def create_mp4_pov(directory, origin_frame=0, fps=5, reverse=True):
filenames = sorted(glob.glob(directory + '\\*.npz'))
r = np.append([10], (np.ones(8) * 4))
r = np.append(r, 3)
r = np.append(r, 2)
c = 'kbbggryrycy'
image_files = []
j = 0
report_progress(len(filenames), title='create_pov_mp4', init=True)
for file in filenames:
j += 1
report_progress(j, title='create_pov_mp4')
dna = HelixPose.from_file(file)
origin_of = nMC.get_of(dna, origin_frame)
tf = nMC.get_transformation(origin_of)
coords = nMC.apply_transformation(dna.coords, tf)
image_files.append(
pov_dna(file, [coords],
range_A=[1000, 1500],
offset_A=[0, 0, 150],
show=False))
create_mp4_images(image_files,
fps=fps,
delete=True,
filename=directory + '.mp4',
reverse=reverse)
return
def create_pov_npz(filename):
filename = change_extension(filename, 'npz')
# directory = 'E:\\Users\\Noort\\data\\20180320\\data_001\\'
# filename = 'E:\\Users\\Noort\\data\\20180320\\data_001\\data_001_0001.npz'
# print(filename)
dna = HelixPose.from_file(filename)
pov_dna(filename, [dna.coords],
range_A=[1500, 2500],
offset_A=[0, 0, 150],
show=True)
return
def plot_step_params(filename, dataset, save=False, wait=0, plot_energy=True):
filename = fileio.change_extension(filename, 'xlsx')
sets, files, _ = contents_xlsx(filename)
if dataset == -1:
filename = sorted(files)[-1]
else:
filename = files[sets.index(dataset)]
dna = HelixPose.from_file(fileio.change_extension(filename, 'npz'))
p0 = np.load(default_step_file)[0]
sigma2 = np.load(default_step_file)[1:]
k = 1 / sigma2
energy_kT = []
for p in dna.params:
energy_kT.append(0.5 * (p - p0) * np.dot(k, p - p0) / kT)
energy_kT = np.asarray(energy_kT)
energy_kT = np.sum(np.abs(energy_kT), axis=1)
i = xrange(len(dna.params))
plt.close()
plt.figure(figsize=(12, 4))
if plot_energy:
plt.plot(i, energy_kT)
plt.ylim(-1, 25)
plt.ylabel('G (kT)')
else:
plt.plot(i, dna.params)
plt.ylim(-2.5, 4.5)
plt.ylabel('step parameters')
plt.legend(['Shift', 'Slide', 'Rise', 'Tilt', 'Roll', 'Twist'], loc=1)
plt.tick_params(axis='both',
which='both',
direction='in',
top=True,
right=True)
plt.title(filename.split('\\')[-2] + '\\' +
filename.split('\\')[-1].split('.')[0],
loc='left',
fontdict={'fontsize': 10})
plt.xlabel('i (bp)')
plt.tight_layout(pad=0.5, w_pad=0.5, h_pad=0.5)
plt.draw()
if wait != 0:
plt.pause(wait)
if save:
filename = fileio.change_extension(filename, '_step.jpg')
plt.savefig(filename, dpi=600, format='jpg')
return
def plot_step_params(filename, dataset, save=False):
filename = change_extension(filename, 'xlsx')
sets, files, _ = contents_xlsx(filename)
if dataset == -1:
filename = sorted(files)[-1]
else:
filename = files[sets.index(dataset)]
dna = HelixPose.from_file(change_extension(filename, 'npz'))
# dna = HelixPose.from_file(change_extension(files[-1], 'npz'))
i = xrange(len(dna.params))
plt.close()
plt.figure(figsize=(12, 4))
plt.plot(i, dna.params)
plt.tick_params(axis='both',
which='both',
direction='in',
top=True,
right=True)
plt.title(filename.split('\\')[-2] + '\\' +
filename.split('\\')[-1].split('.')[0],
loc='left',
fontdict={'fontsize': 10})
plt.xlabel('i (bp)')
plt.ylabel('step parameters')
plt.ylim(-2.5, 4.5)
plt.legend(['Shift', 'Slide', 'Rise', 'Tilt', 'Roll', 'Twist'], loc=1)
plt.tight_layout(pad=0.5, w_pad=0.5, h_pad=0.5)
plt.draw()
plt.pause(5)
if save:
filename = change_extension(filename, '_step.jpg')
plt.savefig(filename, dpi=600, format='jpg')
return
from helixmc.pose import HelixPose
# Run HelixMC #
cmdline = 'helixmc-run '
cmdline += '-params Z-DNA.npz '
cmdline += '-n_bp 100 '
cmdline += '-n_step 10 '
cmdline += '-seq GC '
cmdline += '-force 5 '
cmdline += '-compute_fuller_link '
cmdline += '-out_frame test_run'
print 'Z-DNA command line:', cmdline
subprocess.check_call(cmdline.split())
# Data Analysis #
data = np.load('MC_data.npz')
# avg. z-extension in Å
print 'Avg. Z:', np.average(data['coord_terminal'][:, 2])
# avg. link in radian
print 'Avg. Link:', np.average(data['twist'] + data['writhe'])
# Helix Plotting #
pose = HelixPose.from_file('test_run.npz')
pose.plot_centerline(show=False) # plot the centerline
plt.title('Center line')
pose.plot_helix(show=False, rb_width=15) # plot the entire helix
plt.title('Helix Plot')
plt.show()
# Run HelixMC #
cmdline = 'helixmc-run '
cmdline += '-params Z-DNA.npz '
cmdline += '-n_bp 100 '
cmdline += '-n_step 10 '
cmdline += '-seq GC '
cmdline += '-force 5 '
cmdline += '-compute_fuller_link '
cmdline += '-out_frame test_run'
print 'Z-DNA command line:', cmdline
subprocess.check_call(cmdline.split())
# Data Analysis #
data = np.load('MC_data.npz')
# avg. z-extension in Å
print 'Avg. Z:', np.average(data['coord_terminal'][:, 2])
# avg. link in radian
print 'Avg. Link:', np.average(data['twist'] + data['writhe'])
# Helix Plotting #
pose = HelixPose.from_file('test_run.npz')
pose.plot_centerline(show=False) # plot the centerline
plt.title('Center line')
pose.plot_helix(show=False, rb_width=15) # plot the entire helix
plt.title('Helix Plot')
plt.show()
def plot_energy(filename):
params = np.load(default_step_file)
p0 = params[0]
cov = params[1:]
k = np.linalg.inv(cov)
sets, files, _ = fileio.contents_xlsx(filename)
dna = HelixPose.from_file(fileio.change_extension(files[0], 'npz'))
energy_kT = np.empty((len(files), len(dna.params)))
i = 0
fileio.report_progress(len(files),
title='analyze_step_parameters',
init=True)
for f in files:
dna = HelixPose.from_file(fileio.change_extension(f, 'npz'))
fileio.report_progress(i + 1)
j = 0
for p in dna.params:
energy_kT[i, j] = (np.sum(0.5 * (p - p0) * np.dot(k, p - p0)))
j += 1
i += 1
F_data = fileio.read_param_xlsx(filename, 'F_pN')
forces = np.linspace(10, 0, 4)
energy_F = []
for force in forces:
selected = (np.abs(F_data - force) < 2.5)
energy_F.append(np.mean(np.abs(energy_kT[selected]), axis=0))
energy_F = np.asarray(energy_F)
print(forces)
i = xrange(len(dna.params))
plt.close()
plt.figure(figsize=(12, 3))
# plt.plot(i, energy_kT)
plt.plot(i, energy_F.T)
energy_thermal = np.ones(len(dna.params)) * 3
plt.plot(i, energy_thermal, color='k', linestyle=':', linewidth=0.8)
plt.xlim(0, len(dna.params))
plt.ylim(-1, 26)
plt.ylabel('G (kT)')
plt.tick_params(axis='both',
which='both',
direction='in',
top=True,
right=True)
plt.title(filename.split('\\')[-2] + '\\' +
filename.split('\\')[-1].split('.')[0],
loc='left',
fontdict={'fontsize': 10})
plt.xlabel('i (bp)')
plt.tight_layout(pad=0.5, w_pad=0.5, h_pad=0.5)
plt.draw()
plt.pause(5)
filename = fileio.change_extension(filename, '_Edna.jpg')
plt.savefig(filename, dpi=600, format='jpg')
return
from helixmc.pose import HelixPose
import matplotlib.pyplot as plt
import mpl_toolkits.mplot3d.axes3d as p3
# Here we have the final frames of 3 independent HelixMC runs,
# named data0.npz, data1.npz and data3.npz. We will plot these
# data in this example.
# Load data #
pose_list = []
pose_list.append(HelixPose.from_file('data0.npz'))
pose_list.append(HelixPose.from_file('data1.npz'))
pose_list.append(HelixPose.from_file('data2.npz'))
coords = [pose.coord / 10 for pose in pose_list]
colors = 'kbrgycm'
# Top View #
plt.figure()
for i, coord in enumerate(coords):
plt.plot(coord[:, 0], coord[:, 1], color=colors[i])
plt.ylabel('Y (nm)')
plt.xlabel('X (nm)')
plt.title('Top view')
# Side View #
plt.figure()
for i, coord in enumerate(coords):
plt.plot(coord[:, 0], coord[:, 2], color=colors[i])
plt.ylabel('Z (nm)')
plt.xlabel('X (nm)')
def main():
# Define fiber params
pars = Parameters()
pars.add('F_pN', value=0)
pars.add('z_nm', value=0)
pars.add('L_bp', value=800)
pars.add('n_nuc', value=4)
pars.add('NRL', value=167)
pars.add('P_nm', value=50)
pars.add('dyad0_bp', value=0)
pars.add('diameter_A', value=330)
pars.add('rise_A', value=100)
pars.add('nld_A', value=25)
pars.add('chirality', value=-1)
pars.add('Unwrapped_bp', value=30)
pars.add('face', value=1)
pars.add('g_wrap_kT', value=3)
pars.add('g_stack_kT', value=25)
pars.add('fiber_start', value=2)
g_wrap_kT = pars['g_wrap_kT'].value
g_stack_kT = pars['g_stack_kT'].value
# Setup files and forces
filename = fileio.get_filename(incr=True, root='3nucs')
print(filename)
n_step = 250
n_substeps = 10
fmax_pN = 10
fmin_pN = 0.1
# forces = np.linspace(fmin_pN, fmax_pN, n_step / 2)
forces = np.logspace(np.log10(fmin_pN), np.log10(fmax_pN), n_step / 2)
forces = np.append(forces, forces[::-1])
get_from_file = False
if get_from_file:
# Get from file
file_in = 'E:\\Users\\noort\\data\\20180321\\data_003.xlsx'
dataset = 0
pars, datafile = fileio.read_xlsx(file_in, dataset, pars=pars)
dna, dyads, nucl = fMC.create_nuc_array(p=pars)
dna = HelixPose.from_file(fileio.change_extension(datafile, 'npz'))
else:
# Initialize fiber pose
dna, dyads, nucl = fMC.create_nuc_array(p=pars)
pars['dyad0_bp'].value = dyads[0]
fileio.plot_dna(dna,
title='Initial conformation\n',
range_nm=100,
save=True)
pars.pretty_print(columns=['value'])
# Get stack and wrap parameters
fixed_wrap_params = nMC.get_wrap_params(nucl.dna, nucl.dyad, nucl.fixed)
fiber_dna, dyads, w = fMC.create_folded_fiber(pars, nucl)
fixed_stack_params = fMC.get_stack_pars(fiber_dna, dyads)[0]
fiber_start = pars['fiber_start'].value
# Initialize random steps
random_step = RandomStepSimple.load_gaussian_params('DNA_gau.npy')
basepairs = np.asarray(xrange(pars['L_bp'] - 1))
accept = 0
all_coord = np.empty((n_step, 3))
current_step = 0
fileio.report_progress(n_step, title='RunMC3', init=True)
for force in forces:
fileio.report_progress(current_step + 1, title='RunMC3')
scorefxn = ScoreTweezers(force)
previous_bp = 0
for sub_step in xrange(n_substeps):
for bp in basepairs:
accept += MC_move(dna, bp, previous_bp, scorefxn,
fixed_wrap_params, fixed_stack_params, dyads,
nucl, random_step, g_wrap_kT, g_stack_kT,
fiber_start)
previous_bp = bp
basepairs = basepairs[::-1]
fileio.plot_dna(dna,
update=True,
title='F = {:.1f} pN\n'.format(force),
save=True)
pars['F_pN'].value = force
pars['z_nm'].value = dna.coord_terminal[2]
fileio.write_xlsx(fileio.get_filename(sub=True),
str(current_step),
pars,
report_file=filename)
dna.write2disk(fileio.get_filename(sub=True, ext='npz'))
all_coord[current_step] = dna.coord_terminal
current_step += 1
z = all_coord[:, 2] / 10
wlc = 1 - 0.5 * np.sqrt(0.1 * kT / (forces * pars['P_nm']))
grid = []
for i in xrange(1, pars['n_nuc'] + 1):
grid.append(wlc * (pars['L_bp'] - 80 * i) / 3)
grid.append(wlc * (pars['L_bp'] - (pars['n_nuc'] * 80 + i *
(147 - 80))) / 3)
wlc *= pars['L_bp'] / 3
selected = np.diff(np.append([-1], forces)) > 0
fileio.save_plot((forces, z, wlc, selected),
filename=filename,
ax_labels=['z (nm)', 'F (pN)'],
grid=grid,
transpose=True,
xrange=[0, 1.1 * pars['L_bp'] / 3])
if n_step > 0:
print('Accept rate = %.1f %%' % (100 * float(accept) /
(n_step * n_substeps *
(pars['L_bp'] - 1))))
try:
fileio.create_mp4_pov(fileio.get_filename(sub=True, folder=True),
origin_frame=0,
reverse=False)
except Exception, e:
print(Exception, e)