different trajectory formats.
"""
# from MDAnalysis.tests.datafiles import PRMpbc,TRJpbc_bz2
from MDAnalysis.tests.datafiles import PRM, TRJ_bz2
from MDAnalysis import Universe, Writer
from MDAnalysis.core.util import greedy_splitext
import os.path
topol = PRM # PRMpbc
intrj = TRJ_bz2 # TRJpbc_bz2
ext = '.dcd' # output format determined by extension
root, oldext = greedy_splitext(os.path.basename(intrj))
outtrj = root + ext
outpdb = root + '.pdb'
u = Universe(topol, intrj)
# create a writer instance for the output trajectory
w = Writer(outtrj, u.trajectory.numatoms)
# loop through the trajectory and write a frame for every step
for ts in u.trajectory:
w.write(ts)
print "Converted frame %d" % ts.frame
w.close_trajectory()
print "Converted %r --> %r" % (intrj, outtrj)
def Run(topol, intrj):
ext = '.dcd'
atom_l = Simple_atom.Get_Simple_atom_list(topol)
new_list, store_list = Check(atom_l)
NUM = store_list[0][2]
for a in store_list:
if NUM > a[2]:
NUM = a[2]
root, oldext = greedy_splitext(os.path.basename(intrj))
outpdb = root + '.pdb'
u = Universe(topol, intrj)
NUM_ATOMS = len(new_list)
# create a writer instance for the output trajectory
outtrj = [root + str(i) + ext for i in range(NUM)]
w = [Writer(outtrj[i], NUM_ATOMS) for i in range(NUM)]
Atom_list = [copy.deepcopy(new_list) for i in range(NUM)]
'''
NUM copies new_list
'''
# loop through the trajectory and write a frame for every step
for ts in u.trajectory:
for i in range(NUM_ATOMS):
if i < store_list[0][0] - 1:
for s in range(NUM):
Atom_list[s][i].atom_coor_x = ts._x[i]
Atom_list[s][i].atom_coor_y = ts._y[i]
Atom_list[s][i].atom_coor_z = ts._z[i]
elif i > store_list[-1][1] - 1:
LENGTH = 0
for a in store_list:
LENGTH = LENGTH + (a[2] - 1) * (a[1] - a[0] + 1)
for s in range(NUM):
Atom_list[s][i].atom_coor_x = ts._x[i + LENGTH]
Atom_list[s][i].atom_coor_y = ts._y[i + LENGTH]
Atom_list[s][i].atom_coor_z = ts._z[i + LENGTH]
else:
LENGTH = 0
for j in range(len(store_list)):
if i > store_list[j][0] - 2 and i < store_list[j][1]:
if j > 0:
for a in store_list[:j]:
LENGTH = LENGTH + (a[2] - 1) * (a[1] - a[0] +
1)
else:
LENGTH = 0
for s in range(NUM):
Atom_list[s][i].atom_coor_x = ts._x[
store_list[j][0] - 1 + LENGTH + s +
(i + 1 - store_list[j][0]) * store_list[j][2]]
Atom_list[s][i].atom_coor_y = ts._y[
store_list[j][0] - 1 + LENGTH + s +
(i + 1 - store_list[j][0]) * store_list[j][2]]
Atom_list[s][i].atom_coor_z = ts._z[
store_list[j][0] - 1 + LENGTH + s +
(i + 1 - store_list[j][0]) * store_list[j][2]]
for j in range(len(store_list) - 1):
if i > store_list[j][1] - 1 and i < store_list[j +
1][0] - 1:
for a in store_list[:j + 1]:
LENGTH = LENGTH + (a[2] - 1) * (a[1] - a[0] + 1)
for s in range(NUM):
Atom_list[s][i].atom_coor_x = ts._x[i + LENGTH]
Atom_list[s][i].atom_coor_y = ts._y[i + LENGTH]
Atom_list[s][i].atom_coor_z = ts._z[i + LENGTH]
new_ts = [Timestep(NUM_ATOMS) for i in range(NUM)]
for i in range(NUM_ATOMS):
for s in range(NUM):
new_ts[s]._x[i] = Atom_list[s][i].atom_coor_x
new_ts[s]._y[i] = Atom_list[s][i].atom_coor_y
new_ts[s]._z[i] = Atom_list[s][i].atom_coor_z
for s in range(NUM):
w[s].write(new_ts[s])
usage.echo("Converted frame %d\r" % ts.frame)
for s in range(NUM):
w[s].close_trajectory()
print "Converted %r --> %r" % (intrj, outtrj)
# make a pdb file as a simple 'topology'
u.trajectory.rewind()
for atom in Atom_list[0]:
atom.atom_coor_x = atom.atom_coor_x / 10
atom.atom_coor_y = atom.atom_coor_y / 10
atom.atom_coor_z = atom.atom_coor_z / 10
Simple_atom.Save_file(outpdb, Atom_list[0])
print "Created %r to be used with the trajectory" % outpdb
def Run(topol,intrj):
ext='.dcd'
atom_l=Simple_atom.Get_Simple_atom_list(topol)
new_list,store_list=Check(atom_l)
NUM=store_list[0][2]
for a in store_list:
if NUM> a[2]:
NUM=a[2]
root, oldext = greedy_splitext(os.path.basename(intrj))
outpdb = root + '.pdb'
u = Universe(topol, intrj)
NUM_ATOMS=len(new_list)
# create a writer instance for the output trajectory
outtrj = [root+str(i)+ ext for i in range(NUM)]
w =[ Writer(outtrj[i], NUM_ATOMS) for i in range(NUM)]
Atom_list=[copy.deepcopy(new_list) for i in range(NUM)]
'''
NUM copies new_list
'''
# loop through the trajectory and write a frame for every step
for ts in u.trajectory:
for i in range(NUM_ATOMS):
if i < store_list[0][0]-1 :
for s in range(NUM):
Atom_list[s][i].atom_coor_x=ts._x[i]
Atom_list[s][i].atom_coor_y=ts._y[i]
Atom_list[s][i].atom_coor_z=ts._z[i]
elif i > store_list[-1][1]-1:
LENGTH=0
for a in store_list:
LENGTH=LENGTH+(a[2]-1)*(a[1]-a[0]+1)
for s in range(NUM):
Atom_list[s][i].atom_coor_x=ts._x[i+LENGTH]
Atom_list[s][i].atom_coor_y=ts._y[i+LENGTH]
Atom_list[s][i].atom_coor_z=ts._z[i+LENGTH]
else:
LENGTH=0
for j in range(len(store_list)):
if i > store_list[j][0]-2 and i < store_list[j][1]:
if j > 0:
for a in store_list[:j]:
LENGTH=LENGTH+(a[2]-1)*(a[1]-a[0]+1)
else:
LENGTH=0
for s in range(NUM):
Atom_list[s][i].atom_coor_x=ts._x[store_list[j][0]-1+LENGTH+s+(i+1-store_list[j][0])*store_list[j][2]]
Atom_list[s][i].atom_coor_y=ts._y[store_list[j][0]-1+LENGTH+s+(i+1-store_list[j][0])*store_list[j][2]]
Atom_list[s][i].atom_coor_z=ts._z[store_list[j][0]-1+LENGTH+s+(i+1-store_list[j][0])*store_list[j][2]]
for j in range(len(store_list)-1):
if i > store_list[j][1]-1 and i < store_list[j+1][0]-1:
for a in store_list[:j+1]:
LENGTH=LENGTH+(a[2]-1)*(a[1]-a[0]+1)
for s in range(NUM):
Atom_list[s][i].atom_coor_x=ts._x[i+LENGTH]
Atom_list[s][i].atom_coor_y=ts._y[i+LENGTH]
Atom_list[s][i].atom_coor_z=ts._z[i+LENGTH]
new_ts=[Timestep(NUM_ATOMS) for i in range(NUM)]
for i in range(NUM_ATOMS):
for s in range(NUM):
new_ts[s]._x[i]=Atom_list[s][i].atom_coor_x
new_ts[s]._y[i]=Atom_list[s][i].atom_coor_y
new_ts[s]._z[i]=Atom_list[s][i].atom_coor_z
for s in range(NUM):
w[s].write(new_ts[s])
usage.echo("Converted frame %d\r" % ts.frame)
for s in range(NUM):
w[s].close_trajectory()
print "Converted %r --> %r" % (intrj, outtrj)
# make a pdb file as a simple 'topology'
u.trajectory.rewind()
for atom in Atom_list[0]:
atom.atom_coor_x=atom.atom_coor_x/10
atom.atom_coor_y=atom.atom_coor_y/10
atom.atom_coor_z=atom.atom_coor_z/10
Simple_atom.Save_file(outpdb,Atom_list[0])
print "Created %r to be used with the trajectory" % outpdb
"""
#from MDAnalysis.tests.datafiles import PRMpbc,TRJpbc_bz2
#from MDAnalysis.tests.datafiles import PRM,TRJ_bz2
from MDAnalysis import Universe, Writer
from MDAnalysis.core.util import greedy_splitext
from MDPackage import Simple_atom
import os.path
import sys
pdbfile = sys.argv[1] #PRMpbc
#intrj =sys.argv[2] #TRJpbc_bz2
ext = '.xtc' # output format determined by extension
root, oldext = greedy_splitext(os.path.basename(pdbfile))
outtrj = root + ext
outpdb = root + '_new.pdb'
u = Universe(pdbfile, )
# create a writer instance for the output trajectory
w = Writer(outtrj, u.trajectory.numatoms)
aa = Simple_atom.Get_Simple_atom_list(pdbfile)
NUM_FRAMES = len(aa) / u.trajectory.numatoms
# loop through the trajectory and write a frame for every step
ts = u.trajectory[0]
for i in range(NUM_FRAMES):
for j in range(u.trajectory.numatoms):
ts._x[j] = aa[i * u.trajectory.numatoms + j].atom_coor_x * 10
ts._y[j] = aa[i * u.trajectory.numatoms + j].atom_coor_y * 10
"""
#from MDAnalysis.tests.datafiles import PRMpbc,TRJpbc_bz2
#from MDAnalysis.tests.datafiles import PRM,TRJ_bz2
from MDAnalysis import Universe, Writer
from MDAnalysis.core.util import greedy_splitext
import os.path
import sys
topol =sys.argv[1] #PRMpbc
intrj =sys.argv[2] #TRJpbc_bz2
ext = '.xtc' # output format determined by extension
root, oldext = greedy_splitext(os.path.basename(intrj))
outtrj = root + ext
outpdb = root + '.pdb'
u = Universe(topol, intrj)
# create a writer instance for the output trajectory
w = Writer(outtrj, u.trajectory.numatoms)
# loop through the trajectory and write a frame for every step
for ts in u.trajectory:
w.write(ts)
print "Converted frame %d" % ts.frame
w.close_trajectory()
print "Converted %r --> %r" % (intrj, outtrj)
"""
#from MDAnalysis.tests.datafiles import PRMpbc,TRJpbc_bz2
#from MDAnalysis.tests.datafiles import PRM,TRJ_bz2
from MDAnalysis import Universe, Writer
from MDAnalysis.core.util import greedy_splitext
from MDPackage import Simple_atom
import os.path
import sys
pdbfile =sys.argv[1] #PRMpbc
#intrj =sys.argv[2] #TRJpbc_bz2
ext = '.xtc' # output format determined by extension
root, oldext = greedy_splitext(os.path.basename(pdbfile))
outtrj = root + ext
outpdb = root + '_new.pdb'
u = Universe(pdbfile,)
# create a writer instance for the output trajectory
w = Writer(outtrj, u.trajectory.numatoms)
aa=Simple_atom.Get_Simple_atom_list(pdbfile)
NUM_FRAMES=len(aa)/u.trajectory.numatoms
# loop through the trajectory and write a frame for every step
ts = u.trajectory[0]
for i in range(NUM_FRAMES):
for j in range(u.trajectory.numatoms):
ts._x[j]=aa[i*u.trajectory.numatoms+j].atom_coor_x*10
ts._y[j]=aa[i*u.trajectory.numatoms+j].atom_coor_y*10