def init_positions(num_monos, polymer="isotropic", length=50):
"""
Create list of monomer positions to be fed into sim.load()
"""
step_size = 1.0
if polymer == "boxed":
step_size = length / np.sqrt(num_monos)
init_polymer = tools.create_boxed_random_walk(step_size,
num_monos,
max_length=length)
print("polymer is boxed")
elif polymer == "extended":
step_size = length / np.sqrt(num_monos)
init_polymer = polymerutils.create_random_walk(1, num_monos)
print("polymer is extended")
elif polymer == "compact":
init_polymer = polymerutils.grow_rw(num_monos, int(length) - 2)
print("polymer is compact")
else: # isotropic
init_polymer = tools.create_isotropic_random_walk(step_size, num_monos)
print("polymer is isotropic, input was", polymer)
return init_polymer
400, 100, 200, 400, 100, 200, 400, 100, 200, 400, 100, 200, 400, 100, 200,
400, 100, 200, 400, 100, 200, 400, 100, 200
]
'lleft and lright are defined in SMCTranslocator!'
lleft = (np.cumsum(TADSizes, dtype=np.int64) - 1
) #Load in with left arm active
lright = (np.cumsum(TADSizes, dtype=np.int64)[0:-1] + 1
) #Load with right arm active
N = sum(TADSizes) # number of monomers
smcStepsPerBlock = 1 # I take something like 1/steppingprobability, because stepping is not determistic. I usually choose the probability of stepping to be max 0.1. Usually I take 20 for genes speeding up and 10 for genes slowing down
stiff = 0 # Polymer siffness in unit of bead size
dens = 0.2 #float(sys.argv[4]) # 0.2 # density in beads / volume. The density can roughly be estimated by looking at the amount of chromatin in a nuclear volume.
box = (
N / dens
)**0.33 # Define size of the bounding box for Periodic Boundary Conditions
data = polymerutils.grow_rw(N, int(box) - 2) # creates a compact conformation
block = 0 # starting block
kon = 0 #float(sys.argv[5]) # CTCF binding rate
koff = 1 #float(sys.argv[6]) #CTCF unbinding rate
CTCFsites = np.array(
[0]
) #CTCF binding sites (take np.cumsum(TADsizes) if you want to compare to CTCF sites that are stall sites).
CTCFCohesinEn = 0 # float(sys.argv[7]) # Cohesin-CTCF interaction energy in kT, without a neighbouring cohesin, the unbinding rate of CTCF is koff, if a cohesin is right next to a CTCF site, the CTCF unbinding rate is koff*exp(-CTCFCohesinEn)
kswitch = 0 #float(sys.argv[4])
CTCFPause = 1
zloops = 1
'this variable is controlled in smcTranslocator'
steps = int(
200 * (smcStepsPerBlock)
def doPolymerSimulation(steps, dens, stiff, folder):
from openmmlib.openmmlib import Simulation
from openmmlib.polymerutils import grow_rw
import time
SMCTran = initModel()
box = (N / dens)**0.33 # density = 0.1
if os.path.exists(os.path.join(folder, "block10.dat")):
block = scanBlocks(folder)["keys"].max() - 1
data = polymerutils.load(
os.path.join(folder, "block{0}.dat".format(block)))
else:
data = grow_rw(N, int(box) - 2)
block = 0
assert len(data) == N
skip = 0
time.sleep(1)
while True:
SMCTran.steps(3)
if (block % 2000 == 0) and (skip == 0):
print("doing dummy steps")
SMCTran.steps(500000)
skip = 100
print(skip, "blocks to skip")
a = Simulation(timestep=80, thermostat=0.01)
a.setup(platform="CUDA",
PBC=True,
PBCbox=[box, box, box],
GPU=sys.argv[4],
precision="mixed")
a.saveFolder(folder)
a.load(data)
a.addHarmonicPolymerBonds(wiggleDist=0.1)
if stiff > 0:
a.addGrosbergStiffness(stiff)
a.addPolynomialRepulsiveForce(trunc=1.5, radiusMult=1.05)
left, right = SMCTran.getSMCs()
for l, r in zip(left, right):
a.addBond(l,
r,
bondWiggleDistance=0.5,
distance=0.3,
bondType="harmonic")
a.step = block
if skip > 0:
print("skipping block")
a.doBlock(steps, increment=False)
skip -= 1
if skip == 0:
a.doBlock(steps)
block += 1
a.save()
if block == 50000:
break
data = a.getData()
del a
time.sleep(0.1)
def exampleOpenmm(supercoilCompaction=4, plectonemeLength=10, plectonemeGap=0, stifness=2, ind=0, domainNum=30, domainLen=5):
"""
A method that performs one simulation.
"""
a = Simulation(timestep=100, thermostat=0.01)
a.setup(platform="cuda", GPU=sys.argv[1])
foldername = "newSweep_lambda{0}_L{1}_gap{2}_stiff{3}_ind{4}".format(supercoilCompaction, plectonemeLength,
plectonemeGap, stifness, ind)
a.saveFolder(foldername) # folder where to save trajectory
"""
Defining all parameters of the simulation
"""
genomeLengthBp = 4000000
lengthNm = 1500
diamNm = 450
supercoilBpPerNm = 4.5 * supercoilCompaction
supercoilDiameterNm = 3.45 * np.sqrt(supercoilBpPerNm)
supercoilBpPerBall = supercoilBpPerNm * supercoilDiameterNm * 2 # 2 strands
print(supercoilBpPerBall)
print(supercoilDiameterNm)
ballNumber = 2 * int(0.5 * (genomeLengthBp / supercoilBpPerBall))
radiusMon = 0.5 * (diamNm / float(supercoilDiameterNm))
halfLengthMon = 0.5 * (lengthNm / float(supercoilDiameterNm))
N = ballNumber
print(N)
avLength = plectonemeLength
# Growing a circular polymer
bacteria = grow_rw(N, int(halfLengthMon * 2), "line")
bacteria = bacteria - np.mean(bacteria, axis=0)
a.load(bacteria) # filename to load
print(bacteria[0])
a.tetherParticles([0, N - 1])
a.addCylindricalConfinement(r=radiusMon, bottom=-halfLengthMon, top=halfLengthMon, k=1.5)
BD = makeBondsForBrush(chainLength=a.N)
# Coordinates of top highly expressed genes
geneCoord = [1162773, 3509071, 1180887, 543099, 1953250, 2522439, 3328524, 1503879, 900483, 242693, 3677144, 3931680, 3677704, 3762707, 3480870, 3829656, 1424678, 901855, 1439056, 3678537]
particleCoord = [(i / 4042929.) * a.N for i in geneCoord]
particleCoord = [int(i) for i in particleCoord]
particleCoord = sorted(particleCoord)
# Below making sure that if two PFRs overlap, we just create a PFR which is twice longer
gapShift = 7
gaps = []
gapStart = particleCoord[0]
gapEnd = particleCoord[0]
for i in particleCoord:
if i > gapEnd:
gaps.append((gapStart, gapEnd))
gapStart = i
gapEnd = i + gapShift
else:
gapEnd += gapShift
gaps.append((gapStart, gapEnd))
# Adding PFRs at highly expressed genes
M = domainNum
particles = []
for st, end in gaps:
BD.addGap(st, end)
# Making bonds
BD.addBristles(3, plectonemeLength, 0, plectonemeGap)
BD.sortSegments()
print(BD.segments)
BD.createBonds()
BD.checkConnectivity()
BD.save(os.path.join(a.folder, "chains"))
a.setChains(chains=BD.getChains())
a._initHarmonicBondForce()
for i in BD.bonds:
a.addBond(i[0], i[1], bondWiggleDistance=0.15, bondType="Harmonic")
a.addGrosbergStiffness(k=stifness)
a.addGrosbergRepulsiveForce(trunc=1.)
# a.addSoftLennardJonesForce(epsilon=0.46, trunc=2.5, cutoff=2.3)
a.save(os.path.join(a.folder, "start"))
a.localEnergyMinimization()
a.save()
for step in range(500):
a.doBlock(50000)
a.save()
a.printStats()