction. More...
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LinkedList< String > | declareSolutes () |
| Utilised by a solver instance to know the solutes affected by this reaction. More...
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void | fillParameters (Simulator aSim, XMLParser xmlRoot) |
| Reads the reaction information (name, solute yield, particle yield etc) from the XML file and initialises this reaction. More...
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void | addAgent (ActiveAgent anAgent) |
| Register an agent among the guild of this pathway. More...
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void | removeAgent (ActiveAgent anAgent) |
| Remove an agent among the guild of this pathway. More...
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void | applyReaction (SpatialGrid[] concGrid, SpatialGrid[] reacGrid, SpatialGrid[] diffReacGrid, SpatialGrid biomassGrid) |
| Compute reaction rate on each concerned solute grids Assumes same parameters for all the agents of a same guild. More...
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void | fitAgentMassOnGrid (SpatialGrid aSpG) |
| Add the mass of all the agents of the guild on a received grid. The stored value is a CONCENTRATION. More...
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double[] | readConcentrationSeen (ActiveAgent anAgent, SoluteGrid[] concGrid) |
| Return a double array with all concentration seen by an agent on the default solute grid. More...
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void | writeReport (ResultFile bufferState, ResultFile bufferSum) throws Exception |
| Write reaction information to the result file stream. More...
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void | fitGuildOnGrid () |
| Build a grid with mass and mass-growth-rate of all agents of the guild. More...
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double[] | getSoluteYield () |
| Return the solute yield. More...
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int[] | getSoluteIndex () |
| Return the solute index. More...
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double[] | getParticulateYield () |
| Return the particulate yield. More...
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double[] | getKinetic () |
| Return the kinetic parameters used in this reaction. More...
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LinkedList< ActiveAgent > | getGuild () |
| Return the guild of this pathway. More...
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Deprecated. Was used to create pathways described by a simple Monod kinetic y1 S1 -> y2 S2+X where µ=muMax*S1/(Ks+S1)
Deprecated. Was used to create pathways described by a simple Monod kinetic y1 S1 -> y2 S2+X where µ=muMax*S1/(Ks+S1) the substrate used by a monod kinetic is the first one of the solutelist of the current object
- Author
- Laurent Lardon (lardo.nosp@m.nl@s.nosp@m.upagr.nosp@m.o.in.nosp@m.ra.fr), INRA, France