pySTDLM.StandardCells#

Functions

angstrom(*qty)

Returns a representation of a number in angstroms

buildDividingEColiCell(sim[, crowded, ...])

Build a standard E coli cell 0.5 microns across and 4 microns long.

buildEColiCell(sim[, crowded, crowdedMembrane])

Build a standard E coli cell 0.5 microns across and 2 microns long.

buildFilamentousEColiCell(sim[, length, ...])

Build a long filamentous E coli cell where the user can specify the length.

buildSphericalEColiCell([crowded, ...])

Build a Spherical E coli cell, one that lacks the gene for elongation.

cm(*qty)

Returns a representation of a number in centimeters

day(*qty)

Returns a representation of a number in days

getReactionString(rct, prd, rate)

hr(*qty)

Returns a representation of a number in hours

micron(*qty)

Returns a representation of a number in micrometers

microsecond(*qty)

Returns a representation of a number in microseconds

minute(*qty)

Returns a representation of a number in minutes

mm(*qty)

Returns a representation of a number in millimeters

ms(*qty)

Returns a representation of a number in milliseconds

nm(*qty)

Returns a representation of a number in nanometers

ns(*qty)

Returns a representation of a number in nanoseconds

packFastGrowingEcoli(sim)

Pack a cell with the protein distribution for fast growing E coli.

packSlowGrowingEcoli(sim)

Pack a cell with the protein distribution for fast growing E coli.

second(*qty)

Returns a representation of a number in seconds

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

visualizeRDMEInitialConditions(sim)

Visualize the RDME simulation volume inside Jupyter.

writeTable(columnNames, rows)

Classes

IntRDMESimulation(dimensions, spacing[, ...])

RDMERegion(name)

A class that represents a type region of an RDME simulation.

RDMESimulation(dimensions, spacing[, name, ...])

A class that contains all regions, reactions, diffusions and rules for a RDME simulation

tqdm(*_, **__)

Decorate an iterable object, returning an iterator which acts exactly like the original iterable, but prints a dynamically updating progressbar every time a value is requested.
pySTDLM.StandardCells.buildDividingEColiCell(sim, crowded=False, crowdedMembrane=False)[source]#

Build a standard E coli cell 0.5 microns across and 4 microns long.

Parameters:

  • sim – An RDMESimulation object

  • crowded – Should the cytosol be crowded (default: false)

  • crowdedMembrane – Should the membrane be crowded (default: false)

pySTDLM.StandardCells.buildEColiCell(sim, crowded=False, crowdedMembrane=False)[source]#

Build a standard E coli cell 0.5 microns across and 2 microns long.

Parameters:

  • sim – An RDMESimulation object

  • crowded – Should the cytosol be crowded (default: false)

  • crowdedMembrane – Should the membrane be crowded (default: false)

pySTDLM.StandardCells.buildFilamentousEColiCell(sim, length=8.0, crowded=False, crowdedMembrane=False)[source]#

Build a long filamentous E coli cell where the user can specify the length.

Parameters:

  • sim – An RDMESimulation object

  • length – The length of the cell in microns (default: 8)

  • crowded – Should the cytosol be crowded (default: false)

  • crowdedMembrane – Should the membrane be crowded (default: false)

pySTDLM.StandardCells.buildSphericalEColiCell(crowded=False, latticeSpacing=16, crowdedMembrane=False)[source]#

Build a Spherical E coli cell, one that lacks the gene for elongation.

Parameters:

  • sim – An RDMESimulation object

  • crowded – Should the cytosol be crowded (default: false)

  • crowdedMembrane – Should the membrane be crowded (default: false)

pySTDLM.StandardCells.packFastGrowingEcoli(sim)[source]#

Pack a cell with the protein distribution for fast growing E coli.

Parameters:

sim – A RDMESimulation object

pySTDLM.StandardCells.packSlowGrowingEcoli(sim)[source]#

Pack a cell with the protein distribution for fast growing E coli.

Parameters:

sim – A RDMESimulation object