def write_dcd(self,filename):
'''
This method writes data in the Charmm/Xplor data format.
by calling a pre-compiled C module (dcdio).
'''
outfile=dcdio.open_dcd_write(filename)
nset = self._coor[:,0,0].shape[0]
natoms = self._coor[0,:,0].shape[0]
istart = 0 ; nsavc = 1 ; delta = 1.0
headerresult=dcdio.write_dcdheader(outfile,filename,natoms,nset,istart,nsavc,delta)
for frame in xrange(nset):
print ".",
sys.stdout.flush()
tx=self._coor[frame,:,0].astype(numpy.float32)
ty=self._coor[frame,:,1].astype(numpy.float32)
tz=self._coor[frame,:,2].astype(numpy.float32)
stepresult=dcdio.write_dcdstep(outfile,tx,ty,tz,frame+1)
result = dcdio.close_dcd_write(outfile)
return
def write_dcd_frames(self, filename, start, end):
'''
This method writes a single step or multiple frames
in the Charmm/Xplor data format.
by calling a pre-compiled C module (dcdio).
'''
outfile = dcdio.open_dcd_write(filename)
nset = end - start
natoms = self._coor[0, :, 0].shape[0]
istart = 0
nsavc = 1
delta = 1.0
headerresult = dcdio.write_dcdheader(outfile, filename, natoms, nset,
istart, nsavc, delta)
i = 0
for frame in xrange(start, end):
print ".",
sys.stdout.flush()
tx = self._coor[frame, :, 0].astype(numpy.float32)
ty = self._coor[frame, :, 1].astype(numpy.float32)
tz = self._coor[frame, :, 2].astype(numpy.float32)
stepresult = dcdio.write_dcdstep(outfile, tx, ty, tz, i + 1)
i += 1
result = dcdio.close_dcd_write(outfile)
return
def close_dcd_write(self,filepointer):
'''
This method closes a dcd file.
'''
result = dcdio.close_dcd_write(filepointer)
print 'result = ',result
return
for blah in range(nset):
print ".",
sys.stdout.flush()
x = x + 5.0
y = y + 5.0
z = z + 5.0
stepresult = dcdio.write_dcdstep(fp, x, y, z, blah)
end_time = time.time()
dt = end_time - start_time
print '\ntotal time = ', dt, ' time per structure = ', dt / nset
dcdio.close_dcd_write(fp)
filename = '200c.dcd'
filename = 'c7.dcd'
ifp = dcdio.open_dcd_read(filename)
nnatoms = 0
nset = 0
istart = 0
nsavc = 0
delta = 0.0
namnf = 0
freeindexes = []
reverseEndian = 0
charmm = 0
for blah in range(nset):
print ".",
sys.stdout.flush()
x=x+5.0
y=y+5.0
z=z+5.0
stepresult=dcdio.write_dcdstep(fp,x,y,z,blah)
end_time=time.time()
dt=end_time-start_time
print '\ntotal time = ',dt,' time per structure = ',dt/nset
dcdio.close_dcd_write(fp)
filename='200c.dcd'
filename='c7.dcd'
ifp=dcdio.open_dcd_read(filename)
nnatoms=0 ; nset=0 ; istart=0 ; nsavc=0 ; delta=0.0
namnf=0 ; freeindexes=[] ; reverseEndian=0 ; charmm=0
print 'nnatoms = ',nnatoms
print 'nset = ',nset
print 'freeindexes = ',freeindexes
readheaderresult,nnatoms,nset,istart,nsavc,delta,namnf,reverseEndian,charmm=dcdio.read_dcdheader(ifp)
