def main():
args = parse_cmd()
infile = args.infile
if args.outputfile is None:
outputfile = infile[:-4] + '_with_cid.pdb'
else:
outputfile = args.outputfile
cf.backup_file(outputfile)
natoms = int(args.natoms)
exresname = args.exresname
doit(infile, outputfile, natoms, exresname)
def main():
"""
basically it verifies the options and conf_dict first, then loop_xvgs,
passing whatever should be parsed, ugly code!!! aaaaaahhh....
"""
args = parse_cmd()
# Verify the iterms in args
conf = args.conf
if not os.path.exists(conf):
raise IOError("{0} cannot found".format(conf))
conf_dict = ConfigObj(conf)
SEQS, CDTS, TMPS, NUMS = argparse_action.get_sctn(args, conf_dict['system'])
h5filename = conf_dict['data']['h5filename']
title = conf_dict['data']['title']
# About the property
ppty = args.ppty
p_conf = conf_dict['properties'][ppty] # property configuration
property_obj = h5t.Property(ppty) # including table desc & schema
try:
ogd = p_conf['ogd'] # contains xvg_name and table_name patterns
except KeyError:
print "#" * 20
print '"ogd" not specified in {0} in {1}'.format(ppty, conf)
print "#" * 20
sys.exit(1)
if not args.nobk:
backup_file(h5filename) # later when this script matures, this step may not be necessary
# Start dealing with the h5 file now
h5file = tables.openFile(h5filename, mode="a", title=title)
filters = tables.Filters(complevel=8, complib='zlib')
# zx_create_group is redundant and ugly code, I amd looking for a way to
# overwrite creatGroup in table.file.File 2012-03-16
ppty_group = zx_create_group(h5file, '/', ppty, filters=filters, title=property_obj.desc) # property group
ogd_group = zx_create_group(h5file, ppty_group._v_pathname, 'ogd', filters)
ogd_path = ogd_group._v_pathname # should == ogd_path = os.path.join('/', ppty, 'ogd')
# loop through xvg files and create a table for each one
# ugly code!!! aaaaaahhh Should I learn loop? and make it more clear!
# parsing so many args are really confusing
loop_xvgs(SEQS, CDTS, TMPS, NUMS,
ppty, h5file, property_obj, ogd, ogd_path
)
#!/usr/bin/env python
import shutil
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("-f", dest="inf", required=True)
args = parser.parse_args()
from common_func import backup_file
# The script will cause error if comment comtains "="
# But I won't debug now since it's enough for now for personal use
old_file = backup_file(args.inf) # the returned backuped file
lines = []
with open(old_file) as inf:
for line in inf:
if not line.startswith(';') and line.strip():
k, tropov = [i.strip() for i in line.split('=')] # key, tropo_value
if ';' in tropov:
v, comv = tropov.split(';') # comv: comment in the value
v = v.split()
comv = '; ' + comv.strip()
else:
comv = ' '
v = tropov.split()
v = ''.join(i.strip().ljust(15) for i in v)
lines.append("{0:30s} = {1:30s}{2}\n".format(k, v, comv))
else:
lines.append(line)