sys.exit(2)
frame_end = int(sys.argv[3])
if (len(sys.argv) == 5):
frame_stride = 1
else:
frame_stride = int(sys.argv[4])
if frame_stride <= 0:
print('The frame stride is invalid')
sys.exit(2)
frame_num = frame_end - frame_begin + 1
if frame_num < 1:
print('The number of frames is invalid.')
sys.exit(2)
dcd = DcdFile(sys.argv[1])
dcd.open_to_read()
if (len(sys.argv) == 5):
dcd_out = DcdFile(sys.argv[4])
else:
dcd_out = DcdFile(sys.argv[5])
dcd_out.open_to_write()
# header
dcd.read_header()
header = dcd.get_header()
##header.istart = header.nstep_save * (frame_begin - 1)
#header.istart = header.istart + header.nstep_save * frame_begin
##header.nset = int(frame_num / frame_stride)
#header.nset = int((frame_end-frame_begin)/frame_stride) + 1
#header.nstep = header.nstep_save * (frame_num - 1)
else:
print("Error: resid {:d} should not be there".format(i))
sys.exit(2)
for cM in cMs:
filename_dcd = 'cM{:s}.fit{:s}.dcd'.format(cM,name)
filename_dx = 'cM{:s}.fit{:s}.dx'.format(cM,name)
nMg = 0
c = PdbFile('../make_ninfo/16SCD.cM{:s}.cg.ion.pdb'.format(cM),'r').read_all_and_close()[0]
for r in c.residues:
if r.atoms[0].name.strip() == 'MG':
nMg += 1
dcd = DcdFile(filename_dcd)
dcd.open_to_read()
dcd.read_header()
data = []
mm = minmax()
''' Create target volume '''
mm_target = minmax()
c = PdbFile('./16SCD.cg.pdb','r').read_all_and_close()[0]
for i in range(c.num_atom()):
if i+1 in serials:
mm_target.update(c.get_atom(i).xyz.get_as_list())
#print('Target volume:')
f_rst.write('n_replica_all: %i\n' % (Nrep, ))
for i, label in enumerate(replica_labels):
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')
'''
import sys
from cafysis.file_io.dcd import DcdFile
from copy import copy
if __name__ == '__main__':
if len(sys.argv) < 4:
print('Usage: % SCRIPT [DCD1] [DCD2] ([DCD3] ...) [output DCD]')
sys.exit(2)
# Number of input DCD files
num_dcd = len(sys.argv) - 2
# New DCD file
f_out = DcdFile(sys.argv[-1])
f_out.open_to_write()
# Count the total frame number
num_frame = 1
for i in range(1, num_dcd):
f_in = DcdFile(sys.argv[i])
f_in.open_to_read()
f_in.read_header()
num_frame += f_in.get_header().nset
f_in.close()
# Get the total step number from final DCD file
f_in = DcdFile(sys.argv[num_dcd])
f_in.open_to_read()
f_in.read_header()
'''
Created on 2013/08/20
@author: Naoto Hori
'''
import sys
from cafysis.file_io.dcd import DcdFile
from cafysis.file_io.ts import TsFile
if len(sys.argv) != 4:
print('Usage: % SCRIPT [input DCD] [ts file] [output DCD]')
sys.exit(2)
# Open DCD and read the header
dcd_filename = sys.argv[1]
dcd = DcdFile(dcd_filename)
dcd.open_to_read()
dcd.read_header()
header = dcd.get_header()
#header.istart = header.nstep_save * (frame_begin - 1)
#header.istart = header.istart + header.nstep_save * frame_begin
#header.nset = int(frame_num / frame_stride)
#header.nset = int((frame_end-frame_begin)/frame_stride) + 1
#header.nstep = header.nstep_save * (frame_num - 1)
#header.nstep_save = header.nstep_save * frame_stride
# Open DCD and read the header
dcd_out = DcdFile(sys.argv[-1])
dcd_out.open_to_write()
dcd_out.set_header(header)
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()
@author: Naoto Hori
'''
import sys
import math
from cafysis.file_io.dcd import DcdFile
from cafysis.file_io.drid import DridFile, DridHeader
import cafysis.lib_f2py.py_drid as py_drid
import numpy as np
if len(sys.argv) not in (4,5):
print('Usage: % SCRIPT [input DCD] [mask file] [output DRID]')
print(' or : % SCRIPT [input DCD] [mask file] [# solute in DCD] [output DRID]')
sys.exit(2)
dcd = DcdFile(sys.argv[1])
dcd.open_to_read()
dcd.read_header()
mask = []
for l in open(sys.argv[2]):
lsp = l.strip().split()
a = []
for x in lsp:
a.append( float(x) )
mask.append( a )
if len(sys.argv) == 5:
flg_solute = True
nsolute = int(sys.argv[3])
if len(mask) != nsolute or len(mask[0]) != nsolute:
#i = 0
#for chain in ref_chains :
# for residue in chain.residues:
# for atom in residue.atoms :
# (ref[0][i], ref[1][i], ref[2][i]) = atom.xyz.get_as_tuple()
# i += 1
#
#ref_idx = []
#pre_idx = []
# all to all
#for i in range(num_atom) :
# ref_idx.append(i + 1)
# pre_idx.append(i + 1)
dcd = DcdFile(filename_dcd)
dcd.open_to_read()
dcd.read_header()
bf = zeros((num_atom, 3), dtype=float64)
bf_2 = zeros((num_atom, 3), dtype=float64)
k = 0
while dcd.has_more_data():
k += 1
data = array(dcd.read_onestep())
bf += data
bf_2 += data**2
dcd.close()
if args.frame_stride <= 0:
print('Error: Frame stride must be > 0')
sys.exit(2)
# Read the reference PDB
pdb = PdbFile(args.pdb)
pdb.open_to_read()
chains = pdb.read_all()
pdb.close()
# Output PDB
movie = PdbFile(args.out)
movie.open_to_write()
# Open DCD and read the header
dcd = DcdFile(args.dcd)
dcd.open_to_read()
dcd.read_header()
num_dcd_frames = dcd.count_frame()
if args.frame_end == -1:
frame_end = num_dcd_frames - 1
elif args.frame_end > num_dcd_frames - 1:
print('Warning: There are only %i frames found in the dcd while you specified --to %i' % (num_dcd_frames, args.frame_end))
print(' Output only %i frames.' % (num_dcd_frames))
frame_end = num_dcd_frames - 1
else:
frame_end = args.frame_end
pdb.close()
num_atom = 0
for chain in ref_chains :
num_atom += chain.num_atom()
ref = zeros((3, num_atom), dtype=float64, order='F')
i = 0
for chain in ref_chains :
for residue in chain.residues:
for atom in residue.atoms :
(ref[0][i], ref[1][i], ref[2][i]) = atom.xyz.get_as_tuple()
i += 1
dcd = DcdFile(filename_dcd)
dcd.open_to_read()
dcd.read_header()
out_dcd = DcdFile(filename_out_dcd)
out_dcd.open_to_write()
out_dcd.set_header(dcd.get_header())
out_dcd.write_header()
k = 0
while dcd.has_more_data() :
k += 1
data = dcd.read_onestep_np()
rmsd = superimpose(ref, data.T)
print(k, rmsd)
#!/usr/bin/env python
'''
@author: Naoto Hori
'''
import sys
from cafysis.file_io.dcd import DcdFile
if (len(sys.argv) != 2):
print('Usage: % SCRIPT [filename]')
sys.exit(2)
dcd = DcdFile(sys.argv[1])
dcd.open_to_read()
dcd.read_header()
dcd.show_header()
dcd.close()
print('The frame stride is invalid')
sys.exit(2)
frame_num = frame_end - frame_begin + 1
if frame_num < 1 :
print('The number of frames is invalid.')
sys.exit(2)
# Output PDB
f_out = open(sys.argv[-1],'w')
# Open DCD and read the header
dcd_filename = sys.argv[1]
dcd = DcdFile(dcd_filename)
dcd.open_to_read()
dcd.read_header()
def error_no_data() :
print('The number of frames is invalid.')
print('Header information:')
dcd.show_header()
sys.exit(2)
# skip
dcd.skip(frame_begin)
#dcd.skip(frame_begin - 1) ## 2013/10/26
i_org = frame_begin
# read and write
help='first particle ID')
parser.add_argument(
'--PosCor',
dest='flg_poscor',
default=False,
action='store_true',
help='Consider only the length which has positive correlation')
parser.add_argument('dcd', help='target DCD file')
parser.add_argument('out', help='output file')
args = parser.parse_args()
################################################################################
dcd = DcdFile(args.dcd)
dcd.open_to_read()
dcd.read_header()
nmp = dcd.get_header().nmp_real
unit_len_sq = 0.0
n_unit_len_sq = 0
sum_cos_theta = [0.0] * (nmp - 1)
num_n = [0] * (nmp - 1)
dcd.skip(args.frame_skip)
first = True
while dcd.has_more_data():
data = dcd.read_onestep_np()
print(' # #')
print(' #polar com1 #')
print(' # : : : #')
print(' # #')
print(' #rg mol #')
print(' # : : : #')
print(' # #')
print(' #dt_hb name r theta1 theta2 phi phi1 phi2#')
print(' ##########################################')
sys.exit(2)
JUDGE_CONTACT = 1.2
JUDGE_CONTACT_2 = JUDGE_CONTACT**2.0
DISPLAY_PROCEDURE_DCD_STEP = 0
dcd = DcdFile(sys.argv[1])
dcd.open_to_read()
dcd.read_header()
nmp = dcd.get_header().nmp_real
f_cmd = open(sys.argv[2], 'r')
# Read command file
cmds = []
defs = {}
ninfo_files = {}
frameskip = 1
display = 0
out_time = 0
for line in f_cmd:
if line.find('#') != -1:
pdb.open_to_read()
chains = pdb.read_all()
pdb.close()
header = DcdHeader()
header.nset = 1
header.istart = 1
header.nstep_save = 1
header.nstep = 1
header.nunit_real = len(chains)
header.delta = 0.0
header.title = [' ' * 80, ' ' * 80]
header.tempk = 0.0
header.lunit2mp = []
imp = 0
xyzs = []
for c in chains:
for r in c.residues:
for a in r.atoms:
imp += 1
xyzs.append([a.xyz.x, a.xyz.y, a.xyz.z])
header.lunit2mp.append(imp)
header.nmp_real = imp
dcd = DcdFile(sys.argv[-1])
dcd.open_to_write()
dcd.set_header(header)
dcd.write_header()
dcd.write_onestep(xyzs)
dcd.close()
from cafysis.file_io.ts import TsFile
if __name__ == '__main__':
if len(sys.argv) < 5:
print('Usage: % SCRIPT [name] [Dir 1] [Dir 2] ([Dir 3] ...) [output dir]')
sys.exit(2)
name = sys.argv[1]
dirs = sys.argv[2:-1]
dir_out = sys.argv[-1]
# Prepare output files
out_ts = TsFile( '%s/%s.ts' % (dir_out, name) )
out_ts.open_to_write()
out_dcd = DcdFile( '%s/%s.dcd' % (dir_out, name) )
out_dcd.open_to_write()
nstep_total_ts = 0
nstep_total_dcd = 0
for (i_dir, d) in enumerate(dirs):
in_ts = TsFile( '%s/%s.ts' % (d, name) )
in_ts.open_to_read()
in_ts.read_header()
in_dcd = DcdFile( '%s/%s.dcd' % (d, name) )
in_dcd.open_to_read()
in_dcd.read_header()
# For the first directory
if i_dir == 0:
f_out.write('\n\n')
# Member of cluster
f_out.write('### Members of cluster\n')
for i in range(1,ncls+1):
f_out.write('#cluster %i\n' % (i,))
for iframe, f in enumerate(fcls):
if f == i:
f_out.write("%i %i\n" % (iframe, iframe*nskip))
f_out.write('\n\n')
f_out.close()
############################# Center
dcd_ref = DcdFile(dcd_ref_filepath)
dcd_ref.open_to_read()
dcd_ref.read_header()
data_ref = dcd_ref.read_onestep_np()
dcd_ref.close()
dcd = DcdFile(dcd_filepath)
dcd.open_to_read()
dcd.read_header()
nmp = dcd._header.nmp_real
cls_centroids = []
for icls in range(ncls):
cls_centroids.append( np.zeros((nmp,3)) )
k = 0
dir_in = sys.argv[1]
name = sys.argv[2]
id_end = int(sys.argv[3])
dir_out = sys.argv[-1]
#Open input files
in_ts_files = []
in_dcd_files = []
for id_rep in range(1, id_end + 1):
ts = TsFile('%s/%s_%04i.ts' % (dir_in, name, id_rep))
ts.open_to_read()
#ts.read_header() ## Commented out since the header will be read later
in_ts_files.append(ts)
dcd = DcdFile('%s/%s_%04i.dcd' % (dir_in, name, id_rep))
dcd.open_to_read()
#dcd.read_header() ## Commented out since the header will be read later
in_dcd_files.append(dcd)
id_finish = 0
while id_finish < id_end:
id_begin_now = id_finish + 1
id_end_now = id_finish + NUM_OUTFILE_OPEN
if id_end_now > id_end:
id_end_now = id_end
id_finish = id_end_now
# Prepare output files
list_id_out = list(range(id_begin_now, id_end_now + 1))
help='log scale time')
parser.add_argument('--maxint',
dest='max_interval',
action='store',
type=int,
help='maximum frame interval')
parser.add_argument('dcd', help='target DCD file')
parser.add_argument('out', help='output file')
args = parser.parse_args()
################################################################################
n_frame = count(args.dcd) # e.g. 501 (i=0, 1, 2,..., 500)
dcd = DcdFile(args.dcd)
dcd.open_to_read()
dcd.read_header()
f_out = open(args.out, 'w')
sum_rmsd = [0.0] * (n_frame - args.skip + 1)
count_rmsd = [0.0] * (n_frame - args.skip + 1)
iframe_max = n_frame - 1 # 500 (= 501 - 1)
for iframe_ref in range(args.skip, iframe_max): # iframe_ref = 5, 6, ...., 499
dcd.rewind()
dcd.skip(iframe_ref)
print('Usage: % SCRIPT [input DCD] [ts file] [reference PDB] [output movie]')
sys.exit(2)
# Read the reference PDB
pdb = PdbFile(sys.argv[-2])
pdb.open_to_read()
chains = pdb.read_all()
pdb.close()
# Output PDB
pdb = PdbFile(sys.argv[-1])
pdb.open_to_write()
# Open DCD and read the header
dcd_filename = sys.argv[1]
dcd = DcdFile(dcd_filename)
dcd.open_to_read()
dcd.read_header()
# Open TS and read the header
ts = TsFile(sys.argv[2])
ts.open_to_read()
ts.read_header()
# read and write
imodel = 0
i_org = 0
while dcd.has_more_data():
if not ts.has_more_data():
print('Not enough data in .ts file (1)')
sys.exit(2)
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
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
if len(sys.argv) != 9:
print('Usage: SCRIPT [input DCD] [input PDB] [ID domain begin] [ID domain end] [ID for fit begin] [ID for fit end] [Box size] [output DCD]')
sys.exit(2)
ID_DOM_INI = int(sys.argv[3]) - 1 # 重心を求める際に必要
ID_DOM_END = int(sys.argv[4]) - 1
ID_DOM_INI_FIT = int(sys.argv[5]) - 1 # 重心を求める際に必要
ID_DOM_END_FIT = int(sys.argv[6]) - 1
BOXSIZE = float(sys.argv[7])
BOXMAX = 0.5 * BOXSIZE
BOXMIN = -0.5 * BOXSIZE
### Files
dcd = DcdFile(sys.argv[1])
dcd.open_to_read()
pdb = PdbFile(sys.argv[2])
pdb.open_to_read()
dcd_out = DcdFile(sys.argv[-1])
dcd_out.open_to_write()
### Read the reference pdb
ref_chains = pdb.read_all()
num_atom = 0
for chain in ref_chains :
num_atom += chain.num_atom()
for chain in ref_chains :
for residue in chain.residues:
for atom in residue.atoms :
#(ref[0][i], ref[1][i], ref[2][i]) = atom.xyz.get_as_tuple()
(ref[i][0], ref[i][1], ref[i][2]) = atom.xyz.get_as_tuple()
i += 1
# 1 - 77 and 270 - 950
mask = []
for i in range(NATOM_TOTAL):
if i in (309-1, 477-1, 519-1):
mask.append(1)
else:
mask.append(0)
dcd = DcdFile('dcd/cM0.0300.dcd')
dcd.open_to_read()
dcd.read_header()
out_dcd = DcdFile('cM0.0300.fit665.dcd')
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)
prefix = sys.argv[-1]
f_out = open('%s.Pr' % (prefix,), 'w')
f_out.write('#')
f_out.write('%6s' % sys.argv)
f_out.write('\n')
f_out.flush()
nbin = max_r * 10
bin_edges = [x*0.1 for x in range(nbin+1)]
bin_edges_sq = [(x*0.1)**2 for x in range(nbin+1)]
f_out_traj = open('%s.Pr_traj' % (prefix,), 'wb')
dcd = DcdFile(sys.argv[1])
dcd.open_to_read()
dcd.read_header()
hist_all = [0] * nbin
icount = 0
fmt = '%iI' % (nbin,)
while dcd.has_more_data() :
data = dcd.read_onestep_npF()
hist = py_dcd_r2_histogram.dcd_r2_histogram(data[:,:nmp], bin_edges_sq)
hist_all += hist
icount += 1
name = sys.argv[2]
id_end = int(sys.argv[3])
dir_out = sys.argv[-1]
#Open input files
in_ts_files = []
in_dcd_files = []
for id_rep in range(1, id_end + 1):
idx = id_rep - 1
ts = TsFile('%s/%s_%04i.ts' % (dir_in, name, id_rep))
ts.open_to_read()
ts.read_header()
in_ts_files.append(ts)
dcd = DcdFile('%s/%s_%04i.dcd' % (dir_in, name, id_rep))
dcd.open_to_read()
dcd.read_header()
in_dcd_files.append(dcd)
# Loop for output label
for id_lab in range(1, id_end + 1):
#Prepare output files
tsout = TsFile('%s/%s_%04i.ts' % (dir_out, name, id_lab))
tsout.open_to_write()
dcdout = DcdFile('%s/%s_%04i.dcd' % (dir_out, name, id_lab))
dcdout.open_to_write()
#Rewind
for id_rep in range(1, id_end + 1):
#!/usr/bin/env python
'''
Created on 2016/08/05
@author: Naoto Hori
'''
import sys
import math
from cafysis.file_io.dcd import DcdFile
if len(sys.argv) != 5:
print(' Usage: % SCRIPT [input DCD] [ID1] [ID2] [output PDB] ')
sys.exit(2)
dcd = DcdFile(sys.argv[1])
id1 = int(sys.argv[2]) - 1
id2 = int(sys.argv[3]) - 1
dcd.open_to_read()
dcd.read_header()
f_out = open(sys.argv[-1], 'w')
#nframe = 0
while dcd.has_more_data():
data = dcd.read_onestep()
#nframe += 1
d = math.sqrt((data[id1][0] - data[id2][0])**2 +
(data[id1][1] - data[id2][1])**2 +
(data[id1][2] - data[id2][2])**2)
f_out.write('%.2f\n' % d)
dcd.close()
sys.exit(2)
dir_in = sys.argv[1]
name = sys.argv[2]
id_end = int(sys.argv[3])
dir_out = sys.argv[-1]
out_ts_files = []
out_dcd_files = []
#Prepare output files
for id_rep in range(1, id_end + 1):
ts = TsFile('%s/%s_%04i.ts' % (dir_out, name, id_rep))
ts.open_to_write()
out_ts_files.append(ts)
dcd = DcdFile('%s/%s_%04i.dcd' % (dir_out, name, id_rep))
dcd.open_to_write()
out_dcd_files.append(dcd)
in_ts_files = []
in_dcd_files = []
#Open input files
for id_rep in range(1, id_end + 1):
idx = id_rep - 1
ts = TsFile('%s/%s_%04i.ts' % (dir_in, name, id_rep))
ts.open_to_read()
ts.read_header()
in_ts_files.append(ts)
out_ts_files[idx].copy_header(ts)
#!/usr/bin/env python
import sys
import scipy.cluster
import numpy as np
from CalcRMSD import calcrmsd
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:
# Calculate number of steps from file sieze
crdsize = os.path.getsize(filepath_crd)
num_step = crdsize / 8 / 3 / (nmp + 1)
crd = CoordFile(filepath_crd, nmp)
crd.open_to_read()
header = DcdHeader()
header.nset = num_step
header.istart = 1
header.nstep_save = 1
header.nstep = 0
header.nunit_real = 0
header.delta = 0.05
header.title = ('', '')
header.tempk = 0.0
header.lunit2mp = []
header.nmp_real = nmp
dcd = DcdFile(filepath_dcd)
dcd.open_to_write()
dcd.set_header(header)
dcd.write_header()
while crd.has_more_data():
dcd.write_onestep(crd.read_onestep())
dcd.close()
crd.close()
