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 open_dcd_write(self,filename):
'''
This method opens a file and writes the headerfile in the Charmm/Xplor data format.
by calling a pre-compiled C module (dcdio).
This function will OVERWRITE a file with the same name without prompting.
'''
filepointer=dcdio.open_dcd_write(filename)
self.write_dcd_header(filepointer,1)
return filepointer
natoms = A.natoms()
x = A.coor()[:, 0]
y = A.coor()[:, 1]
z = A.coor()[:, 2]
#x=[1.0,2.0,3.0] ; y=[1.0,2.0,3.0] ; z=[1.0,2.0,3.0]
x = numpy.array(x, numpy.float32)
y = numpy.array(y, numpy.float32)
z = numpy.array(z, numpy.float32)
filename = 'c7.dcd'
fp = dcdio.open_dcd_write(filename)
nset = 200
istart = 1
nsavc = 1
delta = 1.0
headerresult = dcdio.write_dcdheader(fp, filename, natoms, nset, istart, nsavc,
delta)
print 'writing ' + str(nset) + ' to disk'
start_time = time.time()
for blah in range(nset):
print ".",
sys.stdout.flush()
natoms = A.natoms()
x=A.coor()[:,0]
y=A.coor()[:,1]
z=A.coor()[:,2]
#x=[1.0,2.0,3.0] ; y=[1.0,2.0,3.0] ; z=[1.0,2.0,3.0]
x=numpy.array(x,numpy.float32)
y=numpy.array(y,numpy.float32)
z=numpy.array(z,numpy.float32)
filename='c7.dcd'
fp=dcdio.open_dcd_write(filename)
nset=200; istart=1 ; nsavc=1 ; delta=1.0
headerresult=dcdio.write_dcdheader(fp,filename,natoms,nset,istart,nsavc,delta)
print 'writing '+str(nset)+' to disk'
start_time=time.time()
for blah in range(nset):
print ".",
sys.stdout.flush()
x=x+5.0
y=y+5.0
z=z+5.0