def main(argv=None):
""" Runs the main program.
@param argv: The command line arguments.
:return: The return code for the program's termination.
"""
args, ret = parse_cmdline(argv)
if ret != 0:
return ret
if args.src_file is not None:
proc_data = calc_for_wham(args.src_file)
write_csv(proc_data, create_out_fname(args.src_file, prefix=OUT_PFX), COLVAR_WHAM_KEY_SEQ)
else:
found_files = find_files_by_dir(args.base_dir, args.pattern)
logger.debug("Found '%d' dirs with files to process", len(found_files))
# noinspection PyCompatibility
for f_dir, files in found_files.iteritems():
if not files:
logger.warn("No files found for dir '%s'", f_dir)
continue
for colvar_path in ([os.path.join(f_dir, tgt) for tgt in files]):
proc_data = calc_for_wham(colvar_path)
f_name = create_out_fname(colvar_path, prefix=OUT_PFX)
if allow_write(f_name, overwrite=args.overwrite):
list_to_file([str(d['r']) for d in proc_data if 'r' in d], f_name)
# write_csv(proc_data, f_name, COLVAR_WHAM_KEY_SEQ, extrasaction="ignore")
return 0 # success
def main(argv=None):
""" Runs the main program.
@param argv: The command line arguments.
:return: The return code for the program's termination.
"""
args, ret = parse_cmdline(argv)
if ret != 0:
return ret
if args.src_file is not None:
proc_data = calc_for_wham(args.src_file)
write_csv(proc_data, create_out_fname(args.src_file, prefix=OUT_PFX),
COLVAR_WHAM_KEY_SEQ)
else:
found_files = find_files_by_dir(args.base_dir, args.pattern)
logger.debug("Found '%d' dirs with files to process", len(found_files))
# noinspection PyCompatibility
for f_dir, files in found_files.iteritems():
if not files:
logger.warn("No files found for dir '%s'", f_dir)
continue
for colvar_path in ([os.path.join(f_dir, tgt) for tgt in files]):
proc_data = calc_for_wham(colvar_path)
f_name = create_out_fname(colvar_path, prefix=OUT_PFX)
if allow_write(f_name, overwrite=args.overwrite):
list_to_file([str(d['r']) for d in proc_data if 'r' in d],
f_name)
# write_csv(proc_data, f_name, COLVAR_WHAM_KEY_SEQ, extrasaction="ignore")
return 0 # success
def main(argv=None):
""" Runs the main program.
:param argv: The command line arguments.
:return: The return code for the program's termination.
"""
args, ret = parse_cmdline(argv)
if ret != GOOD_RET or args is None:
return ret
kbt = calc_kbt(args.temp)
if args.src_file is not None:
proc_data = to_zero_point(calc_rad(args.src_file, kbt))
write_csv(proc_data, create_out_fname(args.src_file, prefix=OUT_PFX),
RAD_KEY_SEQ)
else:
found_files = find_files_by_dir(args.base_dir, args.pattern)
logger.debug("Found '{}' dirs with files to process".format(
len(found_files)))
# noinspection PyCompatibility
for f_dir, files in found_files.items():
if not files:
logger.warn("No files found for dir '{}'".format(f_dir))
continue
for pmf_path in ([os.path.join(f_dir, tgt) for tgt in files]):
proc_data = to_zero_point(calc_rad(pmf_path, kbt))
f_name = create_out_fname(pmf_path, prefix=OUT_PFX)
if allow_write(f_name, overwrite=args.overwrite):
write_csv(proc_data, f_name, RAD_KEY_SEQ)
return GOOD_RET # success
def main(argv=None):
""" Runs the main program.
:param argv: The command line arguments.
:return: The return code for the program's termination.
"""
args, ret = parse_cmdline(argv)
if ret != GOOD_RET or args is None:
return ret
kbt = calc_kbt(args.temp)
if args.src_file is not None:
proc_data = to_zero_point(calc_rad(args.src_file, kbt))
write_csv(proc_data, create_out_fname(args.src_file, prefix=OUT_PFX), RAD_KEY_SEQ)
else:
found_files = find_files_by_dir(args.base_dir, args.pattern)
logger.debug("Found '{}' dirs with files to process".format(len(found_files)))
# noinspection PyCompatibility
for f_dir, files in found_files.iteritems():
if not files:
logger.warn("No files found for dir '{}'".format(f_dir))
continue
for pmf_path in ([os.path.join(f_dir, tgt) for tgt in files]):
proc_data = to_zero_point(calc_rad(pmf_path, kbt))
f_name = create_out_fname(pmf_path, prefix=OUT_PFX)
if allow_write(f_name, overwrite=args.overwrite):
write_csv(proc_data, f_name, RAD_KEY_SEQ)
return GOOD_RET # success
def write_avg_rmsd(tgt_dir, rmsd, overwrite=False):
"""
Writes out all of the described RMSD files into the given target directory.
:param tgt_dir: The data where the files will go.
:param rmsd: A dict of an array of floats keyed by file name.
:param overwrite: Whether to overwrite existing files.
"""
for rmsd_fname, data in rmsd.items():
f_name = os.path.join(tgt_dir, rmsd_fname)
if allow_write(f_name, overwrite=overwrite):
write_rmsd(data, f_name)
def write_avg_rmsd(tgt_dir, rmsd, overwrite=False):
"""
Writes out all of the described RMSD files into the given target directory.
:param tgt_dir: The data where the files will go.
:param rmsd: A dict of an array of floats keyed by file name.
:param overwrite: Whether to overwrite existing files.
"""
for rmsd_fname, data in rmsd.items():
f_name = os.path.join(tgt_dir, rmsd_fname)
if allow_write(f_name, overwrite=overwrite):
write_rmsd(data, f_name)
def write_result(result, src_file, overwrite=False, basedir=None):
"""Writes the result to a file named for the given source file.
:param result: The result to write.
:param src_file: The original source file name.
:param overwrite: Whether to overwrite an existing file name.
:param basedir: The base directory to target (uses the source file's base directory
if not specified)
"""
f_name = create_out_fname(src_file, prefix=OUT_PFX, base_dir=basedir)
if allow_write(f_name, overwrite=overwrite):
write_csv(result, f_name, OUT_KEY_SEQ)
def write_submit(tgt_dir, sub_tpl_base, sub_tpl_line, step, overwrite=False):
"""
Uses the given templates and step number to write a submit script to the given target file location.
:param sub_tpl_base: The base template.
:param sub_tpl_line: The line template.
:param step: The step number.
:param tgt_dir: The target directory.
:param overwrite: Whether to allow overwrites.
"""
sub_file = os.path.join(tgt_dir, STEP_SUBMIT_FNAME.format(step))
if allow_write(sub_file, overwrite):
wham_fill = fill_submit_wham(sub_tpl_base, sub_tpl_line, step, use_part=False)
str_to_file(wham_fill, sub_file)
def write_submit(tgt_dir, sub_tpl_base, sub_tpl_line, step, overwrite=False):
"""
Uses the given templates and step number to write a submit script to the given target file location.
:param sub_tpl_base: The base template.
:param sub_tpl_line: The line template.
:param step: The step number.
:param tgt_dir: The target directory.
:param overwrite: Whether to allow overwrites.
"""
sub_file = os.path.join(tgt_dir, STEP_SUBMIT_FNAME.format(step))
if allow_write(sub_file, overwrite):
wham_fill = fill_submit_wham(sub_tpl_base, sub_tpl_line, step, use_part=False)
str_to_file(wham_fill, sub_file)
def rmsd_split(meta_file,
steps,
tpl_dir=DEF_TPL_DIR,
overwrite=False,
base_dir=None):
"""
Reads the given meta file, fetches the RMSD files in the inventory, and creates a succession
of directories that split the original RMSD files into a larger number of chunks for each step
such that step 1 will create a split of 2 in 01_01 and 01_02, etc.
:param meta_file: The initial meta file.
:param steps: The number of averaging steps to perform.
:param tpl_dir: The directory that contains the submit templates.
:param overwrite: Whether to overwrite existing files.
:param base_dir: The base directory to write to (defaults to the meta file's dir)
"""
meta = read_meta(meta_file)
rmsd = read_meta_rmsd(meta)
sub_tpl_base = read_tpl(os.path.join(tpl_dir, DEF_BASE_SUBMIT_TPL))
sub_tpl_line = read_tpl(os.path.join(tpl_dir, DEF_PART_LINE_SUBMIT_TPL))
if not base_dir:
base_dir = meta[DIR_KEY]
for step in range(1, steps + 1):
for rmsd_fname, data in rmsd.items():
data_len = len(data)
chunk_num = step + 1
chunk_size = math.floor(data_len / chunk_num)
logger.debug(STEP_DBG_MSG, step, data_len, rmsd_fname, chunk_num,
chunk_size)
rmsd_chunks = [ch for ch in chunk(data, chunk_size, list)]
for step_part in range(1, chunk_num + 1):
rmsd_tgt_dir = os.path.join(
base_dir, SPLIT_DIR_FMT.format(step, step_part))
if not os.path.exists(rmsd_tgt_dir):
os.makedirs(rmsd_tgt_dir)
f_name = os.path.join(rmsd_tgt_dir, rmsd_fname)
if allow_write(f_name, overwrite=overwrite):
write_rmsd(rmsd_chunks[step_part - 1], f_name)
write_meta(base_dir, meta, step, overwrite)
write_submit(base_dir, sub_tpl_base, sub_tpl_line, step, overwrite)
def write_avg_stdev(result, out_fname, overwrite=False, basedir=None):
"""Writes the result to a file named for the given source file.
:param result: The result to write.
:param out_fname: The target out file.
:param overwrite: Whether to overwrite an existing file name.
:param basedir: The base directory to target (uses the source file's base directory
if not specified)
"""
if basedir:
tgt_file = os.path.join(basedir, out_fname)
else:
tgt_file = out_fname
if allow_write(tgt_file, overwrite=overwrite):
with open(tgt_file, 'w') as csv_file:
res_writer = csv.writer(csv_file)
res_writer.writerow(OUT_KEY_SEQ)
for res_row in sorted(result):
res_writer.writerow(res_row)
print("Wrote file: {}".format(tgt_file))
def write_meta(tgt_dir, meta, step, overwrite=False):
"""
Writes out the meta file using the original meta data structure as a beginning.
:param tgt_dir: The target directory for the meta file.
:param meta: The parsed data from the original meta file.
:param step: The step number being processed.
:param overwrite: Whether to overwrite an existing meta file.
"""
step_meta = STEP_META_FNAME.format(step)
f_name = os.path.join(tgt_dir, step_meta)
if allow_write(f_name, overwrite=overwrite):
with open(f_name, 'w') as m_file:
for m_line in meta[LINES_KEY]:
rmsd_loc = os.path.join("{:02d}".format(step),
os.path.basename(m_line[0]))
m_file.write(rmsd_loc)
m_file.write('\t')
m_file.write('\t'.join(m_line[1:]))
m_file.write('\n')
print("Wrote file: {}".format(f_name))
def write_meta(tgt_dir, meta, step, overwrite=False):
"""
Writes out the meta file using the original meta data structure as a beginning.
:param tgt_dir: The target directory for the meta file.
:param meta: The parsed data from the original meta file.
:param step: The step number being processed.
:param overwrite: Whether to overwrite an existing meta file.
"""
step_meta = STEP_META_FNAME.format(step)
f_name = os.path.join(tgt_dir, step_meta)
if allow_write(f_name, overwrite=overwrite):
with open(f_name, 'w') as m_file:
for m_line in meta[LINES_KEY]:
rmsd_loc = os.path.join("{:02d}".format(step),
os.path.basename(m_line[0]))
m_file.write(rmsd_loc)
m_file.write('\t')
m_file.write('\t'.join(m_line[1:]))
m_file.write('\n')
print("Wrote file: {}".format(f_name))
def rmsd_split(meta_file, steps, tpl_dir=DEF_TPL_DIR, overwrite=False, base_dir=None):
"""
Reads the given meta file, fetches the RMSD files in the inventory, and creates a succession
of directories that split the original RMSD files into a larger number of chunks for each step
such that step 1 will create a split of 2 in 01_01 and 01_02, etc.
:param meta_file: The initial meta file.
:param steps: The number of averaging steps to perform.
:param tpl_dir: The directory that contains the submit templates.
:param overwrite: Whether to overwrite existing files.
:param base_dir: The base directory to write to (defaults to the meta file's dir)
"""
meta = read_meta(meta_file)
rmsd = read_meta_rmsd(meta)
sub_tpl_base = read_tpl(os.path.join(tpl_dir, DEF_BASE_SUBMIT_TPL))
sub_tpl_line = read_tpl(os.path.join(tpl_dir, DEF_PART_LINE_SUBMIT_TPL))
if not base_dir:
base_dir = meta[DIR_KEY]
for step in range(1, steps + 1):
for rmsd_fname, data in rmsd.items():
data_len = len(data)
chunk_num = step + 1
chunk_size = math.floor(data_len / chunk_num)
logger.debug(STEP_DBG_MSG, step, data_len, rmsd_fname, chunk_num, chunk_size)
rmsd_chunks = [ch for ch in chunk(data, chunk_size, list)]
for step_part in range(1, chunk_num + 1):
rmsd_tgt_dir = os.path.join(base_dir, SPLIT_DIR_FMT.
format(step, step_part))
if not os.path.exists(rmsd_tgt_dir):
os.makedirs(rmsd_tgt_dir)
f_name = os.path.join(rmsd_tgt_dir, rmsd_fname)
if allow_write(f_name, overwrite=overwrite):
write_rmsd(rmsd_chunks[step_part - 1], f_name)
write_meta(base_dir, meta, step, overwrite)
write_submit(base_dir, sub_tpl_base, sub_tpl_line, step, overwrite)