def dcd_concatenate(filepaths):
n_frames = [] # To return the number of frames
# Number of input DCD files
num_dcd = len(filepaths) - 1
# New DCD file
f_out = DcdFile(filepaths[-1])
f_out.open_to_write()
# Count the total frame number
num_frame = 1
for i in range(0, num_dcd - 1):
f_in = DcdFile(filepaths[i])
f_in.open_to_read()
f_in.read_header()
num_frame += f_in.get_header().nset - 1
f_in.close()
# Get the total step number from final DCD file
f_in = DcdFile(filepaths[num_dcd - 1])
f_in.open_to_read()
f_in.read_header()
num_frame += f_in.get_header().nset - 1
num_step = f_in.get_header().nstep
f_in.close()
f_in = DcdFile(filepaths[0])
f_in.open_to_read()
f_in.read_header()
header = copy(f_in.get_header())
header.nset = num_frame
header.nstep = num_step
f_out.set_header(header)
f_out.write_header()
#print filepaths[0], f_in.get_header().nset
n_frames.append(f_in.get_header().nset)
while f_in.has_more_data():
f_out.write_onestep(f_in.read_onestep())
f_in.close()
for i in range(1, num_dcd):
f_in = DcdFile(filepaths[i])
f_in.open_to_read()
f_in.read_header()
f_in.skip_onestep() # skip the first step
#print filepaths[i], f_in.get_header().nset - 1
n_frames.append(f_in.get_header().nset - 1)
while f_in.has_more_data():
f_out.write_onestep(f_in.read_onestep())
f_in.close()
f_out.close()
return n_frames
def dcd_fit(filename_dcd, filename_dcd_out, natom_total, serials,
filename_rmsd):
f_out = open(filename_rmsd, 'w')
# Coord1
pdb = PdbFile('16SCD.cg.pdb')
pdb.open_to_read()
ref_chains = pdb.read_all()
pdb.close()
#num_atom = 0
#for chain in ref_chains :
# for residue in chain.residues :
# num_atom += len(residue.atoms)
ref = zeros((natom_total, 3), dtype=float64, order='C')
i = 0
for chain in ref_chains:
for residue in chain.residues:
for atom in residue.atoms:
(ref[i][0], ref[i][1], ref[i][2]) = atom.xyz.get_as_tuple()
i += 1
mask = []
for i in range(natom_total):
# the serial ID starts from 1, thus i+1 is the serial ID
if i + 1 in serials:
mask.append(1)
else:
mask.append(0)
dcd = DcdFile(filename_dcd)
dcd.open_to_read()
dcd.read_header()
out_dcd = DcdFile(filename_dcd_out)
out_dcd.open_to_write()
out_dcd.set_header(dcd.get_header())
out_dcd.write_header()
#dcd.show_header()
k = 0
while dcd.has_more_data():
k += 1
coords_dcd = dcd.read_onestep_np()
rmsd = superimpose(ref.T, coords_dcd.T, mask)
f_out.write('{:8d} {:6.2f}\n'.format(k, rmsd))
out_dcd.write_onestep(coords_dcd)
dcd.close()
out_dcd.close()
def count_frame(path):
dcd = DcdFile(path)
dcd.open_to_read()
dcd.read_header()
icount = 0
while dcd.has_more_data():
try:
dcd.skip(1)
icount += 1
except EOFError:
icount += 1
print(
'There is another frame at the end, that is not written completely.'
)
break
except:
break
dcd.close()
return icount
from cafysis.file_io.dcd import DcdFile
if len(sys.argv) != 4:
print('Usage: % SCRIPT [input DCD] [#frame to skip] [output prefix]')
sys.exit(2)
nskip = int(sys.argv[2])
prefix = sys.argv[-1]
dcd = DcdFile(sys.argv[1])
dcd.open_to_read()
dcd.read_header()
dist_array = []
while dcd.has_more_data():
ref = dcd.read_onestep_np()
dcd.set_mark()
if dcd.has_more_data():
while dcd.has_more_data():
data = dcd.read_onestep_np()
dist_array.append(calcrmsd(ref.T, data.T))
dcd.go_mark()
else:
break
dcd.close()
print(len(dist_array))
f_rst.write('rep2lab: %5i %5i\n' % (i + 1, label))
#### Step
f_rst.write('# step\n')
f_rst.write('istep_sim: 1\n')
f_rst.write('istep: %i\n' % (step, ))
#### coordinates of each replicas
for irep in range(1, Nrep + 1):
f_rst.write('# xyz_mp_rep\n')
f_rst.write('grep: %i\n' % (irep, ))
dcd = DcdFile(file_path + '_%04i.dcd' % (irep, ))
dcd.open_to_read()
header = dcd.read_header()
while dcd.has_more_data():
data = dcd.read_onestep()
if len(data) != nmp:
print(('Error len(data) != nmp in replica %i. len(data)=%i' %
(irep, len(data))))
sys.exit(2)
f_rst.write('nmp_all: %i\n' % (nmp, ))
for imp in range(nmp):
f_rst.write('%f %f %f\n' % (data[imp][0], data[imp][1], data[imp][2]))
f_rst.write('# velo_mp\n')
f_rst.write('grep: %i\n' % (irep, ))
f_rst.write('nmp_real: %i\n' % (nmp, ))
for imp in range(nmp):
# Check for ev
for v in ev :
if len(v) != num_dimension :
print('len(v) != num_dimension, %i' % num_dimension)
sys.exit(2)
#debug
#for i in xrange(num_ev):
# print '# ev %i' % i
# for value in ev[i] :
# print value
# Calculate average structure (data_ave)
data_ave = [0.0 for i in range(num_dimension)]
num_data = 0
while f_dcd.has_more_data() :
num_data += 1
data = f_dcd.read_onestep()
idx = 0
for iatom, atom in enumerate(data) :
if not fil[iatom]:
continue
for xyz in atom :
data_ave[idx] += xyz
idx += 1
for i in range(len(data_ave)) :
data_ave[i] /= float(num_data)
f_ave.write('%12.5f\n' % data_ave[i])
f_ave.close()
f_in.open_to_read()
f_in.read_header()
num_frame += f_in.get_header().nset
num_step = f_in.get_header().nstep
f_in.close()
f_in = DcdFile(sys.argv[1])
f_in.open_to_read()
f_in.read_header()
header = copy(f_in.get_header())
header.nset = num_frame
header.nstep = num_step
f_out.set_header(header)
f_out.write_header()
print(sys.argv[1], f_in.get_header().nset)
while f_in.has_more_data():
f_out.write_onestep(f_in.read_onestep())
f_in.close()
for i in range(2, num_dcd + 1):
f_in = DcdFile(sys.argv[i])
f_in.open_to_read()
f_in.read_header()
#f_in.skip_onestep() # skip the first step
print(sys.argv[i], f_in.get_header().nset)
while f_in.has_more_data():
f_out.write_onestep(f_in.read_onestep())
f_in.close()
f_out.close()
in_dcd.read_header()
# For the first directory
if i_dir == 0:
out_ts.header_lines = in_ts.header_lines
out_ts.copy_header( in_ts )
out_ts.write_header()
out_dcd.set_header( in_dcd.get_header() )
out_dcd.write_header()
else:
# restartの場合は、最初のフレームを除外
in_ts.read_onestep()
in_dcd.read_onestep()
nstep_dcd = 0
while in_dcd.has_more_data():
out_dcd.write_onestep( in_dcd.read_onestep() )
nstep_dcd += 1
nstep_ts = 0
while in_ts.has_more_data():
tsdata, tslines = in_ts.read_onestep()
out_ts.write_onestep( tslines )
nstep_ts += 1
if i_dir == 0:
print(('TS in %s: #frame = %i' % (d, nstep_ts)))
print(('DCD in %s: #frame = %i' % (d, nstep_dcd)))
else:
print(('TS in %s: #frame = %i (the first step is eliminated.)' % (d, nstep_ts)))
print(('DCD in %s: #frame = %i (the first step is eliminated.)' % (d, nstep_dcd)))
else:
frame_end = args.frame_end
# skip
skipped = dcd.skip_as_many_as_possible_upto(args.frame_begin)
if skipped < args.frame_begin:
print('Only %i frames could be read from the dcd file, which is less than the one specified as --from %i.' % (skipped, args.frame_begin))
print('No output file generated.')
sys.exit(2)
frame_num = frame_end - args.frame_begin + 1
i_orig = args.frame_begin
# read and write
for iframe in range(frame_num) :
if not dcd.has_more_data() :
print('The number of frames is invalid.')
print('Header information:')
dcd.show_header()
dcd.close()
movie.close()
sys.exit(2)
if iframe % args.frame_stride != 0 :
dcd.skip(1)
i_orig += 1
continue
struct = dcd.read_onestep()
""" Move to the origin """
