mpacts.predicates. cellcycle_predicates

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

import mpacts.predicates.cellcycle_predicates
#or assign it to a shorter name
import mpacts.predicates.cellcycle_predicates as cel

InitBinaryFission_Directed

class mpacts.predicates.cellcycle_predicates.InitBinaryFission_Directed

Bases: mpacts.predicates.predicates.PredicateBase, mpacts.core.baseobject.BaseObject

Initialize the direction of two dividing cells in a given direction. The given vector will be normalized, and the daughter cell with be randomly displaced with either in ‘direction’ or minus ‘direction’
Has no default location.
  • Required keywords:
    • direction — Array of vectors (will be normalized) giving the initial direction of cell division
    • init_offset — Initial offset used for displacing the daughter cell, ensuring it is not exactly overlapping its mother. Expressed as a fraction of the cell’s radius
  • Optional keywords:
    • allow_manager_change (default value = 0) — Boolean that decides whether or not a predicate will allow you to change the manager it is currently working on.This is a safety check, disable only when you know what you are doing.
    • child_predicate (default value = None) — child predicate
    • init_division_time (default value = 0) — Initial value of the division time
object __init__(tuple args, dict kwds) :
args: name, parent kwds: init_offset, direction, [child_predicate, allow_manager_change, init_division_time]
InitBinaryFission_Directed(name, parent, **kwargs)

InitBinaryFission_Random

class mpacts.predicates.cellcycle_predicates.InitBinaryFission_Random

Bases: mpacts.predicates.predicates.PredicateBase, mpacts.core.baseobject.BaseObject

Initialize the direction of two dividing cells in a random direction. This should be used if there is not clear directionality prescribed to the dividing cells.
Has no default location.
  • Required keywords:
    • init_offset — Initial offset used for displacing the daughter cell, ensuring it is not exactly overlapping its mother. Expressed as a fraction of the cell’s radius
  • Optional keywords:
    • allow_manager_change (default value = 0) — Boolean that decides whether or not a predicate will allow you to change the manager it is currently working on.This is a safety check, disable only when you know what you are doing.
    • child_predicate (default value = None) — child predicate
    • init_division_time (default value = 0) — Initial value of the division time
    • restrict_to_plane (default value = 0 0 0) — If a plane normal is given, the command will project its direction in the plane.
object __init__(tuple args, dict kwds) :
args: name, parent kwds: init_offset, [child_predicate, allow_manager_change, init_division_time, restrict_to_plane]
InitBinaryFission_Random(name, parent, **kwargs)

InitBudding_Random

class mpacts.predicates.cellcycle_predicates.InitBudding_Random

Bases: mpacts.predicates.predicates.PredicateBase, mpacts.core.baseobject.BaseObject

The bud is placed at the spherical hull of the mother cell in a random location.
Has no default location.
  • Required keywords:
    • radius_init — Initial radius of a new bud
    • state_mother — State which should be given to the mother cell
  • Optional keywords:
    • allow_manager_change (default value = 0) — Boolean that decides whether or not a predicate will allow you to change the manager it is currently working on.This is a safety check, disable only when you know what you are doing.
    • child_predicate (default value = None) — child predicate
    • init_division_time (default value = 0) — Initial value of the division time
object __init__(tuple args, dict kwds) :
args: name, parent kwds: radius_init, state_mother, [child_predicate, allow_manager_change, init_division_time]
InitBudding_Random(name, parent, **kwargs)

Predicate_BinaryFissionFinished

class mpacts.predicates.cellcycle_predicates.Predicate_BinaryFissionFinished

Bases: mpacts.predicates.predicates.PredicateBase, mpacts.core.baseobject.BaseObject

Signals that a given cell part of a dividing complex has finished dividing, i.e. it has physically detached from its division partner.
Has no default location.
  • Required keywords:
    • predicate_running — Predicate which signals whether the cell is actually dividing. We can only ‘finish’ dividing when we are actually dividing and not doing something else.
  • Optional keywords:
    • allow_manager_change (default value = 0) — Boolean that decides whether or not a predicate will allow you to change the manager it is currently working on.This is a safety check, disable only when you know what you are doing.
    • child_predicate (default value = None) — child predicate
    • split_cutoff (default value = 1) — relative distance [0,1] = [0,2*r] between the cells at which the binary fission will be completed and the two cells split
object __init__(tuple args, dict kwds) :
args: name, parent kwds: predicate_running, [child_predicate, allow_manager_change, split_cutoff]
Predicate_BinaryFissionFinished(name, parent, **kwargs)

Predicate_BinaryFissionFinished_Spheroid

class mpacts.predicates.cellcycle_predicates.Predicate_BinaryFissionFinished_Spheroid

Bases: mpacts.predicates.predicates.PredicateBase, mpacts.core.baseobject.BaseObject

Signals that a given z-spheroidal cell part of a dividing complex has finished dividing, i.e. it has physically detached from its division partner.
Has no default location.
  • Required keywords:
    • predicate_running — Predicate which signals whether the cell is actually dividing. We can only ‘finish’ dividing when we are actually dividing and not doing something else.
  • Optional keywords:
    • allow_manager_change (default value = 0) — Boolean that decides whether or not a predicate will allow you to change the manager it is currently working on.This is a safety check, disable only when you know what you are doing.
    • child_predicate (default value = None) — child predicate
object __init__(tuple args, dict kwds) :
args: name, parent kwds: predicate_running, [child_predicate, allow_manager_change]
Predicate_BinaryFissionFinished_Spheroid(name, parent, **kwargs)

Predicate_BuddingFinished

class mpacts.predicates.cellcycle_predicates.Predicate_BuddingFinished

Bases: mpacts.predicates.predicates.PredicateBase, mpacts.core.baseobject.BaseObject

Signals that a bud is ready to separate from its mother cell.
Has no default location.
  • Required keywords:
    • predicate_running — Predicate which signals whether the cell is actually dividing. We can only ‘finish’ dividing when we are actually dividing and not doing something else.
    • state_bud — State index given to the bud
  • Optional keywords:
    • allow_manager_change (default value = 0) — Boolean that decides whether or not a predicate will allow you to change the manager it is currently working on.This is a safety check, disable only when you know what you are doing.
    • child_predicate (default value = None) — child predicate
    • overlap (default value = 0) — Overlap between the spheres beyond which the division will be finished.
object __init__(tuple args, dict kwds) :
args: name, parent kwds: predicate_running, state_bud, [child_predicate, allow_manager_change, overlap]
Predicate_BuddingFinished(name, parent, **kwargs)

Predicate_GrowthCapsuleFinished

class mpacts.predicates.cellcycle_predicates.Predicate_GrowthCapsuleFinished

Bases: mpacts.predicates.predicates.PredicateBase, mpacts.core.baseobject.BaseObject

Growth of a capsule-like bacterium is finished when its length exceeds a given maximal length which is stored in the array maxsize.
Has no default location.
  • Required keywords:
    • predicate_running — Predicate that signals whether this cell is actually currently growing. We can only finish the growth when we are actually growing at the moment and not doing something else
  • Optional keywords:
    • allow_manager_change (default value = 0) — Boolean that decides whether or not a predicate will allow you to change the manager it is currently working on.This is a safety check, disable only when you know what you are doing.
    • child_predicate (default value = None) — child predicate
object __init__(tuple args, dict kwds) :
args: name, parent kwds: predicate_running, [child_predicate, allow_manager_change]
Predicate_GrowthCapsuleFinished(name, parent, **kwargs)

Predicate_GrowthQuFinished

class mpacts.predicates.cellcycle_predicates.Predicate_GrowthQuFinished

Bases: mpacts.predicates.predicates.PredicateBase, mpacts.core.baseobject.BaseObject

Signals that a given cell, according to the Qu et al 2005 growth model, has reached its maximum size and should not further grow.
Has no default location.
  • Required keywords:
    • predicate_running — Predicate that signals whether this cell is actually currently growing. We can only finish the growth when we are actually growing at the moment and not doing something else
  • Optional keywords:
    • allow_manager_change (default value = 0) — Boolean that decides whether or not a predicate will allow you to change the manager it is currently working on.This is a safety check, disable only when you know what you are doing.
    • child_predicate (default value = None) — child predicate
object __init__(tuple args, dict kwds) :
args: name, parent kwds: predicate_running, [child_predicate, allow_manager_change]
Predicate_GrowthQuFinished(name, parent, **kwargs)