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
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)
dcd_out.write_header()
# Open TS and read the header
ts = TsFile(sys.argv[2])
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()
header = copy(f_in.get_header())
header.nset = num_frame
for icls in range(ncls):
cls_average_RMSD[icls] /= float(cls_num_node[icls])
f_out = open('%s.cls_%s.centroids' % (prefix, cutoff_char),'w')
f_out.write('#clsID node RMSD RMSD/sqrt(nmp) <RMSD> <RMSD>/sqrt(nmp)\n')
for icls in range(ncls):
f_out.write('%i %i %5.2f %f %5.2f %f\n' % (icls+1, cls_nearest_node[icls],
cls_nearest_RMSD[icls], cls_nearest_RMSD[icls]/math.sqrt(nmp),
cls_average_RMSD[icls], cls_average_RMSD[icls]/math.sqrt(nmp)) )
f_out.write('\n')
dcd_out = DcdFile('%s.cls_%s.centroids.dcd' % (prefix, cutoff_char))
dcd_out.open_to_write()
dcd_out.set_header( dcd.get_header() )
dcd_out.write_header()
for icls in range(ncls):
dcd_out.write_onestep( cls_centroids[icls] )
dcd_out.close()
#f_out.write('#centroid DCD\n')
#for icls in range(ncls):
# f_out.write('%i' % (icls+1,))
# for c in cls_centroids[icls]:
# f_out.write(' %f' % (c,))
# f_out.write('\n')
#f_out.write('\n')
#
#f_out.write('#nearest DCD\n')
Created on 2011/05/25
@author: Naoto Hori
'''
import sys
from cafysis.file_io.dcd import DcdFile
from cafysis.file_io.pdb import PdbFile
if len(sys.argv) != 4:
print(' Usage: % SCRIPT [input DCD] [input PDB] [output PDB] ')
sys.exit(2)
dcd = DcdFile(sys.argv[1])
dcd.open_to_read()
dcd.read_header()
nmp = dcd.get_header().nmp_real
f_pdb = PdbFile(sys.argv[2])
f_pdb.open_to_read()
chains = f_pdb.read_all()
f_pdb.close()
f_out = PdbFile(sys.argv[3])
f_out.open_to_write()
ave = []
for i in range(nmp):
xyz = [0.0, 0.0, 0.0]
ave.append(xyz)
nframe = 0
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)
out_ts_files[idx].write_header()
dcd = DcdFile('%s/%s_%04i.dcd' % (dir_in, name, id_rep))
dcd.open_to_read()
dcd.read_header()
in_dcd_files.append(dcd)
out_dcd_files[idx].set_header(dcd.get_header())
out_dcd_files[idx].write_header()
while in_dcd_files[0].has_more_data():
for idx in range(id_end):
(tsdata, tslines) = in_ts_files[idx].read_onestep()
coord_matrix = in_dcd_files[idx].read_onestep()
step = int(tsdata[0][in_ts_files[idx].head_col.step])
label = int(tsdata[0][in_ts_files[idx].head_col.label])
idx_out = label - 1
if step == 1:
(tsdata, tslines) = in_ts_files[idx].read_onestep()
step = int(tsdata[0][in_ts_files[idx].head_col.step])
label = int(tsdata[0][in_ts_files[idx].head_col.label])
# 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)
print(k, rmsd)
out_dcd.write_onestep(coords_dcd)
dcd.close()
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
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 )
