def myLoad(filename, dummy=None):
#ugly workaround for simulating HU:
if filename[:4] == "_HU_":
HU = "HU"
filename = filename[4:]
elif filename[:4] == "_GY_":
HU = "GY"
filename = filename[4:]
else:
HU = False
bonds = makeBondsForBrush()
bonds.load(os.path.join(os.path.split(filename)[0], "chains"))
data = polymerutils.load(filename)
converted = bonds.convertChain(data)
if HU == "HU":
converted += gaussian_filter1d(10 * np.random.randn(*converted.shape),
sigma=2.8,
axis=0)
elif HU == "GY":
converted += gaussian_filter1d(7 * np.random.randn(*converted.shape),
sigma=2.8,
axis=0)
#using only one arm for scalings
if np.random.random() < 0.5:
return converted[:int(0.4 * len(converted))]
else:
return converted[int(0.6 * len(converted)):]
def __init__(
self,
filenames,
mapStarts,
mapN,
cutoff=1.7,
loadFunction=None,
exceptionsToIgnore=[],
contactFunction=None,
):
"""
Init accepts arguments to initialize the iterator.
filenames will be one of the items in the inValues list of the "averageContacts" function
cutoff and loadFunction should be provided either in classInitArgs or classInitKwargs of averageContacts
When initialized, the iterator should store these args properly and create all necessary constructs
"""
from openmmlib import contactmaps
self.contactmaps = contactmaps
self.filenames = filenames
self.cutoff = cutoff
self.exceptionsToIgnore = exceptionsToIgnore
self.mapStarts = mapStarts
self.mapN = mapN
if loadFunction is None:
import polymerutils
loadFunction = polymerutils.load()
if contactFunction is None:
contactFunction = self.contactmaps.giveContacts
self.contactFunction = contactFunction
self.loadFunction = loadFunction
self.i = 0
self.curStarts = []
def saveToPdb(input):
i, dataPath = input
d = polymerutils.load(dataPath)
pdbFilename = '{0:0{width}}.pdb'.format(i, width=numDigits)
savePath = pdbFolder + '/' + pdbFilename
polymerutils.save(d, savePath, mode='pdb', pdbGroups=colorArray)
return os.path.abspath(savePath)
def showOneChain():
data = load("L_201_num_1.0_final_protocol/block500.dat")
#data = load("../globules_expanded/crumpled1.dat_expanded")
balls = cPickle.load(open("L_201_num_1.0_final_protocol/coreParticles"))
balls = np.array(balls)
balls = balls[(balls > 47000) * (balls < 53000)] - 47000
data = data[47000:53000]
pymol_show.show_chain(data,
dataMult=1.1,
spherePositions=balls,
sphereRadius=.02)
def highlightThreeRegions():
folder = "L_200_num_8.0_final_protocol"
filenum = 500
offset = 3
data = load(folder + "/block%d.dat" % filenum)
#data = data[30000:80000]
newData = interpolateData(data, targetN=90000)
pymol_show.do_coloring(newData[0], [(40000, 40400), (44000, 44400),
(48000, 48400), (52000, 52400),
(56000, 56400)],
["green", "red", "blue", "brown", "orange"],
[0, 0, 0, 0, 0],
chain_radius=.07,
subchain_radius=.2,
chain_transparency=0.5,
multiplier=.8)
exit()
def myLoad(filename, dummy=None):
# ugly workaround:
if filename[:4] == "_HU_":
HU = "HU"
filename = filename[4:]
elif filename[:4] == "_GY_":
HU = "GY"
filename = filename[4:]
else:
HU = False
bonds = makeBondsForBrush()
bonds.load(os.path.join(os.path.split(filename)[0], "chains"))
data = polymerutils.load(filename)
converted = bonds.convertChain(data)
if HU == "HU":
converted += gaussian_filter1d(10 * np.random.randn(*converted.shape),
sigma=2.8,
axis=0)
elif HU == "GY":
converted += gaussian_filter1d(7 * np.random.randn(*converted.shape),
sigma=2.8,
axis=0)
return converted
def do_polymer_simulation(steps, dens, stiff, folder, N, SEPARATION,
LIFETIME, forw, rev, save_blocks=2000, smc_steps=3,
no_SMC=False, randomize_SMC=False,
gpu_number='default', cpu_simulation=False,
skip_start=100, save_mode='joblib'):
"""Do the polymer simulation given all the parameters."""
i = 0
SMCTran = initModel(i, N, SEPARATION, LIFETIME, forw, rev)
box = (N / dens) ** 0.33 # density = 0.1
if exists(join(folder, "block10.dat")):
block = scanBlocks(folder)["keys"].max() - 1
data = polymerutils.load(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(0.1)
while True:
SMCTran.steps(smc_steps)
if randomize_SMC:
SMCTran.steps(500000)
if (block % 2000 == 0) and (skip == 0):
print("doing dummy steps")
SMCTran.steps(500000)
skip = skip_start
print(skip, "blocks to skip")
# initialize a polymer for the 3D simualton step.
a = Simulation(timestep=80, thermostat=0.01)
if cpu_simulation:
a.setup(platform="cpu", PBC=True, PBCbox=[
box, box, box], precision="mixed")
else:
a.setup(platform="OpenCL", PBC=True, PBCbox=[
box, box, box], precision="mixed", GPU=gpu_number)
# 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)
# get positions of SMCs, add bonds to polymer
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(mode=save_mode)
if block == save_blocks:
break
data = a.getData()
del a
time.sleep(0.1)
numLoops = 5 * (N / avLoopSize)
lens = np.random.randn(numLoops) * avLoopSize
lens = lens[(lens > minLoopSize) * (lens < maxLoopSize)]
lens = np.array(lens, dtype=int)
lens = np.cumsum(lens)
lens = lens[lens < N - avLoopSize / 2]
lens = np.r_[0, lens , N - 1]
return lens
pancakeWidth = 30
pancakeSize = 15000
foldername = "L_{0}_num_{1}_len_{2}".format(L, num, intLen)
if not os.path.exists(foldername): os.mkdir(foldername)
shutil.copy(sys.argv[0], foldername)
data = load("globule32")[:30000]
polymerutils.save(data, os.path.join(foldername, "block0.dat"))
N = len(data)
pancakeNum = N / float(pancakeSize)
coreParticles = numpy.nonzero(numpy.random.random(N) < (1. / L))[0]
smcStep = 5
stepsPerSmc = 6000
bondBlocks = 70
minBondLen = 5
maxBondLen = 20
bondNum = 3
secondSmcGap = 2
def showCoreParticles():
folder = "L_100_num_1_len_30"
#"L_100_num_11_final_protocol"
filenum = 400
offset = 40
coreParticles = cPickle.load(open(os.path.join(folder, "coreParticles")))
data = load(folder + "/block%d.dat" % filenum)
#data = load("../globules_expanded/crumpled1.dat_expanded")
colorArray = np.zeros(len(data), int)
loopArray = np.zeros(len(data), int)
for j, i in enumerate(coreParticles):
if (j < len(coreParticles) - 1) and (j % 25 == 2):
colorArray[max(i + offset +
1, 0):min(coreParticles[j + 1] - offset -
1, len(data))] = 2
colorArray[max(i - offset, 0):min(i + offset + 1, len(data))] = 1
newData = interpolateData(data, targetN=90000, colorArrays=[colorArray])
coords = newData[0]
colorArray = newData[1][0]
colorArray = np.ceil(colorArray)
"""
greenColors = np.zeros_like(colors)
greenColors[40000:65000] = 1
greenColors[colors] = 0
greenRegions = pymol_show.create_regions(greenColors)
greenRegions = list(greenRegions)
greenColors = ["green"] * len(greenRegions)
greenTransparencies = [0] * len(greenColors)
"""
regions = pymol_show.createRegions(colorArray == 1)
regions = list(regions)
colors = ["blue"] * len(regions)
transparencies = [0] * len(regions)
regions2 = pymol_show.createRegions(colorArray == 2)
M = len(regions2)
print M
allColors = ["br{0}".format(i) for i in range(10)]
S = len(allColors)
colors2 = [
allColors[int(float(i) * float(S) / float(M))] for i in range(M)
]
transparencies2 = [0 for i in colors2]
pymol_show.do_coloring(coords,
list(regions) + list(regions2),
colors + colors2,
transparencies + transparencies2,
showChain="worm",
chainRadius=.4,
subchainRadius=.4,
chainTransparency=0.6,
multiplier=.8,
pdbGroups=colorArray,
support="""
bg black
set orthoscopic, 0
set field_of_view, 70
create back, chain 1
color brown, back
show surface, back
""")
exit()
pymol_show.do_coloring(coords,
regions,
colors,
transparencies,
chain_radius=.1,
subchain_radius=.2,
chain_transparency=0.2,
multiplier=.8)
def showAllChain():
data = load("L_100_num_1_len_30/block500.dat")
#data = data[25000:50000]
pymol_show.show_chain(data, dataMult=1.1)
def makeCoverFigure():
folder = "L_100_num_16_len_30"
filenum = 550
#folder = "../026_controls_loopSize/ConsScaff133_3"
#filenum = 250
offset = 1
coreParticles = cPickle.load(open(os.path.join(folder, "coreParticles")))
print len(coreParticles)
data = load(folder + "/block%d.dat" % filenum)
coreArray = np.zeros(len(data), dtype=float)
coreArray[coreParticles] = 2
#data = data[::-1]
#coreParticles = len(data) - coreParticles
#data = data[:30000]
#coreParticles = coreParticles[coreParticles < 30000 ]
if len(data) > 90000:
data, (coreArray, ) = interpolateData(data,
90000,
colorArrays=[coreArray])
coreArray[np.nonzero(coreArray > 0.4)[0] + 1] = 0
coreParticles = np.nonzero(coreArray > .4)[0]
data = np.dot(
data,
np.array([[
0.782993197,
-0.090055801,
0.615476012,
], [
0.042767350,
0.994917035,
0.091168165,
], [
-0.620556772,
-0.045062274,
0.782866657,
]]))
#data = np.dot(data, np.array([[0.829197228, -0.461252242, -0.315715969, ],
# [0.031428415, 0.602414608, -0.797561765, ],
# [0.558069587, 0.651413143, 0.514018297, ]]
#))
#data = load("../globules_expanded/crumpled1.dat_expanded")
colorArray = np.zeros(len(data), int)
loopArray = np.zeros(len(data), int)
for S, offset in enumerate(range(5, 0, -2)):
for j, i in enumerate(coreParticles):
colorArray[max(i - offset, 0):min(i + offset +
1, len(data))] = S + 1
inds = np.diff(colorArray) != 0
print inds
indCumsum = np.r_[0, np.cumsum(inds)]
newdata = np.zeros(shape=(len(data) + indCumsum[-1], 3), dtype=float)
newcolorarray = np.zeros(shape=(len(data) + indCumsum[-1], ), dtype=float)
newdata[np.arange(len(data), dtype=int) + indCumsum] = data
newcolorarray[np.arange(len(data), dtype=int) + indCumsum] = colorArray
mask = newdata[:, 0] == 0
newdata[mask] = data[np.nonzero(inds)[0] + 1]
newcolorarray[mask] = colorArray[np.nonzero(inds)[0]]
coords, colorArray = newdata, newcolorarray
colorStrings = []
for colorInd in range(0, int(max(colorArray) + 1))[::-1]:
colorFloat = colorInd / (float(max(colorArray) + 1))
colorString = "[{0}, {0}, {1}]".format(max(1. - colorFloat * 1.2, 0),
1.)
colorName = "bubu{0}".format(colorInd)
chainName = "subset{0}".format(colorInd)
#transp = [0.55, 0.55, 0.55, 0.55, 0., 0., 0., 0.][colorInd]
transp = [0.75, 0.75, 0.75, 0., 0., 0., 0.][colorInd]
colorStrings.append("""
set_color {color}, {colorString}
create {chain}, chain {chainNum}
color {color}, {chain}
set cartoon_trace_atoms,1, {chain}
set cartoon_tube_radius, 0.3, {chain}
set cartoon_transparency, {transp}, {chain}
set cartoon_tube_quality, 6
cartoon tube, {chain}
show cartoon, {chain}
""".format(chain=chainName,
color=colorName,
colorString=colorString,
chainNum=colorInd,
transp=transp))
colorStrings = "".join(colorStrings)
pymol_show.new_coloring(coords, [], [], [],
showChain="none",
chainRadius=.4,
subchainRadius=.4,
chainTransparency=1.0,
pdbGroups=colorArray,
transparentBackground=True,
multiplier=.8,
support="""
bg white
""" + colorStrings + """
run axes.py
axes
set spec_direct, 0.1
set spec_reflect, 2.
set spec_power, 100
set spec_direct_power, 100
set ray_max_passes, 2000
set ray_shadow, off
zoom
set antialias, 1
set light, [0,-1,-0.3]
""",
presupport="""
""")
exit()
def loadFunction(x, y):
return polymerutils.load(x, y)
start = numpy.random.randint(0, 80000)
end = start + 20000
return polymerutils.load(x, y)[start:end]
def exampleOpenmm(x):
"""
You need to have a OpenMM-compatible GPU and OpenMM installed to run this script.
Otherwise you can switch to "reference" platform
a.setup(platform = "reference")
But this will be extremely slow...
Installing OpenMM may be not easy too... but you can try
"""
a = SimulationWithCrosslinks(timestep=80, thermostat=0.005)
a.setup(platform="OpenCL", verbose=True)
a.saveFolder("sizes_12_200_2500") # folder where to save trajectory
#a.load("trajectory2/start.dat") #filename to load
g1 = polymerutils.load(
"/net/evolution/home/magus/trajectories/globule_creation/128000_SAW/crumpled%d.dat"
% (x + 1))
#Comment out two lines below for a full-length chain
print "using shorter chain for protocol refinement"
g1 = g1[:40000] # for faster developement of the protocol
a.load(g1)
a.setLayout(mode="chain")
a.addHarmonicPolymerBonds(wiggleDist=0.1)
a.addGrosbergRepulsiveForce(trunc=1.4)
a.addGrosbergStiffness(k=5)
pancakeWidth = 20
pancakeSize = 20000
pancakeNum = a.N / float(pancakeSize)
print pancakeNum
a.addCylindricalConfinement(r=34,
bottom=0,
top=pancakeWidth * pancakeNum,
k=0.7)
a.fixParticlesZCoordinate(particles=range(0, a.N, 10),
zCoordinates=(0, pancakeWidth * pancakeNum),
k=0.03,
mode="quadratic",
gap=pancakeWidth)
#a.addRgLimitations(num = 13,volumeParameter = 0.05,relativeSmeer = 0.60,pancakeLength = 35000)
#a.addConsecutiveRandomBonds(12,0.3,0.5,0.5,distanceBetweenBonds = 2)
#a.addConsecutiveRandomBonds(200,0.3,0.5,0.5,distanceBetweenBonds = 5)
a.addConsecutiveRandomBonds(12, 0.3, 0.5, 0.5, distanceBetweenBonds=2)
a.addConsecutiveRandomBonds(200, 0.3, 0.5, 0.5, distanceBetweenBonds=6)
a.addConsecutiveRandomBonds(2500, 1, 0.5, 0.5, distanceBetweenBonds=100)
#coreParticles = numpy.nonzero(numpy.random.random(a.N) < 0.01)[0]
#a.addAttractionToTheCore(.5,6, coreParticles)
a.energyMinimization(stepsPerIteration=30, force=True)
for _ in xrange(200):
a.doBlock(10000)
a.save()
a.printStats()
def showCoreParticles():
folder = "L_100_num_12_len_30"
filenum = 25
offset = 1
coreParticles = cPickle.load(open(os.path.join(folder, "coreParticles")))
data = load(folder + "/block%d.dat" % filenum)
#data = load("../globules_expanded/crumpled1.dat_expanded")
colorArray = np.zeros(len(data), int)
for j, i in enumerate(coreParticles):
if (j < len(coreParticles) - 1) and (j % 20 == 1):
colorArray[max(i, 0):min(coreParticles[j + 1] - 1, len(data))] = 2
colorArray[max(i - offset, 0):min(i + offset + 1, len(data))] = 1
loopArray = np.zeros(len(data), int)
coords = data
regions1 = pymol_show.createRegions(colorArray == 1)
M = len(regions1)
print M
colors1 = ["brown" for i in range(M)]
transparencies1 = [0 for i in colors1]
regions2 = pymol_show.createRegions(colorArray == 2)
M = len(regions2)
print M
allColors = ["br{0}".format(i) for i in range(10)]
S = len(allColors)
colors2 = [
allColors[int(float(i) * float(S) / float(M))] for i in range(M)
]
transparencies2 = [0 for i in colors2]
return pymol_show.do_coloring(
coords,
list(regions2),
list(colors2),
list(transparencies2),
chainRadius=.25,
subchainRadius=.35,
chainTransparency=0.85,
returnScriptName="mov",
showChain="worm",
pdbGroups=colorArray,
showGui=True,
# saveTo="bla.png",
multiplier=.8,
support="""
create back, chain 1
set cartoon_transparency,0.000000,back
set cartoon_trace_atoms,1, back
set cartoon_tube_radius,0.280000, back
cartoon tube, back
color brown, back
set depth_cue, 0
set_view (\
_ 0.572576821, -0.411692470, -0.708985031,\
_ -0.745704532, 0.097847328, -0.659046650,\
_ 0.340698749, 0.906049132, -0.250979245,\
_ 0.000131026, -0.000255849, -401.058715820,\
_ 49.410499573, 50.416854858, 58.617347717,\
_ 315.981750488, 458.882690430, -20.000000000 )
"""), colorArray
def showAllChain():
data = load("L_200_num_5.0_final_protocol/block500.dat")
#data = data[25000:50000]
pymol_show.show_chain(data, dataMult=1.1)
def smallFunction(x):
i, dataPath = x
savePath = imgFolder + '/{0:0{width}}.png'.format(i, width=numDigits)
coreParticles = cPickle.load(
open(os.path.join(os.path.split(dataPath)[0], "coreParticles")))
data = load(dataPath)
#data = load("../globules_expanded/crumpled1.dat_expanded")
colorArray = np.zeros(len(data), int)
for j, i in enumerate(coreParticles):
if (j < len(coreParticles) - 1) and (j % 20 == 1):
colorArray[max(i, 0):min(coreParticles[j + 1] -
1, len(data))] = 2
colorArray[max(i - offset, 0):min(i + offset + 1, len(data))] = 1
loopArray = np.zeros(len(data), int)
coords = data
regions1 = pymol_show.createRegions(colorArray == 1)
M = len(regions1)
print M
colors1 = ["brown" for i in range(M)]
transparencies1 = [0 for i in colors1]
regions2 = pymol_show.createRegions(colorArray == 2)
M = len(regions2)
print M
allColors = ["br{0}".format(i) for i in range(10)]
S = len(allColors)
colors2 = [
allColors[int(float(i) * float(S) / float(M))] for i in range(M)
]
transparencies2 = [0 for i in colors2]
pymol_show.do_coloring(
coords,
list(regions2),
list(colors2),
list(transparencies2),
chainRadius=.25,
subchainRadius=.35,
chainTransparency=0.9,
#returnScriptName="mov",
showChain="worm",
pdbGroups=colorArray,
showGui=True,
#saveTo=savePath,
multiplier=.8,
support="""
create back, chain 1
set cartoon_transparency,0.000000,back
set cartoon_trace_atoms,1, back
set cartoon_tube_radius,0.280000, back
cartoon tube, back
color brown, back
set depth_cue, 0
set field_of_view, 10
set_view (\
0.362947434, -0.752908945, 0.548998356,\
-0.843832374, -0.015661031, 0.536378920,\
-0.395252228, -0.657936990, -0.641013563,\
-0.000659317, 0.000253409, -788.783874512,\
81.561027527, 81.701515198, 121.653610229,\
615.844299316, 961.749450684, -10.000000000 )
png {savepath}
quit
""".format(savepath=savePath))