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
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
print 'nsavc = ', nsavc
print 'delta = ', delta
print 'namnf = ', namnf
print 'reverseEndian = ', reverseEndian
print 'charmm = ', charmm
x = numpy.zeros((nset, nnatoms), dtype=numpy.float32)
y = numpy.zeros((nset, nnatoms), dtype=numpy.float32)
z = numpy.zeros((nset, nnatoms), dtype=numpy.float32)
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 print 'nsavc = ',nsavc print 'delta = ',delta print 'namnf = ',namnf print 'reverseEndian = ',reverseEndian print 'charmm = ',charmm x=numpy.zeros((nset,nnatoms),dtype=numpy.float32) y=numpy.zeros((nset,nnatoms),dtype=numpy.float32) z=numpy.zeros((nset,nnatoms),dtype=numpy.float32)
