pySTDLM.CellArranger.CellArranger Class Reference

Inheritance diagram for pySTDLM.CellArranger.CellArranger:

Public Member Functions
	__init__ (self, cellType=None, cellAttributes=None, arrangerAttributes=None, name='Unknown')
	cellFactory (self)
	packVolume (self, sim, volume=None)
	addToSimulation (self, sim)
	Add packed volume to RDME simulation.

Public Attributes
list	allowedCellTypes = ["Sphere", "Capsule", "Box", "CapsuleShell"]
list	allowedForms = ["Random", "RandomSpherical", "TightGrid", "LooseGrid", "SkewedGrid"]
str	cellType = cellType
	cellAttributes = cellAttributes
list	cells = []
	packerName = name
	arrangerAttributes = arrangerAttributes

Detailed Description

A base class for laying out cells in a 3D space.

Args:
    cellType:
        The type of cell this packer represents, can be one of: ["Sphere", "Capsule", "Box", "CapsuleShell"]
    cellAttributes:
        A dictionary with the required attributes specified for the cell and the form
    arrangerAttributes:
        A dictionary with the required/optional requirements for the individiual arranger

Constructor & Destructor Documentation

__init__()

pySTDLM.CellArranger.CellArranger.__init__	(		self,
			cellType = None,
			cellAttributes = None,
			arrangerAttributes = None,
			name = 'Unknown' )

Member Function Documentation

addToSimulation()

pySTDLM.CellArranger.CellArranger.addToSimulation	(		self,
			sim )

Add packed volume to RDME simulation.

Parameters

self
sim	An RDMESimulation object

cellFactory()

pySTDLM.CellArranger.CellArranger.cellFactory

(

self

)

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packVolume()

pySTDLM.CellArranger.CellArranger.packVolume	(		self,
			sim,
			volume = None )

Pack a specified volume with cells

Args:
    volume:
        A volume specified as [[xmin,ymin,zmin],[xmax,ymax,zmax]] (TODO: Add angles)
    form:
        The form of the packing, which can one of: ["Random", "RandomSpherical", "TightGrid", "LooseGrid", "SkewedGrid"]
Returns:
    A tuple of the form [volumePacked, volumePercent, numberCells]

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Member Data Documentation

allowedCellTypes

list pySTDLM.CellArranger.CellArranger.allowedCellTypes = ["Sphere", "Capsule", "Box", "CapsuleShell"]

allowedForms

list pySTDLM.CellArranger.CellArranger.allowedForms = ["Random", "RandomSpherical", "TightGrid", "LooseGrid", "SkewedGrid"]

arrangerAttributes

pySTDLM.CellArranger.CellArranger.arrangerAttributes = arrangerAttributes

cellAttributes

pySTDLM.CellArranger.CellArranger.cellAttributes = cellAttributes

cells

list pySTDLM.CellArranger.CellArranger.cells = []

cellType

pySTDLM.CellArranger.CellArranger.cellType = cellType

packerName

pySTDLM.CellArranger.CellArranger.packerName = name

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

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