Namespace for objects of species, reactions and diffusions, as well as their containers.
Class diagram for steps.model namespace.
Top-level container for the objects in a kinetic model.
Construction:
m = steps.model.Model()
Create a model container object.
Remove the steps.model.Spec species object with identifier string spec_id (if defined) from the model.
Syntax:
delSpec(spec_id)
Remove the steps.model.Surfsys surface system object with identifier string ssys_id (if defined) from the model.
Syntax:
delSurfsys(ssys_id)
Remove the steps.model.Volsys volume system object with identifier string vsys_id (if defined) from the model.
Syntax:
delVolsys(vsys_id)
Returns a list of steps.model.Spec object references of all species in the model.
Syntax:
getAllSpecs()
Returns a reference to the steps.model.Spec species object with identifier string spec_id (if defined).
Syntax:
getSpec(spec_id)
Returns a reference to the steps.model.Surfsys surface system object with identifier string ssys_id (if defined).
Syntax:
getSurfsys(ssys_id)
Returns a reference to the steps.model.Volsys volume system object with identifier string vsys_id (if defined).
Syntax:
getVolsys(vsys_id)
A chemical species which can be a reactant and/or product in reaction stoichiometry and/or associated with a diffusion rule.
Construction:
s = steps.model.Spec(id, mdl)
Create a species object with identifier string id and assign the object mdl as its parent model.
Get the identifier string of the species.
Syntax:
getID()
Returns a reference to the parent steps.model.Model container object.
Syntax:
getModel()
Set the identifier string of the species.
Syntax:
setID(name)
A container that groups reactions involving reactants embedded in a volume.
Construction:
v = steps.model.Volsys(id, mdl)
Construct a volume system object with identifier string id and assign the object mdl as its parent model.
Remove the steps.model.Diff diffusion-rule object with identifier diff_id from the volume system.
Syntax:
delDiff(diff_id)
Remove the steps.model.Reac reaction-rule object with identifier reac_id (if defined) from the volume system.
Syntax:
delReac(reac_id)
Returns a list of references to all steps.model.Diff diffusion-rule objects defined in the volume system.
Syntax:
getAllDiffs()
Returns a list of references to all steps.model.Spec objects in this volume system; that is all reactants, products or diffusing species in the reaction and diffusion rules belonging to this volume system. No duplicate member is included.
Syntax:
getAllReacs()
Returns a list of references to all steps.model.Spec objects in this volume system; that is all reactants, products or diffusing species in the reaction and diffusion rules belonging to this volume system. No duplicate member is included.
Syntax:
getAllSpecs()
Returns a reference to the steps.model.Diff diffusion-rule object with identifier diff_id (if defined in the volume system).
Syntax:
getDiff(diff_id)
Get the identifier string of the volume system.
Syntax:
getID()
Returns a reference to the parent steps.model.Model container object.
Syntax:
getModel()
Returns a reference to the steps.model.Reac reaction-rule object with identifier string reac_id (if defined in the volume system).
Syntax:
getReac(reac_id)
Set the identifier string of the volume system.
Syntax:
setID(name)
A container that groups reactions involving a reactant embedded in a membrane.
Construction:
s = steps.model.Surfsys(id, mdl)
Construct a surface system object with identifier string id and assign the object mdl as its parent model.
Remove the steps.model.SReac surface-reaction object with identifier sreac_id from the surface system.
Syntax:
delSReac(sreac_id)
Returns a list of references to all steps.model.SReac surface-reaction objects defined in the surface system.
Syntax:
getAllSReacs()
Returns a list of references to all steps.model.Spec species objects included in the surface system; that is all reactants and products in the surface reactions belonging to this surface system. No duplicate member is included.
Syntax:
getAllSpecs()
Get the identifier string of the surface system.
Syntax:
getID()
Returns a reference to the parent steps.model.Model container object.
Syntax:
getModel()
Returns a reference to the steps.model.SReac surface-reaction object with identifier sreac_id (if defined in the surface system.
Syntax:
getSReac(sreac_id)
Set the identifier string of the surface system.
Syntax:
setID(name)
A kinetic reaction rule in a volume.
The reaction rule is specified by: * Species on the left hand side of the reaction: the reactants (lhs). * Species on the right hand side of the reaction: the products (rhs). * Rate constant for the reaction, supplied in s.i. units (kcst).
Construction:
reac = steps.model.Reac(id, volsys, lhs = [ ], rhs = [ ], kcst = 0.0)
Construct a reaction rule object with identifier string id and assign volsys as the parent volume system. A list of left hand side reactants may be assigned with lhs, whilst a list of right hand side products may be assigned with rhs, the kinetic reaction rate constant is set by kcst.
Returns a list of references to all steps.model.Spec species objects in the reaction; that is all reactants and products. No duplicate member is included.
Syntax:
getAllSpecs()
Get the identifier string of the reaction rule.
Syntax:
getID()
Get the kinetic reaction rate constant, in s.i. units, where the actual units depend on the order of the reaction.
Syntax:
getKcst()
Get a list of references to steps.model.Spec species objects on the left hand side of the reaction: the reactants.
Syntax:
getLHS()
Returns a reference to the parent steps.model.Model container object.
Syntax:
getModel()
Returns the order of this reaction.
Syntax:
getOrder()
Get a list of references to steps.model.Spec species objects on the right hand side of the reaction: the reactants.
Syntax:
getRHS()
Returns a reference to the parent steps.model.Volsys volume system object.
Syntax:
getVolsys()
Set the identifier string of the reaction rule.
Syntax:
setID(name)
Set the kinetic reaction rate constant, in s.i. units, where the actual units depend on the order of the reaction.
Syntax:
setKcst(kcst)
Set a list of references to steps.model.Spec species objects on the left hand side of the reaction: the reactants.
Syntax:
setLHS(lhs)
Set a list of references to steps.model.Spec species objects on the right hand side of the reaction: the reactants.
Syntax:
setRHS(rhs)
A reaction rule where at least one reactant is embedded in a surface.
In a surface reaction, the species can be classified as:
The reaction rate is defined by kcst, supplied in s.i. units.
Construction:
sreac = steps.model.Reac(id, surfsys,
ilhs = [ ], olhs = [ ], slhs = [ ],
irhs = [ ], orhs = [ ], srhs = [ ],
kcst = 0.0)
Construct a surface reaction rule object with identifier string id and assign surfsys as the parent surface system. A list of left hand reactants are assigned with ilhs, olhs and slhs (default for each is an empty list). A list of right hand side products are assigned with irhs, orhs and srhs (default for each is an empty list). The kinetic reaction rate constant is set with kcst.
Returns a list of references to all steps.model.Spec species objects in the surface reaction; that is all reactants and products. No duplicate member is included.
Syntax:
getAllSpecs()
Get the identifier string of the surface reaction rule.
Syntax:
getID()
Get a list of references to steps.model.Spec species objects; the left hand side inner volume reactants.
Syntax:
getILHS()
Get a list of references to steps.model.Spec species objects; the right hand side inner volume reactants.
Syntax:
getIRHS()
Get the kinetic reaction rate constant, in s.i. units, where the actual units depend on the order of the surface reaction.
Syntax:
getKcst()
Returns a reference to the parent steps.model.Model container object.
Syntax:
getModel()
Get a list of references to steps.model.Spec species objects; the left hand side outer volume reactants.
Syntax:
getOLHS()
Get a list of references to steps.model.Spec species objects; the right hand side outer volume reactants.
Syntax:
getORHS()
Returns the order of this surface reaction.
Syntax:
getOrder()
Get a list of references to steps.model.Spec species objects; the left hand side surface reactants.
Syntax:
getSLHS()
Get a list of references to steps.model.Spec species objects; the right hand side surface reactants.
Syntax:
getSRHS()
Returns a reference to the parent steps.model.Surfsys surface system object.
Syntax:
getSurfsys()
Set the identifier string of the surface reaction rule.
Syntax:
setID(name)
Set a list of references to steps.model.Spec species objects; the left hand side inner volume reactants.
Syntax:
setILHS(ilhs)
Set a list of references to steps.model.Spec species objects; the right hand side inner volume reactants.
Syntax:
setIRHS(irhs)
Set the kinetic reaction rate constant, in s.i. units, where the actual units depend on the order of the surface reaction.
Syntax:
setKcst(kcst)
Set a list of references to steps.model.Spec species objects; the left hand side outer volume reactants.
Syntax:
setOLHS(olhs)
Get a list of references to steps.model.Spec species objects; the right hand side outer volume reactants.
Syntax:
setORHS(orhs)
Set a list of references to steps.model.Spec species objects; the left hand side surface reactants.
Syntax:
setSLHS(slhs)
Set a list of references to steps.model.Spec species objects; the right hand side surface reactants.
Syntax:
setSRHS(srhs)
A diffusion rule for a chemical species in a volume.
A diffusion rule is described by: * Species to which the diffusion rule applies (lig). * Diffusion constant (dcst) specified in s.i. units.
Construction:
diff = steps.model.Diff(id, volsys, lig, dcst = 0.0)
Construct a diffusion rule object with identifier string id applied to species lig and assign volsys as the parent volume system. Diffusion constant is set by dcst.
Get the diffusion constant for the diffusion rule, in s.i. units.
Syntax:
getDcst()
Get the identifier string of the diffusion rule.
Syntax:
getID()
get a reference to the steps.model.Spec species object to which this diffusion rule is applied.
Syntax:
getLig()
Returns a reference to the parent steps.model.Model container object.
Syntax:
getModel()
Returns a reference to the parent steps.model.Volsys volume system object.
Syntax:
getVolsys()
Set the diffusion constant for the diffusion rule, in s.i. units.
Syntax:
setDcst(dcst)
Set the identifier string of the diffusion rule.
Syntax:
setID(name)
Set a reference to the steps.model.Spec species object to which this diffusion rule is applied.
Syntax:
setLig(lig)