def main(args):
if args.debug:
main_load()
# check the validity of output file name, do backup
output = args.optf
if output is None:
outputfile = '{0:s}.output.xvg'.format(args.grof)
else:
outputfile = output
backup_old_output(outputfile)
# Do some logging at the beginning
outputf = open(outputfile, 'w')
beginning_time = write_header(outputf)
# do calculation
result = calc_bond_length(args.grof, args.xtcf, args.btime, args.etime,
args.debug)
# write results to the outputfile
for r in result:
outputf.write(r)
# Do some logging at the end
write_footer(outputf, beginning_time)
outputf.close()
def main(ARGS):
if ARGS.debug:
main_load()
# check the validity of output file name, do backup
output = ARGS.optf
if output is None:
outputfile = '{0:s}.output.xvg'.format(ARGS.grof)
else:
outputfile = output
backup_old_output(outputfile)
# Do some logging at the beginning
outputf = open(outputfile, 'w')
beginning_time = write_header(outputf)
# do calculation
result = count_interactions(
ARGS.grof,
ARGS.xtcf,
ARGS.btime,
ARGS.cutoff * 10, # convert to angstrom from nm
ARGS.debug)
# write results to the outputfile
outputf.write('# {0:>10s}{1:>8s}\n'.format('time', 'num'))
for r in result:
outputf.write(r)
# Do some logging at the end
write_footer(outputf, beginning_time)
outputf.close()
def main(args):
utils.main_load()
# check the validity of output file name, do backup
output = args.optf
if output is None:
outputfile = '{0:s}.output.xvg'.format(args.grof)
else:
outputfile = output
utils.backup(outputfile)
# Do some logging at the beginning
outputf = open(outputfile, 'w')
beginning_time = utils.write_header(outputf)
# do calculation
result = calc_dihedral(args.grof, args.xtcf, args.btime, args.etime)
# write results to the outputfile
for r in result:
outputf.write(r)
# Do some logging at the end
utils.write_footer(outputf, beginning_time)
outputf.close()
def main(args):
utils.main_load()
# check the validity of output file name, do backup
output = args.optf
if output is None:
outputfile = '{0:s}.output.xvg'.format(args.grof)
else:
outputfile = output
utils.backup(outputfile)
# Do some logging at the beginning
outputf = open(outputfile, 'w')
beginning_time = utils.write_header(outputf)
# do calculation
result = calc_dihedral(args.grof, args.xtcf, args.btime, args.etime)
# write results to the outputfile
for r in result:
outputf.write(r)
# Do some logging at the end
utils.write_footer(outputf, beginning_time)
outputf.close()
def main(ARGS):
if ARGS.debug:
main_load()
# check the validity of output file name, do backup
output = ARGS.optf
if output is None:
outputfile = '{0:s}.output.xvg'.format(ARGS.grof)
else:
outputfile = output
backup_old_output(outputfile)
# Do some logging at the beginning
outputf = open(outputfile, 'w')
beginning_time = write_header(outputf)
# do calculation
result = count_interactions(
ARGS.grof,
ARGS.xtcf,
ARGS.btime,
ARGS.cutoff * 10, # convert to angstrom from nm
ARGS.debug)
# write results to the outputfile
outputf.write('# {0:>10s}{1:>8s}\n'.format('time', 'num'))
for r in result:
outputf.write(r)
# Do some logging at the end
write_footer(outputf, beginning_time)
outputf.close()
def main(args):
utils.main_load()
outputfile = args.optf if args.optf else '{0:s}.sespacing.xvg'.format(args.grof)
utils.backup(outputfile)
outputf = open(outputfile, 'w')
beginning_time = utils.write_header(outputf)
# This line will be used when there is a better code design
# if ARGS.atom_sel is None:
# raise ValueError("atom_selection must be specified, check --atom_selection option!")
# do calculation
ijdist_dict = sequence_spacing(args.grof, args.xtcf, args.btime, args.etime,
args.peptide_length, args.atom_sel)
# cannot yield from sequence_spacing function because the result cannot be
# calculated until all frames have been looped through
# write headers
outputf.write('# {0:8s}{1:20s}{2:20s}{3:10s}\n'.format('i-j', 'average', 'std', 'num_of_data_points'))
# write results to the outputfile
for k in sorted(ijdist_dict.keys()):
data = np.array(ijdist_dict[k])
mean = data.mean() # mean of ijdist
std = data.std() # standard deviation of ijdist
num = len(data) # num of data in that ijdist
outputf.write('{0:8d}{1:20.8f}{2:20.8f}{3:10d}\n'.format(k, mean, std, num))
# Do some logging at the end
utils.write_footer(outputf, beginning_time)
outputf.close()
def main(args):
utils.main_load()
outputfile = args.optf if args.optf else '{0:s}.sespacing.xvg'.format(
args.grof)
utils.backup(outputfile)
outputf = open(outputfile, 'w')
beginning_time = utils.write_header(outputf)
# This line will be used when there is a better code design
# if ARGS.atom_sel is None:
# raise ValueError("atom_selection must be specified, check --atom_selection option!")
# do calculation
ijdist_dict = sequence_spacing(args.grof, args.xtcf, args.btime,
args.etime, args.peptide_length,
args.atom_sel)
# cannot yield from sequence_spacing function because the result cannot be
# calculated until all frames have been looped through
# write headers
outputf.write('# {0:8s}{1:20s}{2:20s}{3:10s}\n'.format(
'i-j', 'average', 'std', 'num_of_data_points'))
# write results to the outputfile
for k in sorted(ijdist_dict.keys()):
data = np.array(ijdist_dict[k])
mean = data.mean() # mean of ijdist
std = data.std() # standard deviation of ijdist
num = len(data) # num of data in that ijdist
outputf.write('{0:8d}{1:20.8f}{2:20.8f}{3:10d}\n'.format(
k, mean, std, num))
# Do some logging at the end
utils.write_footer(outputf, beginning_time)
outputf.close()
def main(args):
if args.debug:
main_load()
# check the validity of output file name, do backup
output = args.optf
if output is None:
outputfile = '{0:s}.output.xvg'.format(args.grof)
else:
outputfile = output
backup_old_output(outputfile)
# Do some logging at the beginning
outputf = open(outputfile, 'w')
beginning_time = write_header(outputf)
# do calculation
result = calc_bond_length(
args.grof,
args.xtcf,
args.btime,
args.etime,
args.debug)
# write results to the outputfile
for r in result:
outputf.write(r)
# Do some logging at the end
write_footer(outputf, beginning_time)
outputf.close()
def main(args):
main_load()
output = args.optf
if output is None:
outputfile = '{0:s}.output.xtc'.format(args.tprf)
else:
outputfile = output
backup(outputfile)
# do calculation
trjcat_plus(args.xtcf, args.tprf, outputfile)
def main(args):
U.main_load()
outputfile = args.optf if args.optf else '{0:s}.rama.xvg'.format(args.grof)
U.backup(outputfile)
outputf = open(outputfile, 'w')
beginning_time = U.write_header(outputf)
result = calc_rama(args.grof, args.xtcf, args.btime, args.etime)
# write headers
outputf.write('# {0:>10s}{1:>8s}\n'.format('phi', 'psi', 'resname-resid'))
# write results to the outputfile
for r in result:
outputf.write(r)
# Do some logging at the end
U.write_footer(outputf, beginning_time)
outputf.close()
def main(args):
utils.main_load()
outputfile = args.optf if args.optf else '{0:s}.unun.xvg'.format(args.grof)
utils.backup(outputfile)
outputf = open(outputfile, 'w')
beginning_time = utils.write_header(outputf)
result = count_interactions(args.grof, args.xtcf, args.btime, args.etime, args.cutoff)
# write headers
outputf.write('# {0:>10s}{1:>8s}\n'.format('time', 'num'))
# write results to the outputfile
for r in result:
outputf.write(r)
# Do some logging at the end
utils.write_footer(outputf, beginning_time)
outputf.close()
def main(args):
U.main_load()
outputfile = args.optf if args.optf else '{0:s}.rama.xvg'.format(args.grof)
U.backup(outputfile)
outputf = open(outputfile, 'w')
beginning_time = U.write_header(outputf)
result = calc_rama(args.grof, args.xtcf, args.btime, args.etime)
# write headers
outputf.write('# {0:>10s}{1:>8s}\n'.format('phi', 'psi', 'resname-resid'))
# write results to the outputfile
for r in result:
outputf.write(r)
# Do some logging at the end
U.write_footer(outputf, beginning_time)
outputf.close()
def main(args):
utils.main_load()
outputfile = args.optf if args.optf else '{0:s}.unun.xvg'.format(args.grof)
utils.backup(outputfile)
outputf = open(outputfile, 'w')
beginning_time = utils.write_header(outputf)
result = count_interactions(args.grof, args.xtcf, args.btime, args.etime,
args.cutoff)
# write headers
outputf.write('# {0:>10s}{1:>8s}\n'.format('time', 'num'))
# write results to the outputfile
for r in result:
outputf.write(r)
# Do some logging at the end
utils.write_footer(outputf, beginning_time)
outputf.close()
def main(cmd_args):
args = get_args(cmd_args)
utils.main_load()
output = args.optf
if output is None:
# it's a log since the results are written to the h5 file directly
outputfile = '{0:s}.output.log'.format(args.grof)
else:
outputfile = output
utils.backup(outputfile)
outputf = open(outputfile, 'w')
beginning_time = utils.write_header(outputf)
A = args
if not os.path.exists(A.h5):
raise IOError('{0} does not exist'.format(A.h5))
# *10: convert to angstrom from nm
result = count_interactions(A)
path = os.path.join('/', os.path.dirname(A.xtcf))
tb_name = os.path.join(path, 'unun_map')
h5 = tables.openFile(A.h5, mode='a')
if h5.__contains__(tb_name):
logger.info(
'found {0} already in {0}, replacing with new calculated values'.
format(tb_name, A.h5))
_ = h5.getNode(tb_name)
_.remove()
h5.createArray(where=path, name='unun_map', object=result)
h5.close()
utils.write_footer(outputf, beginning_time)
outputf.close()
def main(cmd_args):
args = get_args(cmd_args)
utils.main_load()
output = args.optf
if output is None:
# it's a log since the results are written to the h5 file directly
outputfile = '{0:s}.output.log'.format(args.grof)
else:
outputfile = output
utils.backup(outputfile)
outputf = open(outputfile, 'w')
beginning_time = utils.write_header(outputf)
A = args
if not os.path.exists(A.h5):
raise IOError('{0} does not exist'.format(A.h5))
# *10: convert to angstrom from nm
result = count_interactions(A)
path = os.path.join('/', os.path.dirname(A.xtcf))
tb_name = os.path.join(path, 'unun_map')
h5 = tables.openFile(A.h5, mode='a')
if h5.__contains__(tb_name):
logger.info('found {0} already in {0}, replacing with new calculated values'.format(tb_name, A.h5))
_ = h5.getNode(tb_name)
_.remove()
h5.createArray(where=path, name='unun_map', object=result)
h5.close()
utils.write_footer(outputf, beginning_time)
outputf.close()