Lattice Microbes 2.5
This is for whole cell modeling
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jLM.JupyterDisplay.JupyterDisplayMixin Class Reference

Public Member Functions

 construct (sim)
 Model builder context manager.
 displayGeometry (self, filterFunctions=None, mode="widget")
 Site lattice viewer.
 showRegion (self, plane="xz", planeIndex=None)
 showRegionStack (self, plane='xz', scl=None, maxWidth=600, maxHeight=600)
 showAllParameters (self)
 showRateConstants (self)
 showDiffusionConstants (self)
 showSpecies (self, sps)
 showAllSpecies (self)
 showReactions (self, rxnList=None)

Public Attributes

 regionList
 siteLattice
 rxnRateList
 diffRateList
 reactionList

Protected Member Functions

 _repr_html_ (self)
 _speciesJ2context (self, sps, cs)
 _reactionJ2context (self, rxns)
 _regionJ2context (self, plane, planeIndex, maxWidth=600, maxHeight=600)
 _modelJ2context (self)
 _x3dJ2context (self, filterFunctions=None)
 _paramTable (self, title, params)

Protected Attributes

 _transitionRates
 _keys0 = self._getKeys()

Member Function Documentation

◆ _modelJ2context()

jLM.JupyterDisplay.JupyterDisplayMixin._modelJ2context ( self)
protected

◆ _paramTable()

jLM.JupyterDisplay.JupyterDisplayMixin._paramTable ( self,
title,
params )
protected

◆ _reactionJ2context()

jLM.JupyterDisplay.JupyterDisplayMixin._reactionJ2context ( self,
rxns )
protected

◆ _regionJ2context()

jLM.JupyterDisplay.JupyterDisplayMixin._regionJ2context ( self,
plane,
planeIndex,
maxWidth = 600,
maxHeight = 600 )
protected

◆ _repr_html_()

jLM.JupyterDisplay.JupyterDisplayMixin._repr_html_ ( self)
protected

◆ _speciesJ2context()

jLM.JupyterDisplay.JupyterDisplayMixin._speciesJ2context ( self,
sps,
cs )
protected

◆ _x3dJ2context()

jLM.JupyterDisplay.JupyterDisplayMixin._x3dJ2context ( self,
filterFunctions = None )
protected

◆ construct()

jLM.JupyterDisplay.JupyterDisplayMixin.construct ( sim)

Model builder context manager. 

Track newly created model objects and display in Notebook.

Context manager which tracks new species, reactions, etc., and displays
a HTML summary when used in Jupyter

◆ displayGeometry()

jLM.JupyterDisplay.JupyterDisplayMixin.displayGeometry ( self,
filterFunctions = None,
mode = "widget" )

Site lattice viewer. 

3-D site type lattice viewer

The display mode can be "widget", which displays in the 
notebook, "download_x3d", which opens a download link in the 
notebook to the X3D scene, or "download_html", which opens a 
download link in the notebook to a standalone HTML file. 

To hide parts of the lattice, `filterFunctions` can be 
specified. This option takes a list of functions which map 
from a (x,y,z) mesh grid to a [nx,ny,nz] boolean mask 
where only subvolumes marked True are shown. To only show
volumes whose z coordinate are less than 32, the function

>>> def zfilter(x,y,z):
>>>     return z<32

is used. Here the arguments x,y,z are 
of type :py:class:`numpy.ndarray` and a boolean lattice is
returned.

Args:
    filterFunctions (dict):
        Dict of functions which take a (nx,ny,nz) mesh to a 
        bool [nx,ny,nz] mask
    mode (str):
        View mode

◆ showAllParameters()

jLM.JupyterDisplay.JupyterDisplayMixin.showAllParameters ( self) 
Display a table of reaction rates and diffusion constants

◆ showAllSpecies()

jLM.JupyterDisplay.JupyterDisplayMixin.showAllSpecies ( self) 
Inspect all species interactively

◆ showDiffusionConstants()

jLM.JupyterDisplay.JupyterDisplayMixin.showDiffusionConstants ( self) 
Display a table of diffusion constants

◆ showRateConstants()

jLM.JupyterDisplay.JupyterDisplayMixin.showRateConstants ( self) 
Display a table of reaction rates

◆ showReactions()

jLM.JupyterDisplay.JupyterDisplayMixin.showReactions ( self,
rxnList = None ) 
Display a table of all reactions

◆ showRegion()

jLM.JupyterDisplay.JupyterDisplayMixin.showRegion ( self,
plane = "xz",
planeIndex = None ) 
Display a slice of the site lattice

Args:
    plane (str):
        Viewing plane, e.g. "xy"
    planeIndex (int):
        Index along the normal direction to the plane

◆ showRegionStack()

jLM.JupyterDisplay.JupyterDisplayMixin.showRegionStack ( self,
plane = 'xz',
scl = None,
maxWidth = 600,
maxHeight = 600 ) 
Display all slices of the site lattice interactively

Args:
    plane (str):
        Viewing plane, e.g. "xy"
    scl (int):
        Scale pixels by this amount
    maxWidth (int):
        Maximum width of image
    maxHeight (int):
        Maximum height of image

◆ showSpecies()

jLM.JupyterDisplay.JupyterDisplayMixin.showSpecies ( self,
sps ) 
Show details on a species type

Member Data Documentation

◆ _keys0

jLM.JupyterDisplay.JupyterDisplayMixin._keys0 = self._getKeys()
protected

◆ _transitionRates

jLM.JupyterDisplay.JupyterDisplayMixin._transitionRates
protected

◆ diffRateList

jLM.JupyterDisplay.JupyterDisplayMixin.diffRateList

◆ reactionList

jLM.JupyterDisplay.JupyterDisplayMixin.reactionList

◆ regionList

jLM.JupyterDisplay.JupyterDisplayMixin.regionList

◆ rxnRateList

jLM.JupyterDisplay.JupyterDisplayMixin.rxnRateList

◆ siteLattice

jLM.JupyterDisplay.JupyterDisplayMixin.siteLattice
The documentation for this class was generated from the following file: