Moved ratesOfChange to roadrunner
@@ -29,7 +29,6 @@ class ExtendedRoadRunner(roadrunner.RoadRunner):
'getBoundarySpeciesIds',
'getNumBoundarySpecies',
- 'getFloatingSpeciesConcentrations',
'getFloatingSpeciesIds',
'getNumFloatingSpecies',
@@ -85,8 +84,8 @@ class ExtendedRoadRunner(roadrunner.RoadRunner):
vs.__doc__ = roadrunner.ExecutableModel.getCompartmentIds.__doc__
def dv(self):
- return self.model.getStateVectorRate()
- dv.__doc__ = roadrunner.ExecutableModel.getStateVector.__doc__
+ return self.getRatesOfChange()
+ dv.__doc__ = roadrunner.RoadRunner.getRatesOfChange.__doc__
def rv(self):
return self.model.getReactionRates()
@@ -121,7 +120,7 @@ class ExtendedRoadRunner(roadrunner.RoadRunner):
""" Antimony string of the current model state.
See also: :func:`getAntimony`
- :returns: Antimony
+ :returns: Antimony string
:rtype: str
"""
return self.getAntimony(current=True)
@@ -131,7 +130,7 @@ class ExtendedRoadRunner(roadrunner.RoadRunner):
:param current: return current model state
:type current: bool
- :returns: Antimony
+ :returns: CellML string
:rtype: str
"""
sbml = self.__getSBML(current)
@@ -245,21 +244,6 @@ class ExtendedRoadRunner(roadrunner.RoadRunner):
roadrunner.SelectionRecord.FLOATING |
roadrunner.SelectionRecord.GLOBAL_PARAMETER)
- # ---------------------------------------------------------------------
- # Routines flattened from model, aves typing and easier finding of methods
- # ---------------------------------------------------------------------
- def getRatesOfChange(self):
- """ Rate of change of all state variables in the model.
-
- :returns: rate of change of all state variables (eg species) in the model.
- """
- if self.conservedMoietyAnalysis:
- m1 = self.getLinkMatrix()
- m2 = self.model.getStateVectorRate()
- return m1.dot(m2)
- else:
- return self.model.getStateVectorRate()
-
# ---------------------------------------------------------------------
# Plotting Utilities
# ---------------------------------------------------------------------
@@ -323,6 +307,8 @@ class ExtendedRoadRunner(roadrunner.RoadRunner):
:type ytitle: str
:param title: plot title
:type title: str
+ :param linewidth: linewidth of the plot
+ :type linewidth: float
:param xlim: limits on x-axis (tuple [start, end])
:param ylim: limits on y-axis
:param logx: use log scale for x-axis
