pySTDLM.Cells#

Functions

setLMLogConsole([level])

Set the logger to write to the console as the code is working

setLMLogFile(filename[, level])

Set up file handler to print log to file

setLMLoggerLevel(level)

Set the level of the logger for the application

Classes

BoxCell([p1, p2])

A representation for a spherical cell.

CapsuleCell([p1, p2, radius, length])

A representation for a spherical cell.

CapsuleShellCell([p1, p2, radius, length])

A representation for a spherical cell.

CellShape()

Base class for a particular cell type for use in CellArranger (and later more)

SphereCell([origin, radius])

A representation for a spherical cell.
class pySTDLM.Cells.BoxCell(p1=[0.0, 0.0, 0.0], p2=[0.0, 0.0, 0.0])[source]#

Bases: CellShape

A representation for a spherical cell. This cell requires an attribute dictionary that includes “width”, “height”, “depth” and “membraneThickness”

addToSimulation(sim)#

Add the cell to the simulation

Parameters:

sim – An RDMESimulation object

boundingBox()#

Return a bounding box for the cell

computeVolume()[source]#
createModelCell(attr)#

Create model cell

Parameters:

attrs – A dictionary of attributes

getVolume()#

Volume occupied by cell

When overriding this class, you must specify a “computeVolume()” function of no arguments

Returns:

Volume in intrinsic units

internalAddToSim(sim)[source]#
internalModelCell(attr)[source]#
internalTranslateCell(point)[source]#
setRegions(membrane, cytoplasm)#

Set regions

Parameters:

  • membrane – The name of the region in which the membrane should be considered

  • cytoplasm – The name of the region in which the cytoplasm should be considered

translateCell(point)#

Shift a cell in space by the specified amount

Parameters:

  • [x (point) – translation in space

  • y – translation in space

  • z] – translation in space

class pySTDLM.Cells.CapsuleCell(p1=[0.0, 0.0, 0.0], p2=[0.0, 0.0, 0.0], radius=0.0, length=0.0)[source]#

Bases: CellShape

A representation for a spherical cell. This cell requires an attribute dictionary that includes “radius”, “length”, and “membraneThickness”

addToSimulation(sim)#

Add the cell to the simulation

Parameters:

sim – An RDMESimulation object

boundingBox()#

Return a bounding box for the cell

computeVolume()[source]#
createModelCell(attr)#

Create model cell

Parameters:

attrs – A dictionary of attributes

getVolume()#

Volume occupied by cell

When overriding this class, you must specify a “computeVolume()” function of no arguments

Returns:

Volume in intrinsic units

internalAddToSim(sim)[source]#
internalModelCell(attr)[source]#
internalTranslateCell(point)[source]#
setRegions(membrane, cytoplasm)#

Set regions

Parameters:

  • membrane – The name of the region in which the membrane should be considered

  • cytoplasm – The name of the region in which the cytoplasm should be considered

translateCell(point)#

Shift a cell in space by the specified amount

Parameters:

  • [x (point) – translation in space

  • y – translation in space

  • z] – translation in space

class pySTDLM.Cells.CapsuleShellCell(p1=[0.0, 0.0, 0.0], p2=[0.0, 0.0, 0.0], radius=0.0, length=0.0)[source]#

Bases: CapsuleCell

A representation for a spherical cell. This cell requires an attribute dictionary that includes “radius”, “length” and “membraneThickness”

addToSimulation(sim)#

Add the cell to the simulation

Parameters:

sim – An RDMESimulation object

boundingBox()#

Return a bounding box for the cell

computeVolume()[source]#
createModelCell(attr)#

Create model cell

Parameters:

attrs – A dictionary of attributes

getVolume()#

Volume occupied by cell

When overriding this class, you must specify a “computeVolume()” function of no arguments

Returns:

Volume in intrinsic units

internalAddToSim(sim)[source]#
internalModelCell(attr)[source]#
internalTranslateCell(point)#
setRegions(membrane, cytoplasm)#

Set regions

Parameters:

  • membrane – The name of the region in which the membrane should be considered

  • cytoplasm – The name of the region in which the cytoplasm should be considered

translateCell(point)#

Shift a cell in space by the specified amount

Parameters:

  • [x (point) – translation in space

  • y – translation in space

  • z] – translation in space

class pySTDLM.Cells.CellShape[source]#

Bases: object

Base class for a particular cell type for use in CellArranger (and later more)

addToSimulation(sim)[source]#

Add the cell to the simulation

Parameters:

sim – An RDMESimulation object

boundingBox()[source]#

Return a bounding box for the cell

createModelCell(attr)[source]#

Create model cell

Parameters:

attrs – A dictionary of attributes

getVolume()[source]#

Volume occupied by cell

When overriding this class, you must specify a “computeVolume()” function of no arguments

Returns:

Volume in intrinsic units

setRegions(membrane, cytoplasm)[source]#

Set regions

Parameters:

  • membrane – The name of the region in which the membrane should be considered

  • cytoplasm – The name of the region in which the cytoplasm should be considered

translateCell(point)[source]#

Shift a cell in space by the specified amount

Parameters:

  • [x (point) – translation in space

  • y – translation in space

  • z] – translation in space

class pySTDLM.Cells.SphereCell(origin=[0.0, 0.0, 0.0], radius=0.0)[source]#

Bases: CellShape

A representation for a spherical cell. This cell requires an attribute dictionary that includes “radius” and “membraneThickness”

addToSimulation(sim)#

Add the cell to the simulation

Parameters:

sim – An RDMESimulation object

boundingBox()#

Return a bounding box for the cell

computeVolume()[source]#
createModelCell(attr)#

Create model cell

Parameters:

attrs – A dictionary of attributes

getVolume()#

Volume occupied by cell

When overriding this class, you must specify a “computeVolume()” function of no arguments

Returns:

Volume in intrinsic units

internalAddToSim(sim)[source]#
internalModelCell(attr)[source]#
internalTranslateCell(point)[source]#
setRegions(membrane, cytoplasm)#

Set regions

Parameters:

  • membrane – The name of the region in which the membrane should be considered

  • cytoplasm – The name of the region in which the cytoplasm should be considered

translateCell(point)#

Shift a cell in space by the specified amount

Parameters:

  • [x (point) – translation in space

  • y – translation in space

  • z] – translation in space