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 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 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
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:
break
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
@author: Naoto Hori
'''
import sys
from cafysis.file_io.dcd import DcdFile
if len(sys.argv) < 6:
print('Usage: % SCRIPT [input dcd] [filter file] [ev file] [,ev file ....] [output average file] [output PC file]')
sys.exit(2)
f_dcd = DcdFile(sys.argv[1])
f_dcd.open_to_read()
f_dcd.read_header()
f_out = open(sys.argv[-1], 'w')
f_ave = open(sys.argv[-2], 'w')
# Read eigen values
num_ev = len(sys.argv) - 5
ev = []
for i in range(num_ev) :
f_ev = open(sys.argv[i+3], 'r')
ev_tmp = []
for line in f_ev :
if line.find('#') != -1: continue
ev_tmp.append(float(line.strip()))
ev.append(ev_tmp)
f_ev.close()
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()
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()
# 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
while dcd.has_more_data():
# 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:
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