def write_trajectory(universe, filename):
'''A simplified method for writing trajectories
'''
w = Writer(filename, universe.atoms.numberOfAtoms())
for ts in universe.trajectory:
w.write(ts)
w.close()
def write_trajectory(universe, filename):
'''A simplified method for writing trajectories
'''
w = Writer(filename, universe.atoms.numberOfAtoms())
for ts in universe.trajectory:
w.write(ts)
w.close()
def Move_2_center(top_file, trj_file, trjout_file):
u = Universe(top_file, trj_file)
TRAJ_FRAMES = u.trajectory.numframes
w = Writer(trjout_file, u.trajectory.numatoms)
atoms = Simple_atom.Get_atom_list(top_file)
SOLUTE_COUNT = 0
for atom_ID in atoms:
if atoms[atom_ID].residue_name != "SOL" and atoms[
atom_ID].residue_name != "WAT":
SOLUTE_COUNT += 1
else:
pass
print '''Note: this program will read the pbc condition and use the dimensions \
read from trajectory files. You should make sure the dimensions are right or \
it will create a wrong output trajectory file.'''
START_TIME = Time.time()
NUM_ATOMS = u.trajectory.numatoms
# loop through the trajectory and write a frame for every step
for ts in u.trajectory:
dimensions = ts.dimensions
for i in range(SOLUTE_COUNT):
if ts._x[i] > dimensions[0]:
ts._x[i] = ts._x[i] - dimensions[0]
if ts._x[i] < 0:
ts._x[i] = ts._x[i] + dimensions[0]
if ts._y[i] > dimensions[1]:
ts._y[i] = ts._y[i] - dimensions[1]
if ts._y[i] < 0:
ts._y[i] = ts._y[i] + dimensions[1]
if ts._z[i] > dimensions[2]:
ts._z[i] = ts._z[i] - dimensions[2]
if ts._z[i] < 0:
ts._z[i] = ts._z[i] + dimensions[2]
NOW_TIME = Time.time()
BIN_TIME = NOW_TIME - START_TIME
if ts.frame % 100 == 0:
# usage.echo("%8.4f %8.4f %8.4f\r" %(dimensions[0],dimensions[1],dimensions[2]))
usage.echo(" "*40+"Converted frame %d, time used: %8.2f s, time left: %8.2f s \r" \
% (ts.frame,BIN_TIME,BIN_TIME*(float(TRAJ_FRAMES)/ts.frame-1) ))
# for ts in u.trajectory:
w.write(ts)
# usage.echo("Writting frame %d\r" %ts.frame)
w.close_trajectory()
print "Converted %r --> %r" % (intrj, outtrj)
def write_trajectory(universe, filename, maximum_frames=0):
'''A simplified method for writing trajectories
'''
w = Writer(filename, universe.atoms.numberOfAtoms())
frame_count = 0
for ts in universe.trajectory:
if(maximum_frames != 0 and frame_count == maximum_frames):
break
w.write(ts)
frame_count += 1
w.close()
def Move_2_center(top_file,trj_file,trjout_file):
u=Universe(top_file,trj_file)
TRAJ_FRAMES=u.trajectory.numframes
w = Writer(trjout_file, u.trajectory.numatoms)
atoms=Simple_atom.Get_atom_list(top_file)
SOLUTE_COUNT = 0
for atom_ID in atoms:
if atoms[atom_ID].residue_name != "SOL" and atoms[atom_ID].residue_name != "WAT":
SOLUTE_COUNT +=1
else:
pass
print '''Note: this program will read the pbc condition and use the dimensions \
read from trajectory files. You should make sure the dimensions are right or \
it will create a wrong output trajectory file.'''
START_TIME=Time.time()
NUM_ATOMS = u.trajectory.numatoms
# loop through the trajectory and write a frame for every step
for ts in u.trajectory:
dimensions=ts.dimensions
for i in range(SOLUTE_COUNT):
if ts._x[i] > dimensions[0]:
ts._x[i]=ts._x[i]-dimensions[0]
if ts._x[i] <0:
ts._x[i]=ts._x[i]+dimensions[0]
if ts._y[i] > dimensions[1]:
ts._y[i]=ts._y[i]-dimensions[1]
if ts._y[i] <0:
ts._y[i]=ts._y[i]+dimensions[1]
if ts._z[i] > dimensions[2]:
ts._z[i]=ts._z[i]-dimensions[2]
if ts._z[i] < 0:
ts._z[i]=ts._z[i]+dimensions[2]
NOW_TIME=Time.time()
BIN_TIME=NOW_TIME-START_TIME
if ts.frame % 100 == 0:
# usage.echo("%8.4f %8.4f %8.4f\r" %(dimensions[0],dimensions[1],dimensions[2]))
usage.echo(" "*40+"Converted frame %d, time used: %8.2f s, time left: %8.2f s \r" \
% (ts.frame,BIN_TIME,BIN_TIME*(float(TRAJ_FRAMES)/ts.frame-1) ))
# for ts in u.trajectory:
w.write(ts)
# usage.echo("Writting frame %d\r" %ts.frame)
w.close_trajectory()
print "Converted %r --> %r" % (intrj, outtrj)
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)
# make a pdb file as a simple 'topology'
u.trajectory.rewind()
u.atoms.write(outpdb)
print "Created %r to be used with the trajectory" % outpdb
# coding=utf-8
"""
MDAnalysis example: Convert DCD trajectory into XTC
===================================================
This example shows how one can use MDAnalysis to convert between
different trajectory formats.
"""
from MDAnalysis.tests.datafiles import PDB_small, DCD
from MDAnalysis import Universe, Writer
import os.path
root, ext = os.path.splitext(os.path.basename(DCD))
xtcname = root + '.xtc' # output format determined by extension
u = Universe(PDB_small, DCD)
# create a writer instance for the output trajectory
w = Writer(xtcname, 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 {0:d}".format(ts.frame)
w.close_trajectory()
print "Converted {0!r} --> {1!r}".format(DCD, xtcname)
def Move_2_center(top_file,trj_file,trjout_file,skip=1):
u=Universe(top_file,trj_file)
TRAJ_FRAMES=u.trajectory.numframes
atom_l=Simple_atom.Get_Simple_atom_list(top_file)
while True:
fit_residue=Simple_atom.Get_residue(top_file)
if len(fit_residue) > 1:
print "Only 1 residue is aviliable."
continue
else:
break
while True:
fit_atom=Simple_atom.Get_atom(atom_l,fit_residue[0])
if len(fit_atom) > 1:
print "Only 1 atom is aviliable."
continue
else:
break
fitting_group=Simple_atom.Get_residue(top_file)
fit_atom=fit_atom[0]
w = Writer(trjout_file, u.trajectory.numatoms)
NUM_ATOMS=len(atom_l)
print '''Note: this program will read the pbc condition and use the dimensions \
read from trajectory files. You should make sure the dimensions are right or \
it will create a wrong output trajectory file.'''
START_TIME=Time.time()
# loop through the trajectory and write a frame for every step
for ts in u.trajectory:
if ts.frame % skip != 1:
break
if ts.frame==1:
label_coordinate=[ts._x[fit_atom],ts._y[fit_atom],ts._z[fit_atom]]
# origin_list=list()
# for atom in atom_l:
# if atom.residue_serial in fitting_group:
# origin_list.append([\
# ts._x[atom_l.index(atom)],\
# ts._y[atom_l.index(atom)],\
# ts._z[atom_l.index(atom)],\
# ])
else:
shift=[label_coordinate[0]-ts._x[fit_atom],\
label_coordinate[1]-ts._y[fit_atom],\
label_coordinate[2]-ts._z[fit_atom]]
dimensions=ts.dimensions
usage.echo("%8.4f %8.4f %8.4f\r" %(dimensions[0],dimensions[1],dimensions[2]))
for i in range(NUM_ATOMS):
ts._x[i] =ts._x[i]+shift[0]
if ts._x[i] > dimensions[0]:
ts._x[i]=ts._x[i]-dimensions[0]
if ts._x[i] <0:
ts._x[i]=ts._x[i]+dimensions[0]
ts._y[i] =ts._y[i]+shift[1]
if ts._y[i] > dimensions[1]:
ts._y[i]=ts._y[i]-dimensions[1]
if ts._y[i] <0:
ts._y[i]=ts._y[i]+dimensions[1]
ts._z[i] =ts._z[i]+shift[2]
if ts._z[i] > dimensions[2]:
ts._z[i]=ts._z[i]-dimensions[2]
if ts._z[i] < 0:
ts._z[i]=ts._z[i]+dimensions[2]
# temp_list=list()
# for atom in atom_l:
# if atom.residue_serial in fitting_group:
# temp_list.append([\
# ts._x[atom_l.index(atom)],\
# ts._y[atom_l.index(atom)],\
# ts._z[atom_l.index(atom)],\
# ])
# # [Rotate,shift]=least_squares_fitting.Fitting(temp_list,origin_list)
# atom_matrix=numpy.array([[ts._x[i],ts._y[i],ts._z[i]]for i in range(NUM_ATOMS)])
# # resu_matrix=numpy.matrix(atom_matrix) * numpy.matrix(Rotate).T
# # resu_matrix=numpy.array(resu_matrix)
# # for i in range(NUM_ATOMS):
# # atom_matrix[i,0]=resu_matrix[i,0]+shift[0]
# # atom_matrix[i,1]=resu_matrix[i,1]+shift[1]
# # atom_matrix[i,2]=resu_matrix[i,2]+shift[2]
# for i in range(NUM_ATOMS):
# ts._x[i]=atom_matrix[i,0]
# ts._y[i]=atom_matrix[i,1]
# ts._z[i]=atom_matrix[i,2]
# w.write(ts)
NOW_TIME=Time.time()
BIN_TIME=NOW_TIME-START_TIME
usage.echo(" "*40+"Converted frame %d, time used: %8.2f s, time left: %8.2f s \r" \
% (ts.frame,BIN_TIME,BIN_TIME*(float(TRAJ_FRAMES)/ts.frame-1) ))
# for ts in u.trajectory:
w.write(ts)
# usage.echo("Writting frame %d\r" %ts.frame)
w.close_trajectory()
print "Converted %r --> %r" % (intrj, outtrj)
Index[nst] = [n]
else:
print "Error: ", n, nst, N_str
ifile.close()
print 'number of clusters:', len(N_str)
N_str.sort()
N_str.reverse()
N_write = int(raw_input('How many clusters you want to look at (eg. 8): '))
universe = Universe(pdbfile, pdbfile)
writer = Writer(filename + '_.pdb', universe.atoms.numberOfAtoms())
k = 1
for each in N_str[:N_write]:
if k > N_write:
break
percent = float(each) * 100 / sum(N_str)
for i in Index[each]:
print 'Writing cluster #' + str(i).ljust(3),
universe.trajectory[i - 1]
protein = universe.atoms
writer.write(protein)
print '%3i %5.0f%% %6.2f%%' % (k, percent, percent)
k += 1
writer.close()
def Move_2_center(top_file,trj_file,index_file,trjout_file):
u=Universe(top_file,trj_file)
TRAJ_FRAMES=u.trajectory.numframes
w = Writer(trjout_file, u.trajectory.numatoms)
atoms=Simple_atom.Get_Simple_atom_list(top_file)
index = Index.Read_index_to_Inclass(index_file)
Index.Print_Index(index)
while True:
try:
solute_index=int(raw_input("Choosing the group for centering:"))
# solvent_index = int(raw_input("Choosing the solvent group:"))
break
except:
print "You should input a number."
continue
solute_group = index[solute_index].group_list
# solvent_group = index[solvent_index].group_list
solute_atoms =len(solute_group)
NUM_ATOMS = u.trajectory.numatoms
# print "\t Reading %d frames from trajectory file: %s" %(nframes,traj_file)
START_TIME=Time.time()
for ts in u.trajectory:
ref_com =np.zeros((3),dtype=np.float32)
# sys.stderr.write("\t Reading frame %8d\r" %ts.frame)
# sys.stderr.flush()
for i,ai in list(enumerate(solute_group)):
ref_com[0] += ts._x[ai-1]
ref_com[1] += ts._y[ai-1]
ref_com[2] += ts._z[ai-1]
ref_com = ref_com/solute_atoms
dimensions=ts.dimensions
ref_com = ref_com - np.array([dimensions[0]/2, dimensions[1]/2, dimensions[2]/2])
# ref_com = np.array([sum(traj_data[:,0])/solute_atoms - dimensions[0]/2,\
# sum(traj_data[:,1])/solute_atoms - dimensions[1]/2,\
# sum(traj_data[:,2])/solute_atoms - dimensions[2]/2])
for i in range(NUM_ATOMS):
ts._x[i] = ts._x[i] - ref_com[0]
ts._y[i] = ts._y[i] - ref_com[1]
ts._z[i] = ts._z[i] - ref_com[2]
if (i+1) in solute_group:
continue
if ts._x[i] > dimensions[0] or ts._x[i] <0:
ts._x[i]=ts._x[i]%dimensions[0]
if ts._y[i] > dimensions[1] or ts._y[i] <0:
ts._y[i]=ts._y[i]%dimensions[1]
if ts._z[i] > dimensions[2] or ts._z[i] < 0:
ts._z[i]=ts._z[i]%dimensions[2]
NOW_TIME=Time.time()
BIN_TIME=NOW_TIME-START_TIME
# if ts.frame % 10 == 0:
# usage.echo("%8.4f %8.4f %8.4f\r" %(dimensions[0],dimensions[1],dimensions[2]))
usage.echo(" "*40+"Converted frame %d, time used: %8.2f s, time left: %8.2f s \r" \
% (ts.frame,BIN_TIME,BIN_TIME*(float(TRAJ_FRAMES)/ts.frame-1) ))
# for ts in u.trajectory:
w.write(ts)
# del traj_data
# usage.echo("Writting frame %d\r" %ts.frame)
w.close_trajectory()
print "Converted %r --> %r" % (intrj, outtrj)