def next(self):
if len(self.filenames) == 0:
raise StopIteration
data = polymerutils.load(self.filenames.pop())
contacts = self.method(data, cutoff=self.cutoff) // self.coarsegrain
return contacts
def getCmap(prefix = "", radius = 6):
"""
This is a function to calculate a simulated Hi-C contact map from one or several folders with conformations, defined by "prefix".
"""
n = 20 # number of processes to use = number of cores
coarsegrainBy = 5 # how many monomers per pixel in a heatmap
print(os.getcwd())
folders = [i for i in os.listdir(".") if i.startswith(prefix)]
foldes = [i for i in folders if os.path.exists(i)]
print(folders)
files = sum([polymerutils.scanBlocks(i)["files"] for i in folders], [])
filegroups = [files[i::n] for i in range(n)]
data = polymerutils.load(files[0])
N = len(data)
method = contactmaps.findMethod(data,radius)
cmapN = int(np.ceil(N / coarsegrainBy))
cmap = averageContacts(contactCalculator, filegroups, cmapN, classInitArgs=[radius, coarsegrainBy, method ], nproc=n,
bucketNum = 60, useFmap=True)
pickle.dump(cmap, open("cmaps/cmap{0}_r={1}.pkl".format(prefix, radius), 'wb'))
#!/usr/bin/env python import sys from openmmlib import pymol_show from openmmlib.polymerutils import load inFile = sys.argv[1] data = load(inFile) pymol_show.show_chain(data)
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 load(filename):
from openmmlib import polymerutils
return polymerutils.load(filename)