#
# University of Illinois Open Source License
# Copyright 2008-2018 Luthey-Schulten Group,
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#
# Developed by: Luthey-Schulten Group
# University of Illinois at Urbana-Champaign
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# Author(s): Michael J. Hallock and Joseph R. Peterson
#
#
import pyLM
from pyLM.RDME import *
from pyLM.units import *
# #########
# E. coli #
# #########
[docs]
def buildEColiCell(sim, crowded=False, crowdedMembrane=False ):
"""Build a standard E coli cell 0.5 microns across and 2 microns long.
Args:
sim:
An RDMESimulation object
crowded:
Should the cytosol be crowded (default: false)
crowdedMembrane:
Should the membrane be crowded (default: false)
"""
# Sanity check
if not isinstance(sim, RDMESimulation):
LMLogger.error('Could not build an E. coli cell in the sim which is not of type \'RDMESimulation\'')
# Create the cell
sim.buildCapsidCell(length=micron(2), diameter=micron(0.5), membraneThickness=nm(32))
# Pack the cell
if crowded is True:
packFastGrowingEcoli(sim)
# Pack the membrane
if crowdedMembrane is True:
pass
# Give the simulation back
return sim
[docs]
def buildDividingEColiCell(sim, crowded=False, crowdedMembrane=False ):
"""Build a standard E coli cell 0.5 microns across and 4 microns long.
Args:
sim:
An RDMESimulation object
crowded:
Should the cytosol be crowded (default: false)
crowdedMembrane:
Should the membrane be crowded (default: false)
"""
# Sanity check
if not isinstance(sim, RDMESimulation):
LMLogger.error('Could not build an E. coli cell in the sim which is not of type \'RDMESimulation\'')
# Create the cell
sim.buildCapsidCell(length=micron(4), diameter=micron(0.5), membraneThickness=nm(32))
# Pack the cell
if crowded is True:
packFastGrowingEcoli(sim)
# Pack the membrane
if crowdedMembrane is True:
pass
# Give the simulation back
return sim
[docs]
def buildSphericalEColiCell(crowded=False, latticeSpacing=16, crowdedMembrane=False ):
"""Build a Spherical E coli cell, one that lacks the gene for elongation.
Args:
sim:
An RDMESimulation object
crowded:
Should the cytosol be crowded (default: false)
crowdedMembrane:
Should the membrane be crowded (default: false)
"""
# Sanity check
if not isinstance(sim, RDMESimulation):
LMLogger.error('Could not build an E. coli cell in the sim which is not of type \'RDMESimulation\'')
# Create the cell
sim.buildSphericalCell(diameter=micron(0.5), membraneThickness=nm(32))
# Pack the cell
if crowded is True:
packFastGrowingEcoli(sim)
# Pack the membrane
if crowdedMembrane is True:
pass
# Give the simulation back
return sim
[docs]
def buildFilamentousEColiCell(sim, length=8.0, crowded=False, crowdedMembrane=False ):
"""Build a long filamentous E coli cell where the user can specify the length.
Args:
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)
"""
# Sanity check
if not isinstance(sim, RDMESimulation):
LMLogger.error('Could not build an E. coli cell in the sim which is not of type \'RDMESimulation\'')
# Create the cell
sim.buildCapsidCell(length=micron(length), diameter=micron(0.5), membraneThickness=nm(32))
# Pack the cell
if crowded is True:
packFastGrowingEcoli(sim)
# Pack the membrane
if crowdedMembrane is True:
pass
# Give the simulation back
return sim
[docs]
def packFastGrowingEcoli(sim):
"""Pack a cell with the protein distribution for fast growing E coli.
Args:
sim:
A RDMESimulation object
"""
if not isinstance(sim, RDMESimulation):
return
# get cytosol region
region='cytoplasm'
# pack the cell
sim.packRegion(region, nm(10.4), 17.8, 1)
sim.packRegion(region, nm(5.2), 18.6, 2)
sim.packRegion(region, nm(4.3), 0.7, 3)
sim.packRegion(region, nm(4.1), 0.3, 4)
sim.packRegion(region, nm(4.0), 1.7, 5)
sim.packRegion(region, nm(3.8), 1.2, 6)
sim.packRegion(region, nm(3.5), 0.9, 7)
sim.packRegion(region, nm(3.4), 2.5, 8)
sim.packRegion(region, nm(3.0), 2.0, 9)
sim.packRegion(region, nm(2.7), 2.0, 10)
sim.packRegion(region, nm(2.3), 1.8, 11)
sim.packRegion(region, nm(1.7), 0.4, 12)
return sim
[docs]
def packSlowGrowingEcoli(sim):
"""Pack a cell with the protein distribution for fast growing E coli.
Args:
sim:
A RDMESimulation object
"""
if not isinstance(sim, RDMESimulation):
return
# get cytosol region
region='cytoplasm'
# pack the cell
sim.packRegion(region, nm(10.4), 5.7, 1)
sim.packRegion(region, nm(5.2), 25.5, 2)
sim.packRegion(region, nm(4.3), 1.2, 3)
sim.packRegion(region, nm(4.1), 0.4, 4)
sim.packRegion(region, nm(4.0), 2.4, 5)
sim.packRegion(region, nm(3.8), 1.8, 6)
sim.packRegion(region, nm(3.5), 1.3, 7)
sim.packRegion(region, nm(3.4), 3.6, 8)
sim.packRegion(region, nm(3.0), 2.8, 9)
sim.packRegion(region, nm(2.7), 2.7, 10)
sim.packRegion(region, nm(2.3), 2.3, 11)
sim.packRegion(region, nm(1.7), 0.6, 12)
return sim