def read_single_dcd_step(self, filename, frame):
'''
This method reads a single dcd step in the Charmm/Xplor data format.
The method simply reads all frames up until frame and then assigns
coordinates to the last frame (no seek option is utilizied)
'''
infile = dcdio.open_dcd_read(filename)
num_fixed = 0
result = 1
print 'calling read dcd header'
readheaderresult, nnatoms, nset, istart, nsavc, delta, namnf, reverseEndian, charmm = dcdio.read_dcdheader(
infile)
if (readheaderresult != 0):
print 'failed to read header'
print 'readheaderresult = ', readheaderresult
print 'done with read dcd header'
coor = numpy.zeros((1, nnatoms, 3), numpy.float)
tx = numpy.zeros(nnatoms, dtype=numpy.float32)
ty = numpy.zeros(nnatoms, dtype=numpy.float32)
tz = numpy.zeros(nnatoms, dtype=numpy.float32)
first = 1 # since num_fixed = 0 ; the "first" variable is inconsequential
print 'calling read_dcdstep'
for i in xrange(frame):
result = dcdio.read_dcdstep(infile, tx, ty, tz, num_fixed, first,
reverseEndian, charmm)
print 'back from read_dcdstep'
print 'result = ', result
coor[0, :, 0] = tx.astype(numpy.float)
coor[0, :, 1] = ty.astype(numpy.float)
coor[0, :, 2] = tz.astype(numpy.float)
result = dcdio.close_dcd_read(infile)
self._coor = numpy.array(coor)
if (result != 0):
print 'failed to read coordinates'
print 'result = ', result
return
def read_dcd(self, filename):
'''
This method reads data in the Charmm/Xplor data format.
'''
infile = dcdio.open_dcd_read(filename)
nnatoms = 0
nset = 0
istart = 0
nsavc = 0
delta = 0.0
namnf = 0
freeindexes = []
reverseEndian = 0
charmm = 0
readheaderresult, nnatoms, nset, istart, nsavc, delta, namnf, reverseEndian, charmm = dcdio.read_dcdheader(
infile)
coor = numpy.zeros((nset, nnatoms, 3), numpy.float)
num_fixed = 0
result = 1
sum = 0.0
for i in xrange(nset):
print '.',
sys.stdout.flush()
read_start_time = time.time()
tx = numpy.zeros(nnatoms, dtype=numpy.float32)
ty = numpy.zeros(nnatoms, dtype=numpy.float32)
tz = numpy.zeros(nnatoms, dtype=numpy.float32)
result = dcdio.read_dcdstep(infile, tx, ty, tz, num_fixed, i,
reverseEndian, charmm)
read_end_time = time.time()
sum += read_end_time - read_start_time
coor[i, :, 0] = tx.astype(numpy.float)
coor[i, :, 1] = ty.astype(numpy.float)
coor[i, :, 2] = tz.astype(numpy.float)
result = dcdio.close_dcd_read(infile)
self._coor = numpy.array(coor)
print
return
def read_single_dcd_step(self,filename,frame):
'''
This method reads a single dcd step in the Charmm/Xplor data format.
The method simply reads all frames up until frame and then assigns
coordinates to the last frame (no seek option is utilizied)
'''
infile=dcdio.open_dcd_read(filename)
num_fixed=0
result = 1
print 'calling read dcd header'
readheaderresult,nnatoms,nset,istart,nsavc,delta,namnf,reverseEndian,charmm=dcdio.read_dcdheader(infile)
if(readheaderresult!=0):
print 'failed to read header'
print 'readheaderresult = ',readheaderresult
print 'done with read dcd header'
coor=numpy.zeros((1,nnatoms,3),numpy.float)
tx=numpy.zeros(nnatoms,dtype=numpy.float32)
ty=numpy.zeros(nnatoms,dtype=numpy.float32)
tz=numpy.zeros(nnatoms,dtype=numpy.float32)
first = 1 # since num_fixed = 0 ; the "first" variable is inconsequential
print 'calling read_dcdstep'
for i in xrange(frame):
result=dcdio.read_dcdstep(infile,tx,ty,tz,num_fixed,first,reverseEndian,charmm)
print 'back from read_dcdstep'
print 'result = ',result
coor[0,:,0]=tx.astype(numpy.float) ; coor[0,:,1]=ty.astype(numpy.float) ; coor[0,:,2]=tz.astype(numpy.float)
result = dcdio.close_dcd_read(infile)
self._coor=numpy.array(coor)
if(result!=0):
print 'failed to read coordinates'
print 'result = ',result
return
def read_dcd(self,filename):
'''
This method reads data in the Charmm/Xplor data format.
'''
infile=dcdio.open_dcd_read(filename)
nnatoms=0 ; nset=0 ; istart=0 ; nsavc=0 ; delta=0.0
namnf=0 ; freeindexes=[] ; reverseEndian=0 ; charmm=0
readheaderresult,nnatoms,nset,istart,nsavc,delta,namnf,reverseEndian,charmm=dcdio.read_dcdheader(infile)
coor=numpy.zeros((nset,nnatoms,3),numpy.float)
num_fixed=0
result=1
sum=0.0
print('Reading DCD')
for i in xrange(nset):
sys.stdout.write('\r')
eq = int(numpy.ceil(numpy.true_divide(i*100,nset*5)))
sys.stdout.write("[{:20s}] {}/{} frames ".format('='*eq, i+1,nset))
sys.stdout.flush()
read_start_time=time.time()
tx=numpy.zeros(nnatoms,dtype=numpy.float32)
ty=numpy.zeros(nnatoms,dtype=numpy.float32)
tz=numpy.zeros(nnatoms,dtype=numpy.float32)
result=dcdio.read_dcdstep(infile,tx,ty,tz,num_fixed,i,reverseEndian,charmm)
read_end_time=time.time()
sum+=read_end_time-read_start_time
coor[i,:,0]=tx.astype(numpy.float) ; coor[i,:,1]=ty.astype(numpy.float) ; coor[i,:,2]=tz.astype(numpy.float)
print
result = dcdio.close_dcd_read(infile)
self._coor=numpy.array(coor)
print
return
def open_dcd_read(self,filename):
'''
This method opens a file to read in the Charmm/Xplor data format.
by calling a pre-compiled C module (dcdio).
'''
filepointer=dcdio.open_dcd_read(filename)
num_fixed=0
result = 1
readheaderresult,nnatoms,nset,istart,nsavc,delta,namnf,reverseEndian,charmm=dcdio.read_dcdheader(filepointer)
if(readheaderresult!=0):
print 'failed to read header'
print 'readheaderresult = ',readheaderresult
dcdfile = [filepointer,nnatoms,nset,reverseEndian,charmm]
return dcdfile
def read_dcd(self,filename):
'''
This method reads data in the Charmm/Xplor data format.
'''
infile=dcdio.open_dcd_read(filename)
nnatoms=0 ; nset=0 ; istart=0 ; nsavc=0 ; delta=0.0
namnf=0 ; freeindexes=[] ; reverseEndian=0 ; charmm=0
readheaderresult,nnatoms,nset,istart,nsavc,delta,namnf,reverseEndian,charmm=dcdio.read_dcdheader(infile)
coor=numpy.zeros((nset,nnatoms,3),numpy.float)
num_fixed=0
result=1
sum=0.0
for i in xrange(nset):
print '.',
sys.stdout.flush()
read_start_time=time.time()
tx=numpy.zeros(nnatoms,dtype=numpy.float32)
ty=numpy.zeros(nnatoms,dtype=numpy.float32)
tz=numpy.zeros(nnatoms,dtype=numpy.float32)
result=dcdio.read_dcdstep(infile,tx,ty,tz,num_fixed,i,reverseEndian,charmm)
read_end_time=time.time()
sum+=read_end_time-read_start_time
coor[i,:,0]=tx.astype(numpy.float) ; coor[i,:,1]=ty.astype(numpy.float) ; coor[i,:,2]=tz.astype(numpy.float)
result = dcdio.close_dcd_read(infile)
self._coor=numpy.array(coor)
print
return
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
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)
print 'read header result = ',readheaderresult
print 'nnatoms = ',nnatoms
print 'nset = ',nset
print 'istart = ',istart