def read_dcd_step(self,dcdfile,frame,**kwargs):
'''
This method reads a single dcd step in the Charmm/Xplor data format.
'''
num_fixed=0
filepointer = dcdfile[0]
nnatoms = dcdfile[1]
reverseEndian = dcdfile[3]
charmm = dcdfile[4]
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(filepointer,tx,ty,tz,num_fixed,frame,reverseEndian,charmm)
self._coor[0,:,0]=tx.astype(numpy.float) ; self._coor[0,:,1]=ty.astype(numpy.float) ; self._coor[0,:,2]=tz.astype(numpy.float)
if len(kwargs) < 1:
sys.stdout.write('.',)
elif not kwargs['no_print']:
try:
sys.stdout.write('.',)
except:
pass
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
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 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
i = 0
#try:
print 'reading dcd file'
start_time = time.time()
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(ifp, tx, ty, tz, num_fixed, i, reverseEndian,
charmm)
read_end_time = time.time()
sum += read_end_time - read_start_time
x[i][:] = tx
y[i][:] = ty
z[i][:] = tz
end_time = time.time()
dt = end_time - start_time
print '\nread total_time = ', sum, ' time per structure = ', sum / nset
print 'total_time = ', dt, ' time per structure = ', dt / nset
print 'ratio(total time) = ', dt / sum
print 'ratio(per structure) = ', (dt / nset) / (sum / nset)
i=0 #try: print 'reading dcd file' start_time=time.time() 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(ifp,tx,ty,tz,num_fixed,i,reverseEndian,charmm) read_end_time=time.time() sum+=read_end_time-read_start_time x[i][:]=tx ; y[i][:]=ty ; z[i][:]=tz end_time=time.time() dt=end_time-start_time print '\nread total_time = ',sum,' time per structure = ',sum/nset print 'total_time = ',dt,' time per structure = ',dt/nset print 'ratio(total time) = ',dt/sum print 'ratio(per structure) = ',(dt/nset)/(sum/nset)