pySTDLM.Cells.CellShape Class Reference

Inheritance diagram for pySTDLM.Cells.CellShape:

Public Member Functions
	__init__ (self)
	getVolume (self)
	boundingBox (self)
	addToSimulation (self, sim)
	translateCell (self, point)
	createModelCell (self, attr)
	setRegions (self, membrane, cytoplasm)

Public Attributes
str	name = "Unknown"
float	volume = -1.0
int	mins = 3*[0.]
int	maxs = 3*[0.]
float	membraneThickness = 0.0
str	memtype = "membrane"
str	cyttype = "cytoplasm"

Detailed Description

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

Constructor & Destructor Documentation

__init__()

pySTDLM.Cells.CellShape.__init__

(

self

)

Member Function Documentation

addToSimulation()

pySTDLM.Cells.CellShape.addToSimulation	(		self,
			sim )

Add the cell to the simulation

Args:
    sim:
        An RDMESimulation object

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boundingBox()

pySTDLM.Cells.CellShape.boundingBox

(

self

)

Return a bounding box for the cell

createModelCell()

pySTDLM.Cells.CellShape.createModelCell	(		self,
			attr )

Create model cell

Args:
    attrs:
        A dictionary of attributes

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getVolume()

pySTDLM.Cells.CellShape.getVolume

(

self

)

Volume occupied by cell

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

Returns:
    Volume in intrinsic units

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setRegions()

pySTDLM.Cells.CellShape.setRegions	(		self,
			membrane,
			cytoplasm )

Set regions

Args:
    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()

pySTDLM.Cells.CellShape.translateCell	(		self,
			point )

Shift a cell in space by the specified amount

Args:
    point [x,y,z]:
        translation in space

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Member Data Documentation

cyttype

str pySTDLM.Cells.CellShape.cyttype = "cytoplasm"

maxs

int pySTDLM.Cells.CellShape.maxs = 3*[0.]

membraneThickness

float pySTDLM.Cells.CellShape.membraneThickness = 0.0

memtype

str pySTDLM.Cells.CellShape.memtype = "membrane"

mins

pySTDLM.Cells.CellShape.mins = 3*[0.]

name

str pySTDLM.Cells.CellShape.name = "Unknown"

volume

float pySTDLM.Cells.CellShape.volume = -1.0

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The documentation for this class was generated from the following file:

• /data2/LM_zls_github/Lattice-Microbes/src/pylm/pySTDLM/Cells.py