mpacts.commands.misc. molecularreactions

In order to be able to use this module import it like this:

import mpacts.commands.misc.molecularreactions
#or assign it to a shorter name
import mpacts.commands.misc.molecularreactions as mol

BindingReaction

class mpacts.commands.misc.molecularreactions.BindingReaction

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

A command that will create the product for a given probability of two particles two react, stored in the contact data storage.
Default location: ‘loop_cmds/post_contact_cmds’
  • Required keywords:
    • contacts — ContactDataStorage which contains the reaction probabilities - currently ContactDataStorage_Vector is required!
    • diffusivity1 — Diffusivity of molecules in first particle container in the contact-data.
    • diffusivity2 — Diffusivity of molecules in second particle container in the contact-data.
    • pc — Particle container on which the command is applied
    • r — Radius of product
  • Optional keywords:
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • m (default value = 0) — Mass of product
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, contacts, diffusivity1, diffusivity2, r, [gate, predicate, m]
BindingReaction(name, parent, **kwargs)

CreationReaction

class mpacts.commands.misc.molecularreactions.CreationReaction

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

A command that will create a new product with probability k in the vicinity of a reagent.
Default location: ‘loop_cmds/post_contact_cmds’
  • Required keywords:
    • k — Reaction rate
    • pc — Particle container on which the command is applied
    • product — Particle container of product
    • r — Radius of product
  • Optional keywords:
    • excluded_volume_predicate (default value = None) — If given, exludes particles from a given volume
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • m (default value = 0) — Mass of product
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, product, k, r, [gate, predicate, m, excluded_volume_predicate]
CreationReaction(name, parent, **kwargs)

TransformationReaction

class mpacts.commands.misc.molecularreactions.TransformationReaction

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

A command that will create a new product with probability k and delete the reagent.
Default location: ‘loop_cmds/post_contact_cmds’
  • Required keywords:
    • k — Reaction rate
    • pc — Particle container on which the command is applied
    • product — Particle container of product
  • Optional keywords:
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
    • stimulus (default value = 1) — Stimulus modifying the reaction rate.
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, product, k, [gate, predicate, stimulus]
TransformationReaction(name, parent, **kwargs)

UnbindingReaction

class mpacts.commands.misc.molecularreactions.UnbindingReaction

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

A command that will create two products from one reagent with probability k.
Default location: ‘loop_cmds/post_contact_cmds’
  • Required keywords:
    • k — Reaction rate
    • pc — Particle container on which the command is applied
    • product1 — Particle container of first product - will be in the position of the reagent
    • product2 — Particle container of second product - will be randomly displaced by sum of radii
    • r1 — Radius of product1
    • r2 — Radius of product2
  • Optional keywords:
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • m1 (default value = 0) — Mass of product1
    • m2 (default value = 0) — Mass of product2
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, product1, product2, k, r1, r2, [gate, predicate, m1, m2]
UnbindingReaction(name, parent, **kwargs)