def _parse_header(self):
"""Parses in the first header.
Not for public use
"""
log.debug('---In dcd.py, parse_header()')
#process the first header block
header1 = self._fo.read(92)
header1_format=\
"i---cccci---i---i---i---xxxxxxxxxxxxxxxxxxxxf---i---i---xxxxxxxxxxxxxxxxxxxxxxxxxxxxi---i---"
# |1 |5 |10 |15 |20 |25 |30 |35 |40 |45 |50 |55 |60 |65 |70 |75 |80 |85 |90
#|header size=84 |nframes*tstep |tstep_size |charm_ver
# |CORD=has coordinates |block_a |header_size=84
# |nframes |block_b
# |starting timestep
# |timestep between coord sets
header1_format = string.replace(header1_format, "-", "")
header1 = struct.unpack(header1_format, header1)
header1_size1, c1, c2, c3, c4, self._nframes, self._firsttstep, self._dcdfreq, self._ntsteps, self._tstep_size, self._block_a, self._block_b, self._charm_v, header1_size2 = header1 #unpack the tuple header1
self._dcdtype = "".join((c1,c2,c3,c4)) #get the data-type field. I it should always be cord...
if header1_size1 != 84 or header1_size2 !=84:
log.error("error-- header size fields not correct (should be 84)\n")
if self._block_a != 0 or self._block_b != 0:
log.info("I've found a signal possibly indicating an extra record block")
log.info(" I'll try to parse it, but it might fail. Also, I won't use")
log.info(" any data from them.")
def _parse_unknown_block(self, mode=None):
"""This parses a block, doing nothing with it.
"""
(length1, ) = struct.unpack("i", self._fo.read(4))
data = self._fo.read(length1)
(length2, ) = struct.unpack("i", self._fo.read(4))
if length1 != length2:
log.error("We tried to read the extra block, but it didn't work out quite right.")
if mode:
values = struct.unpack(mode, data)
return values
def _parse_atoms(self):
"""Parses in the natoms record.
Not for public use.
"""
##
##Parse the number of atoms
##
#format: 3 ints, first one is blocksize (must equal 4), second is natoms, third is blocksize (must equal 4)
log.debug("---in dcd.py, parse_atoms()")
blocksize, self._natoms, blocksize2 = struct.unpack("iii", self._fo.read(12))
if blocksize != 4 or blocksize2 != 4:
log.error("blocksizes in the number of atoms record is broken\n")
def _parse_title(self):
"""Parses in the title.
Not for public use.
"""
log.debug('---In dcd.py, parse_title()')
##
##Parse the title field
##
#title field format: int that specifies the block size = 80n + 4
# int that specifies the number of 80-char title blocks = x
# x * 80 char title blocks
# ...
# int that specifies the block size = 80n +4
title = ""
blocksize, n = struct.unpack("ii", self._fo.read(8)) #read in 8 bytes, convert to ints, store in blocksize, n
if blocksize != 80*n+4:
log.error("beginningblock size in title block is wrong\n")
for i in range(0,n):
title = title + self._fo.read(80) # read the next title string onto the current one.
if (blocksize, ) != struct.unpack("i", self._fo.read(4)):
log.error("ending blocksize on the title block is not correct !\n")
self._title = title