def main():
args = read_traj_vmd()
psffile = os.path.splitext(args.psffile)[0]
u = Universe(psffile + '.psf', 'trajectory_nve.dcd')
Nres = len(u.residues)
frame = []
g2 = []
res_g2 = 0.
fig = plt.figure()
plt.ylim(0, 1)
ims = []
for ts in u.trajectory[args.startframe:args.endframe:args.trajskip]:
all_g2 = 0.
k = 0
frame.append(ts.frame)
for res in u.residues:
chords = get_bondlist_coords(res)
res_g2 = get_chain_crystallinity(chords, 4)
all_g2 += res_g2
print("frame %d , g2 = %f" % (ts.frame, all_g2 / float(Nres)))
g2.append(all_g2 / float(Nres))
frame = np.array(frame)
g2 = np.array(g2)
# os.system("convert -delay ")
save_plot(frame, g2, psffile)
def main():
""" the main function"""
args = read_traj_vmd()
psffile = os.path.splitext(args.psffile)[0]
# calc_rdf(args)
plot_rdf(psffile)
def main():
args = read_traj_vmd()
psffile = os.path.splitext(args.psffile)[0]
u = Universe(psffile+'.psf', 'trajectory_nve.dcd')
Nres = len(u.residues)
frame = []
g2 = []
res_g2 = 0.
fig = plt.figure()
plt.ylim(0,1)
ims = []
for ts in u.trajectory[args.startframe:args.endframe:args.trajskip]:
all_g2 = 0.
k = 0
frame.append(ts.frame)
for res in u.residues:
chords = get_bondlist_coords(res)
res_g2 = get_chain_crystallinity(chords,4)
all_g2 += res_g2
print ("frame %d , g2 = %f" %(ts.frame, all_g2 / float(Nres)))
g2.append(all_g2 / float(Nres))
frame = np.array(frame)
g2 = np.array(g2)
# os.system("convert -delay ")
save_plot(frame,g2,psffile)
def main():
"""
analyze equilibration of melt
"""
args = read_traj_vmd()
print " "
print " ====================== "
print " done inputing the trajectory"
print args
print ""
print " ====================== "
print " "
calc_r2n(args)
print " "
print " ====================== "
print " done r2(n)/n"
print ""
print " ====================== "
print " "
calc_rgre(args)
print " "
print " ====================== "
print " done rgre"
print ""
print " ====================== "
print " "
calc_rmsd(args)
print " "
print " ====================== "
print " done rmsd"
print ""
print " ====================== "
print " "
calc_rdf(args)
plot_rdf(args)
print " "
print " ====================== "
print " done rdf"
print ""
print " ====================== "
print " "
# logargs = read_log()
# print " "
# print " ====================== "
# print " done inputing the log"
# print logargs
# print ""
# print " ====================== "
# print " "
# analyze_log(logargs)
return None
def main():
args = read_parameters.read_traj_vmd()
u = Universe(args.psffile+'.psf',args.traj)
trajskip = args.trajskip
box = u.universe.dimensions[:3]
L = box[0]
print (L)
for ts in u.trajectory[1:-1:trajskip]:
atoms,angles = get_angles(u)
g2 = 0.0
# print (atoms,angles)
g2 = Calcg2(atoms,angles,L)
print ("frame %d , g2 = %f" %(ts.frame, g2))
def main():
args = read_traj_vmd()
psffile = os.path.splitext(args.psffile)[0]
u = Universe(psffile + '.psf', args.traj)
ref_atoms = u.selectAtoms("all")
traj_atoms = u.selectAtoms("all")
natoms = traj_atoms.numberOfAtoms()
frame = []
g2 = []
# if performing a mass-weighted alignment/rmsd calculation
#masses = ref_atoms.masses()
#weight = masses/numpy.mean(masses)
# reference centre of mass system
ref_com = ref_atoms.centerOfMass()
ref_coordinates = ref_atoms.coordinates() - ref_com
# diff_coordinates = ref_atoms.coordinates().copy
# allocate the array for selection atom coords
traj_coordinates = traj_atoms.coordinates().copy()
for ts in u.trajectory[args.startframe:args.endframe:args.trajskip]:
# shift coordinates for rotation fitting
# selection is updated with the time frame
x_com = traj_atoms.centerOfMass()
traj_coordinates[:] = traj_atoms.coordinates() - x_com
# diff = calc_rmsd(traj_coordinates,ref_coordinates)
diff = traj_coordinates - ref_coordinates
norm = np.linalg.norm(diff, axis=1)
norm *= norm
# rms = sqrt(mean_squared_error(traj_coordinates, ref_coordinates ))
# diff_coordinates = traj_coordinates - ref_coordinates
# mean = np.mean(LA.norm(diff_coordinates,axis=0))
# difference =
# print diff_coordinates
# print "%5d %8.3f A" % (k, rmsd[k])
print "frame ", ts.frame, " diff ", np.average(norm)
# print "frame " , ts.frame, " n " , rms
frame.append(ts.frame)
g2.append(np.average(norm))
frame = np.array(frame)
g2 = np.array(g2)
# os.system("convert -delay ")
save_plot(frame, g2, psffile)
def main():
"""main programm"""
args = read_traj_vmd()
psffile = os.path.splitext(args.psffile)[0]
u = Universe(psffile + '.psf', args.traj)
# u.trajectory[-1]
angles = u.angles.angles()
ymax = len(angles) / 10
xmax = angles.max() * 1.1
for ts in u.trajectory[args.startframe:args.endframe:args.trajskip]:
print " frame = %d " % ts.frame
angles = u.angles.angles()
plt.cla()
plt.ylim(0., ymax)
plt.xlim(0., xmax)
plt.title("frame = %d" % ts.frame)
plt.hist(angles, bins=100, alpha=0.75)
plt.savefig("angles_hist_%.5d.png" % ts.frame)
os.system("convert -delay 60 angles_*.png anim_angles.gif")
os.system("rm angles*.png")
def main():
args = read_traj_vmd()
psffile = os.path.splitext(args.psffile)[0]
u = Universe(psffile+'.psf', 'trajectory_nve.dcd')
Nres = len(u.residues)
frame = []
g2 = []
chainlengths = []
chaing2s = []
res_g2 = 0.
fig = plt.figure()
plt.ylim(0,1)
ims = []
for ts in u.trajectory[args.startframe:args.endframe:args.trajskip]:
all_g2 = 0.
k = 0
chainlengths = []
chaing2s = []
frame.append(ts.frame)
for res in u.residues:
chords = get_bondlist_coords(res)
res_g2 = get_chain_crystallinity(chords,4)
all_g2 += res_g2
chainlengths.append(len(res))
chaing2s.append(res_g2)
chainlengths = np.array(chainlengths)
chaing2s = np.array(chaing2s)
bins, histogram = create_hist_chainlength(chainlengths,chaing2s)
plt.ylim(0,1)
im = plt.bar(bins,histogram,10.0)
ims.append([im])
plt.savefig('hist'+str(ts.frame)+'.png')
plt.cla()
print ("frame %d , g2 = %f" %(ts.frame, all_g2 / float(Nres)))
g2.append(all_g2 / float(Nres))
frame = np.array(frame)
g2 = np.array(g2)
def main():
args = read_traj_vmd()
psffile = os.path.splitext(args.psffile)[0]
u = Universe(psffile+'.psf', args.traj)
time, g2 = [], []
box = u.universe.dimensions[:3]
L = box[0]
print (L)
for ts in u.trajectory[args.startframe:args.endframe:args.trajskip]:
# bonds, atoms = get_bondlist_coords(u)
atoms,angles = get_angles(u)
# bonds, atoms = get_bonds(u)
N=atoms.shape[0]
g = 0.0
# print (atoms,angles)
g = Calcg2(atoms,angles,L)
# result = ft.sparam(natoms=N,bonds=bonds,atoms=atoms,around=2.0,s=s)
print "frame is " , ts.frame, " order = ", g
time.append(ts.frame)
g2.append(g)
# Rgyr = np.sum(np.array([myres.atoms.radiusOfGyration(pbc=True) for myres in u.residues]))
# Rgyr /= len(u.residues)
# gyr.append(Rgyr*Rgyr)
# R2 = np.sum(np.array([distance_sq_coords(myres.atoms[0].pos,myres.atoms[-1].pos) for myres in u.residues]))
# R2 /= len(u.residues)
# gr2.append(R2)
time = np.array(time)
g2 = np.array(g2)
save_plot_cryst_cos(time,g2,psffile)
def main():
args = read_traj_vmd()
psffile = os.path.splitext(args.psffile)[0]
u = Universe(psffile+'.psf', 'trajectory_nve.dcd')
ref_atoms = u.selectAtoms("all")
traj_atoms = u.selectAtoms("all")
natoms = traj_atoms.numberOfAtoms()
# if performing a mass-weighted alignment/rmsd calculation
#masses = ref_atoms.masses()
#weight = masses/numpy.mean(masses)
# reference centre of mass system
ref_com = ref_atoms.centerOfMass()
ref_coordinates = ref_atoms.coordinates() - ref_com
# diff_coordinates = ref_atoms.coordinates().copy
# allocate the array for selection atom coords
traj_coordinates = traj_atoms.coordinates().copy()
for ts in u.trajectory[args.startframe:args.endframe:args.trajskip]:
# shift coordinates for rotation fitting
# selection is updated with the time frame
x_com = traj_atoms.centerOfMass()
traj_coordinates[:] = traj_atoms.coordinates() - x_com
diff = calc_rmsd(traj_coordinates,ref_coordinates)
# rms = sqrt(mean_squared_error(traj_coordinates, ref_coordinates ))
# diff_coordinates = traj_coordinates - ref_coordinates
# mean = np.mean(LA.norm(diff_coordinates,axis=0))
# difference =
# print diff_coordinates
# print "%5d %8.3f A" % (k, rmsd[k])
print "frame " , ts.frame, " diff " , diff
def main():
args = read_traj_vmd()
analyze_chain_hist(args)
def main():
"""main programm"""
args = read_parameters.read_traj_vmd()
calc_cryst(args)
def main():
args = read_parameters.read_traj_vmd()
print args
u = MDAnalysis.Universe(args.psffile, args.traj)
psffile = get_path_names.get_filename(u.filename)
n_atoms_per_box = args.nAtomsPerBox
Natoms = u.trajectory.numatoms
Nx_atoms = Natoms**(1./3.) # how many atoms in a line
Nsub = int(Nx_atoms / float(n_atoms_per_box)) # how many segements of 3 atoms
cryst_all = 0.0
# box = u.trajectory.ts.dimensions[:-3]
# length_x = box[-1]
u.SYSTEM.packIntoBox()
a = u.selectAtoms("all")
c = a.coordinates()
print c
length_x = a.bbox().max()
grid_1d = np.linspace(0.0, length_x, Nsub+1, endpoint=True)
delta = grid_1d[1] - grid_1d[0]
frame = []
g2 = []
if args.filedumpskip:
dumpskip = AnalyzeLog.get_dumpskip(filename='dumpskip.txt',
keyparameter="dump" +
args.keyparameter+"skip")
# dumpskip = args.dumpskip
timestep = AnalyzeLog.get_timestep(filename='dumpskip.txt',
keyparameter="time" +
args.keyparameter
+ "step")
else:
print "using given parameters"
dumpskip = args.dumpskip
timestep = args.timestep
# decide the skipping information
if args.auto_traj_skip:
trajskip = int(u.trajectory.numframes/120.)
if trajskip < 1:
trajskip = 1
elif args.auto_traj_skip:
trajskip = args.trajskip
else:
raise ValueError("trajskip needs to be provided")
for ts in u.trajectory[args.startframe:args.endframe:trajskip]:
# ar_z is a planar selection
u.SYSTEM.packIntoBox()
for i, z in enumerate(grid_1d[0:-1]):
ar_z = u.selectAtoms("prop z >= "
+ str(z) +
" and prop z < "
+ str(z+delta))
# print " I am in z ", z
# print len(ar_z)
# ater this step ar_y is a line
for j, y in enumerate(grid_1d[0:-1]):
ar_y = ar_z.selectAtoms("prop y >= "
+ str(y) +
" and prop y < "
+ str(y+delta))
# print " I am in y ", y
# print len(ar_y)
# ater this step ar_x is a dot
for k, x in enumerate(grid_1d[0:-1]):
ar_x = ar_y.selectAtoms("prop x >= "
+ str(x)
+ " and prop x < "
+ str(x+delta))
# print " I am in x ", x
# print len(ar_x)
bonds = AnalyzeChain.get_bondlist_coords(ar_x)
cryst_all += get_cryst(bonds, get_eigvec(bonds),
threshold=args.threshold)
frame.append(ts.frame)
cryst_all /= float(Nsub**3.0)
g2.append(cryst_all)
print "frame ", ts.frame, " cryst = ", cryst_all
frame = np.array(frame)
g2 = np.array(g2)
# os.system("convert -delay ")
save_plots.save_plot(frame, g2,
plotname='YC',
name=psffile,
logplot=args.logplot,
dumpskip=dumpskip,
timestep=timestep)
return None
def main():
args = read_traj_vmd()
calc_rgre(args)
calc_rmsd(args)
def main():
args = read_traj_vmd()
psffile = os.path.splitext(args.psffile)[0]
PSF = psffile + '.psf'
DCD = args.traj
u = Universe(PSF, DCD)
userdata = "tmp_viz.txt"
vmdscript = "viz_dat.vmd"
timeseries = []
len_cryst_array = np.zeros(len(u.atoms))
for ts in u.trajectory[args.startframe:args.endframe:args.trajskip]:
for res in u.residues:
len_cryst_array[res.atoms.indices] = len(res)
timeseries.append(len_cryst_array)
print "frame %d" % ts.frame
print "result ", np.average(len_cryst_array)
# serialize: add a marker 'END' after each frame
marker = 'END'
with open(userdata, 'w') as data:
for len_cryst_array in timeseries:
data.write("\n".join([str(x) for x in len_cryst_array]))
data.write("\n{0}\n".format(marker))
# write VMD loader script
parameters = {
'vmdfile': vmdscript,
'datafile': userdata,
'topology': PSF,
'trajectory': DCD,
'startframe': args.startframe,
'endframe': args.endframe,
'trajskip': int(args.trajskip)
}
script = """\
proc loaduserdata { fname } {
set all [atomselect top all]
set frame 0
set data [open $fname r]
while { [gets $data line] != -1 } {
set value [string trim $line]
switch -- [string range $value 0 2] {
END {
$all frame $frame
$all set user $beta
# $all set vx $beta
set beta {}
incr frame
}
default {
lappend beta $line
}
}
}
}
""" + """
mol new "{0[topology]}"
animate read dcd "{0[trajectory]}" skip {0[trajskip]} waitfor all
# mol addfile "{0[trajectory]}" type {{dcd}} first 0 last -2 step 1 waitfor
# mol addfile "{0[trajectory]}" waitfor all
animate goto 0
loaduserdata "{0[datafile]}"
color change rgb 0 0.1 0.2 0.7 ;# blue
color change rgb 1 0.7 0.2 0.1 ;# red
color change rgb 3 0.7 0.4 0.0 ;# orange
color change rgb 4 0.8 0.7 0.1 ;# yellow
color change rgb 7 0.1 0.7 0.2 ;# green
color change rgb 10 0.1 0.7 0.8 ;# cyan
color change rgb 11 0.6 0.1 0.6 ;# purple
# color Display Background white #black
color Display Background white
# mol selupdate 0 0 1
# mol colupdate 0 0 1
mol modcolor 0 top User
mol material AOChalky
mol addrep 0
mol modselect 0 0 user > 150
mol modselect 1 0 user < 50
mol modcolor 1 0 ColorID 0
# mol modstyle 1 0 CPK 1.000000 0.300000 12.000000 12.000000
mol modstyle 1 0 Licorice 0.300000 12.000000 12.000000
mol modmaterial 1 0 Diffuse
# mol modcolor 0 0 ColorID 0
# mol modcolor 0 0 ColorID 1
# # mol modstyle 0 0 Licorice 0.500000 46.000000 58.000000
# # mol material 0 0 AOChalky
# mol modmaterial 0 0 AOChalky
# mol modstyle 0 0 Licorice 0.600000 48.000000 58.000000
# mol modcolor 1 0 ColorID 7
# # mol modstyle 1 0 VDW 0.600000 27.000000
# mol modselect 0 0 user > 0.6
# mol modstyle 0 top Lines
# mol modstyle 0 top VDW
# mol modmaterial 0 0 AOChalky
# box_molecule top
""".format(parameters)
with open(vmdscript, 'w') as tcl:
tcl.write(script + '\n')
print("Wrote data trajectory {0} with len_cryst_array".format(userdata))
print("Wrote VMD script {0}: 'source {0}' to load everything ".format(
vmdscript))
def main():
args = read_traj_vmd()
calc_r2n(args)
def main():
args = read_traj_vmd()
calc_sq(args)
def main():
args = read_parameters.read_traj_vmd()
calc_bondacf(args)
bonds,
threshold=args.threshold,
neigh=args.neigh)
if ci > args.threshold:
# print "segment = %d, | ci = %4.3f" % (i,ci)
Flag = True
atom_indices.append(i)
elif ci > 0.0:
# print "segment = %d, > ci = %4.3f" % (i,ci)
Flag = False
else:
ValueError("crystallinity is negative")
L_array.append(L / float(Nres))
timeframes = np.array(timeframes)
L_array = np.array(L_array)
save_plots.save_plot(timeframes,
L_array,
plotname='lamellae',
name=psffile,
logplot=args.logplot,
dumpskip=dumpskip,
timestep=timestep,
ylabel='frac{N_{stems}}{N_{chains}}')
# print "number of lammelae in the chain 1 is = %f" % float(L/Nres)
if __name__ == '__main__':
args = read_parameters.read_traj_vmd()
main(args)
def main():
"""creates wraped trajectory"""
args = read_traj_vmd()
# psffile = os.path.splitext(args.psffile)[0]
create_wrapdcd(args)
# Purpose: Cuts Trajectory for download (in future will wrap it as well)
# Author: Triandafilidi Vasiliy , MSc student at CHBE UBC, Vancouver
# e-mail: vtriandafilidi(at)chbe(dot)ubc(dot)ca
# Syntax: python CreateCutTraj.py -h for help,
# Requires: read_parameters.py
# Copyright (c) 2014 Vasiliy Triandafilidi
# Released under the GNU Public Licence, v2 or any higher version
# todo: add wrapping feature, make function look nice
from read_parameters import read_traj_vmd
import os
from termcolor import colored
args = read_traj_vmd()
psffile = os.path.splitext(args.psffile)[0]
PSF = psffile + '.psf'
DCD = os.path.splitext(args.traj)[0] + '.dcd'
DATA = os.path.splitext(args.datafile)[0] + '.data'
vmdfile = "create_cuttraj.vmd"
bashfile = "create_cuttraj.sh"
resfolder = psffile + '_results'
# write VMD loader script
parameters = {
'vmdfile': vmdfile,
'topology': PSF,
'datafile': DATA,
'trajectory': os.path.basename(DCD),
'trajskip': args.trajskip,
def main():
args = read_parameters.read_traj_vmd()
def main():
args = read_parameters.read_traj_vmd()
calc_clusters(args)
def main():
args = read_traj_vmd()
# calc_sq_rdf(args)
# print "doing sq direct"
calc_sq(args)
