py4sci

6.1. steps.model

Namespace for objects of species, reactions and diffusions, as well as their containers.

_images/steps.model.jpg

Class diagram for steps.model namespace.

class steps.model.Model(*args)

Top-level container for the objects in a kinetic model.

Construction:

m = steps.model.Model()

Create a model container object.

Arguments:
None
delSpec(*args)

Remove the steps.model.Spec species object with identifier string spec_id (if defined) from the model.

Syntax:

delSpec(spec_id)
Arguments:
string spec_id
Return:
None
delSurfsys(*args)

Remove the steps.model.Surfsys surface system object with identifier string ssys_id (if defined) from the model.

Syntax:

delSurfsys(ssys_id)
Arguments:
string ssys_id
Return:
None
delVolsys(*args)

Remove the steps.model.Volsys volume system object with identifier string vsys_id (if defined) from the model.

Syntax:

delVolsys(vsys_id)
Arguments:
string vsys_id
Return:
None
getAllSpecs(*args)

Returns a list of steps.model.Spec object references of all species in the model.

Syntax:

getAllSpecs()
Arguments:
None
Return:
list<steps.model.Spec>
getSpec(*args)

Returns a reference to the steps.model.Spec species object with identifier string spec_id (if defined).

Syntax:

getSpec(spec_id)
Arguments:
string spec_id
Return:
steps.model.Spec
getSurfsys(*args)

Returns a reference to the steps.model.Surfsys surface system object with identifier string ssys_id (if defined).

Syntax:

getSurfsys(ssys_id)
Arguments:
string ssys_id
Return:
steps.model.Surfsys
getVolsys(*args)

Returns a reference to the steps.model.Volsys volume system object with identifier string vsys_id (if defined).

Syntax:

getVolsys(vsys_id)
Arguments:
string vsys_id
Return:
steps.model.Volsys
class steps.model.Spec(*args)

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.

Arguments:
  • string id
  • steps.model.Model mdl
getID(*args)

Get the identifier string of the species.

Syntax:

getID()
Arguments:
None
Return:
string
getModel(*args)

Returns a reference to the parent steps.model.Model container object.

Syntax:

getModel()
Arguments:
None
Return:
steps.model.Model
Attribute:
model
setID(*args)

Set the identifier string of the species.

Syntax:

setID(name)
Arguments:
string name
Return:
None
id
Identifier string of the species.
model
Reference to parent model.
class steps.model.Volsys(*args)

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.

Arguments:
  • string id
  • steps.model.Model mdl
delDiff(*args)

Remove the steps.model.Diff diffusion-rule object with identifier diff_id from the volume system.

Syntax:

delDiff(diff_id)
Arguments:
string diff_id
Return:
None
delReac(*args)

Remove the steps.model.Reac reaction-rule object with identifier reac_id (if defined) from the volume system.

Syntax:

delReac(reac_id)
Arguments:
string reac_id
Return:
None
getAllDiffs(*args)

Returns a list of references to all steps.model.Diff diffusion-rule objects defined in the volume system.

Syntax:

getAllDiffs()
Arguments:
None
Return:
list<steps.model.Diff>
getAllReacs(*args)

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()
Arguments:
None
Return:
list<steps.model.Reac>
getAllSpecs(*args)

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()
Arguments:
None
Return:
list<steps.model.Spec>
getDiff(*args)

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)
Arguments:
string diff_id
Return:
steps.model.Diff
getID(*args)

Get the identifier string of the volume system.

Syntax:

getID()
Arguments:
None
Return:
string
getModel(*args)

Returns a reference to the parent steps.model.Model container object.

Syntax:

getModel()
Arguments:
None
Return:
steps.model.Model
getReac(*args)

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)
Arguments:
string reac_id
Return:
steps.model.Reac
setID(*args)

Set the identifier string of the volume system.

Syntax:

setID(name)
Arguments:
string name
Return:
None
id
Identifier string of the volume system.
model
Reference to parent model.
class steps.model.Surfsys(*args)

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.

Arguments:
  • string id
  • steps.model.Model mdl
delSReac(*args)

Remove the steps.model.SReac surface-reaction object with identifier sreac_id from the surface system.

Syntax:

delSReac(sreac_id)
Arguments:
string sreac_id
Return:
None
getAllSReacs(*args)

Returns a list of references to all steps.model.SReac surface-reaction objects defined in the surface system.

Syntax:

getAllSReacs()
Arguments:
None
Return:
list<steps.model.SReac>
getAllSpecs(*args)

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()
Arguments:
None
Return:
list<steps.model.Spec>
getID(*args)

Get the identifier string of the surface system.

Syntax:

getID()
Arguments:
None
Return:
string
getModel(*args)

Returns a reference to the parent steps.model.Model container object.

Syntax:

getModel()
Arguments:
None
Return:
steps.model.Model
getSReac(*args)

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)
Arguments:
string sreac_id
Return:
steps.model.SReac
setID(*args)

Set the identifier string of the surface system.

Syntax:

setID(name)
Arguments:
string name
Return:
None
id
Identifier string of the surface system.
model
Reference to parent model.
class steps.model.Reac(*args, **kwargs)

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.

Arguments:
  • string id
  • steps.model.Volsys volsys
  • list(steps.model.Spec) lhs (default = [ ])
  • list(steps.model.Spec) rhs (default = [ ])
  • float kcst (default = 0.0)
getAllSpecs(*args)

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()
Arguments:
None
Return:
list<steps.model.Spec>
getID(*args)

Get the identifier string of the reaction rule.

Syntax:

getID()
Arguments:
None
Return:
string
getKcst(*args)

Get the kinetic reaction rate constant, in s.i. units, where the actual units depend on the order of the reaction.

Syntax:

getKcst()
Arguments:
None
Return:
float
getLHS(*args)

Get a list of references to steps.model.Spec species objects on the left hand side of the reaction: the reactants.

Syntax:

getLHS()
Arguments:
None
Return:
list<steps.model.Spec>
getModel(*args)

Returns a reference to the parent steps.model.Model container object.

Syntax:

getModel()
Arguments:
None
Return:
steps.model.Model
getOrder(*args)

Returns the order of this reaction.

Syntax:

getOrder()
Arguments:
None
Return:
int
getRHS(*args)

Get a list of references to steps.model.Spec species objects on the right hand side of the reaction: the reactants.

Syntax:

getRHS()
Arguments:
None
Return:
list<steps.model.Spec>
getVolsys(*args)

Returns a reference to the parent steps.model.Volsys volume system object.

Syntax:

getVolsys()
Arguments:
None
Return:
steps.model.Volsys
setID(*args)

Set the identifier string of the reaction rule.

Syntax:

setID(name)
Arguments:
string name
Return:
None
setKcst(*args)

Set the kinetic reaction rate constant, in s.i. units, where the actual units depend on the order of the reaction.

Syntax:

setKcst(kcst)
Arguments:
float kcst
Return:
None
setLHS(*args)

Set a list of references to steps.model.Spec species objects on the left hand side of the reaction: the reactants.

Syntax:

setLHS(lhs)
Arguments:
list<steps.model.Spec> lhs
Return:
None
setRHS(*args)

Set a list of references to steps.model.Spec species objects on the right hand side of the reaction: the reactants.

Syntax:

setRHS(rhs)
Arguments:
list<steps.model.Spec> rhs
Return:
None
id
Identifier string of the reaction.
kcst
Reaction constant.
lhs
Left hand side reactants.
model
Reference to parent model.
order
Order of the reaction.
rhs
Right hand side reactants.
volsys
Reference to parent volume system.
class steps.model.SReac(*args, **kwargs)

A reaction rule where at least one reactant is embedded in a surface.

In a surface reaction, the species can be classified as:

  • Reactants on the left hand side of the reaction:
    • Species in the ‘outer’ compartment (olhs)
    • or Species in the ‘inner’ compartment (ilhs)
    • Species on the surface (slhs)
  • Reactants on right hand side of the reaction:
    • Species in the ‘outer’ compartment (orhs)
    • Species in the ‘inner’ compartment (irhs)
    • Species on the surface (srhs)
  • 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.

Arguments:
  • string id
  • steps.model.Surfsys surfsys
  • list(steps.model.Spec) ilhs (default = [ ])
  • list(steps.model.Spec) olhs (default = [ ])
  • list(steps.model.Spec) slhs (default = [ ])
  • list(steps.model.Spec) irhs (default = [ ])
  • list(steps.model.Spec) orhs (default = [ ])
  • list(steps.model.Spec) srhs (default = [ ])
  • float kcst (default = 0.0)
getAllSpecs(*args)

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()
Arguments:
None
Return:
list<steps.model.Spec>
getID(*args)

Get the identifier string of the surface reaction rule.

Syntax:

getID()
Arguments:
None
Return:
string
getILHS(*args)

Get a list of references to steps.model.Spec species objects; the left hand side inner volume reactants.

Syntax:

getILHS()
Arguments:
None
Return:
list<steps.model.Spec>
getIRHS(*args)

Get a list of references to steps.model.Spec species objects; the right hand side inner volume reactants.

Syntax:

getIRHS()
Arguments:
None
Return:
list<steps.model.Spec>
getInner(*args)
Obsolete
getKcst(*args)

Get the kinetic reaction rate constant, in s.i. units, where the actual units depend on the order of the surface reaction.

Syntax:

getKcst()
Arguments:
None
Return:
float
getModel(*args)

Returns a reference to the parent steps.model.Model container object.

Syntax:

getModel()
Arguments:
None
Return:
steps.model.Model
getOLHS(*args)

Get a list of references to steps.model.Spec species objects; the left hand side outer volume reactants.

Syntax:

getOLHS()
Arguments:
None
Return:
list<steps.model.Spec>
getORHS(*args)

Get a list of references to steps.model.Spec species objects; the right hand side outer volume reactants.

Syntax:

getORHS()
Arguments:
None
Return:
list<steps.model.Spec>
getOrder(*args)

Returns the order of this surface reaction.

Syntax:

getOrder()
Arguments:
None
Return:
int
getOuter(*args)
Obsolete
getSLHS(*args)

Get a list of references to steps.model.Spec species objects; the left hand side surface reactants.

Syntax:

getSLHS()
Arguments:
None
Return:
list<steps.model.Spec>
getSRHS(*args)

Get a list of references to steps.model.Spec species objects; the right hand side surface reactants.

Syntax:

getSRHS()
Arguments:
None
Return:
list<steps.model.Spec>
getSurfsys(*args)

Returns a reference to the parent steps.model.Surfsys surface system object.

Syntax:

getSurfsys()
Arguments:
None
Return:
steps.model.Surfsys
setID(*args)

Set the identifier string of the surface reaction rule.

Syntax:

setID(name)
Arguments:
string name
Return:
None
setILHS(*args)

Set a list of references to steps.model.Spec species objects; the left hand side inner volume reactants.

Syntax:

setILHS(ilhs)
Arguments:
list<steps.model.Spec> ilhs
Return:
None
setIRHS(*args)

Set a list of references to steps.model.Spec species objects; the right hand side inner volume reactants.

Syntax:

setIRHS(irhs)
Arguments:
list<steps.model.Spec> irhs
Return:
None
setKcst(*args)

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)
Arguments:
float kcst
Return:
None
setOLHS(*args)

Set a list of references to steps.model.Spec species objects; the left hand side outer volume reactants.

Syntax:

setOLHS(olhs)
Arguments:
list<steps.model.Spec) olhs
Return:
None
setORHS(*args)

Get a list of references to steps.model.Spec species objects; the right hand side outer volume reactants.

Syntax:

setORHS(orhs)
Arguments:
list<steps.model.Spec> orhs
Return:
None
setSLHS(*args)

Set a list of references to steps.model.Spec species objects; the left hand side surface reactants.

Syntax:

setSLHS(slhs)
Arguments:
list<steps.model.Spec> slhs
Return:
None
setSRHS(*args)

Set a list of references to steps.model.Spec species objects; the right hand side surface reactants.

Syntax:

setSRHS(srhs)
Arguments:
list<steps.model.Spec> srhs
Return:
None
id
Identifier string of the surface reaction.
ilhs
Left hand side reactants in inner compartment.
irhs
Right hand side reactants in inner compartment.
kcst
Reaction constant.
model
Reference to parent model.
olhs
Left hand side reactants in outer compartment.
order
Order of the reaction.
orhs
Right hand side reactants in outer compartment.
outer
Obsolete
slhs
Left hand side reactants on surface.
srhs
Right hand side reactants on surface.
surfsys
Reference to parent surface system.
class steps.model.Diff(*args, **kwargs)

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.

Arguments:
  • string id
  • steps.model.Volsys volsys
  • steps.model.Spec lig
  • float dcst (default = 0.0)
getDcst(*args)

Get the diffusion constant for the diffusion rule, in s.i. units.

Syntax:

getDcst()
Arguments:
None
Return:
float
getID(*args)

Get the identifier string of the diffusion rule.

Syntax:

getID()
Arguments:
None
Return:
string
getLig(*args)

get a reference to the steps.model.Spec species object to which this diffusion rule is applied.

Syntax:

getLig()
Arguments:
None
Return:
steps.model.Spec
getModel(*args)

Returns a reference to the parent steps.model.Model container object.

Syntax:

getModel()
Arguments:
None
Return:
steps.model.Model
getVolsys(*args)

Returns a reference to the parent steps.model.Volsys volume system object.

Syntax:

getVolsys()
Arguments:
None
Return:
steps.model.Volsys
setDcst(*args)

Set the diffusion constant for the diffusion rule, in s.i. units.

Syntax:

setDcst(dcst)
Arguments:
float dcst
Return:
None
setID(*args)

Set the identifier string of the diffusion rule.

Syntax:

setID(name)
Arguments:
string name
Return:
None
setLig(*args)

Set a reference to the steps.model.Spec species object to which this diffusion rule is applied.

Syntax:

setLig(lig)
Arguments:
steps.model.Spec lig
Return:
None
dcst
Diffusion constant.
id
Identifier string of the diffusion.
lig
Reference to diffusion species.
model
Reference to parent model.
volsys
Reference to parent volume system.

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