pyLM
v1.1
A Python Problem Solving Environment for the simulation of stochastic biological systems
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- _ -
__init__() :
pyLM.CME.CMESimulation
,
pyLM.RDME.CMESimulation
,
pyLM.RDME.RDMERegion
,
pyLM.RDME.RDMESimulation
,
pySTDLM.CellArranger.CellArranger
,
pySTDLM.CellArranger.LooseGridArranger
,
pySTDLM.CellArranger.RandomArranger
,
pySTDLM.CellArranger.RandomSphericalArranger
,
pySTDLM.CellArranger.TightGridArranger
,
pySTDLM.Cells.BoxCell
,
pySTDLM.Cells.CapsuleCell
,
pySTDLM.Cells.CapsuleShellCell
,
pySTDLM.Cells.CellShape
,
pySTDLM.Cells.SphereCell
,
pySTDLM.Distributions.ParticleGenerator
,
pySTDLM.Fitting.Comparator
,
pySTDLM.Fitting.Fitter
,
pySTDLM.Fitting.MomentComparator
,
pySTDLM.Fitting.SimulatedAnnealingFitter
,
pySTDLM.Fitting.SweepFitter
,
pySTDLM.Fitting.TraceComparator
- a -
addConcentration() :
pyLM.CME.CMESimulation
,
pyLM.RDME.CMESimulation
addCuboidRegion() :
pyLM.RDME.RDMESimulation
addExperiment() :
pySTDLM.Fitting.Fitter
addParameter() :
pySTDLM.Fitting.Fitter
addParticleAt() :
pyLM.RDME.RDMESimulation
addParticleAtIdx() :
pyLM.RDME.RDMESimulation
addParticles() :
pyLM.CME.CMESimulation
,
pyLM.RDME.CMESimulation
,
pyLM.RDME.RDMESimulation
addParticlesToRegion() :
pySTDLM.Distributions.ParticleGenerator
addReaction() :
pyLM.CME.CMESimulation
,
pyLM.RDME.CMESimulation
,
pyLM.RDME.RDMERegion
addRegion() :
pyLM.RDME.RDMESimulation
addShape() :
pyLM.RDME.RDMESimulation
addToSimulation() :
pySTDLM.CellArranger.CellArranger
,
pySTDLM.Cells.CellShape
- b -
boundingBox() :
pySTDLM.Cells.CellShape
buildCapsidCell() :
pyLM.RDME.RDMESimulation
buildDifference() :
pyLM.RDME.RDMESimulation
buildDiffusionModel() :
pyLM.RDME.RDMESimulation
buildEllipse() :
pyLM.RDME.RDMESimulation
buildPoint() :
pyLM.RDME.RDMESimulation
buildReactionModel() :
pyLM.CME.CMESimulation
,
pyLM.RDME.RDMESimulation
buildSpatialModel() :
pyLM.RDME.RDMESimulation
buildSphere() :
pyLM.RDME.RDMESimulation
buildSphericalCell() :
pyLM.RDME.RDMESimulation
buildVector() :
pyLM.RDME.RDMESimulation
- c -
cellFactory() :
pySTDLM.CellArranger.CellArranger
computeMetric() :
pySTDLM.Fitting.Comparator
,
pySTDLM.Fitting.MomentComparator
,
pySTDLM.Fitting.TraceComparator
computeVolume() :
pySTDLM.Cells.BoxCell
,
pySTDLM.Cells.CapsuleCell
,
pySTDLM.Cells.CapsuleShellCell
,
pySTDLM.Cells.SphereCell
createModelCell() :
pySTDLM.Cells.CellShape
- d -
defineSpecies() :
pyLM.CME.CMESimulation
,
pyLM.RDME.CMESimulation
,
pyLM.RDME.RDMESimulation
doesIntersect() :
pySTDLM.CellArranger.RandomArranger
- e -
emit() :
pyLM.LMLogger.NullHandler
- g -
getLattice() :
pyLM.RDME.RDMESimulation
getLatticeSite() :
pyLM.RDME.RDMESimulation
getReactionCount() :
pyLM.RDME.RDMERegion
getVolume() :
pySTDLM.Cells.CellShape
- i -
internalAddToSim() :
pySTDLM.Cells.BoxCell
,
pySTDLM.Cells.CapsuleCell
,
pySTDLM.Cells.CapsuleShellCell
,
pySTDLM.Cells.SphereCell
internalModelCell() :
pySTDLM.Cells.BoxCell
,
pySTDLM.Cells.CapsuleCell
,
pySTDLM.Cells.CapsuleShellCell
,
pySTDLM.Cells.SphereCell
internalTranslateCell() :
pySTDLM.Cells.BoxCell
,
pySTDLM.Cells.CapsuleCell
,
pySTDLM.Cells.SphereCell
intPackVolume() :
pySTDLM.CellArranger.LooseGridArranger
,
pySTDLM.CellArranger.RandomArranger
,
pySTDLM.CellArranger.RandomSphericalArranger
,
pySTDLM.CellArranger.TightGridArranger
- m -
modifyRegion() :
pyLM.RDME.RDMESimulation
- n -
newBBox() :
pySTDLM.CellArranger.RandomArranger
- o -
outsideDomain() :
pySTDLM.CellArranger.RandomArranger
- p -
packRegion() :
pyLM.RDME.RDMESimulation
packVolume() :
pySTDLM.CellArranger.CellArranger
performFit() :
pySTDLM.Fitting.Fitter
,
pySTDLM.Fitting.SimulatedAnnealingFitter
,
pySTDLM.Fitting.SweepFitter
- r -
run() :
pyLM.CME.CMESimulation
,
pyLM.RDME.RDMESimulation
runMPI() :
pyLM.CME.CMESimulation
,
pyLM.RDME.RDMESimulation
runSolver() :
pyLM.CME.CMESimulation
,
pyLM.RDME.RDMESimulation
- s -
save() :
pyLM.CME.CMESimulation
,
pyLM.RDME.RDMESimulation
saveFit() :
pySTDLM.Fitting.Fitter
,
pySTDLM.Fitting.SimulatedAnnealingFitter
,
pySTDLM.Fitting.SweepFitter
setDefaultDiffusionRate() :
pyLM.RDME.RDMERegion
setDiffusionRate() :
pyLM.RDME.RDMERegion
setLatticeSite() :
pyLM.RDME.RDMESimulation
setLatticeWriteInterval() :
pyLM.RDME.RDMESimulation
setParameterDivisions() :
pySTDLM.Fitting.SweepFitter
setRandomSeed() :
pyLM.CME.CMESimulation
,
pyLM.RDME.RDMESimulation
setRegions() :
pySTDLM.Cells.CellShape
setSimulationTime() :
pyLM.CME.CMESimulation
,
pyLM.RDME.RDMESimulation
setTimestep() :
pyLM.CME.CMESimulation
,
pyLM.RDME.RDMESimulation
setTransitionRate() :
pyLM.RDME.RDMESimulation
setTwoWayTransitionRate() :
pyLM.RDME.RDMESimulation
setWriteInterval() :
pyLM.CME.CMESimulation
,
pyLM.RDME.RDMESimulation
siteVolume() :
pyLM.RDME.RDMESimulation
- t -
translateCell() :
pySTDLM.Cells.CellShape
Generated on Wed Nov 9 2016 10:47:46 for pyLM by
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