def rex_map(log_fname, out_dir, dcd_fnames, log_ftype='auto'):
# validate inputs
if not isinstance(log_fname, basestring):
raise TypeError("invalid log_fname")
if not isinstance(out_dir, basestring):
raise TypeError("invalid out_dir")
if not dcd_fnames:
raise ValueError("must specify input dcd files")
# parse rexlog
rexlog = ExchangeLog(fname=log_fname, validate=True, ftype=log_ftype)
# parse nsavc value
nsavc = get_nsavc(*dcd_fnames)
# make nsavc is compatible with step values from log
for entry in rexlog:
if entry.step % nsavc != 0:
raise ValueError("bad value for nsavc, is not multiple of step %d in exchangelog entry %d" % (entry.step, entry.exchange))
# create output fnames
out_dcd_fnames = []
for i, temp in enumerate(rexlog.temp_array):
fname = _myexpandpath(out_dir) + os.path.sep + 'rex_map_%02d_%6.2f.dcd' % (i, temp)
out_dcd_fnames.append(fname)
# write headers
with open_dcd(dcd_fnames[0], mode='r') as fp:
base_header = fp.export_header()
for fname in out_dcd_fnames:
with open_dcd(fname, mode='wb') as fp:
tmp_header = {}
tmp_header.update(base_header)
tmp = ["\x02\x00\x00\x00"]
tmp.append("%-80s" % "* This DCD was generated by rex_map")
tmp.append("%-80s" % "* This DCD index is %d, and temp is %d" % (i,rexlog.temp_array[i]))
tmp_header['title'] = ''.join(tmp)
fp.import_header(tmp_header)
fp.write_header()
# write frames
inp_dcd = [ open_dcd(fname, mode='rb') for fname in dcd_fnames ]
out_dcd = [ open_dcd(fname, mode='ab') for fname in out_dcd_fnames ]
## ignore entries where repeat != 1
iterator = ( entry for entry in rexlog if entry.repeat == 1 )
current_step = 0 # how many steps have we written?
for entry in iterator:
# print "exchange number: %d" % entry.exchange
while current_step < entry.step:
# print " step number: %d" % (current_step + nsavc)
###################
# do work #########
###################
for i, out in enumerate(out_dcd):
# print " reading from: %s" % dcd_fnames[entry.index_array[i]-1]
# print " writing to: %s" % out.name
out.write(inp_dcd[entry.index_array[i]-1].read_frame())
##################
# done with work #
##################
current_step += nsavc
def get_nsavc(*fnames):
if not fnames:
raise ValueError("must specify input dcd files")
nsavc_array = []
for fname in fnames:
with open_dcd(fname, mode='r') as fp:
nsavc_array.append(fp.nsavc)
nsavc0 = nsavc_array[0]
for nsavc in nsavc_array:
if nsavc != nsavc0:
raise ValueError('bad value for nsavc, first dcd has nsavc = %d but dcd file "%s" has value of %d' % (nsavc, dcd_fnames[i], nsav))
return nsavc0
