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:
return ret
deduped = compress_dups(read_csv(args.file, all_conv=float), args.column)
write_csv(deduped, create_out_fname(args.file, prefix=PREFIX),
read_csv_header(args.file))
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:
return ret
deduped = compress_dups(read_csv(args.file, all_conv=float), args.column)
write_csv(deduped, create_out_fname(args.file, prefix=PREFIX),
read_csv_header(args.file))
return GOOD_RET # success
def process_file(base_file, data_file):
# TODO: add in reading vectors
base_dict = read_csv(base_file, quote_style=csv.QUOTE_NONNUMERIC)[0]
data_dict_list = read_csv(data_file, quote_style=csv.QUOTE_NONNUMERIC)
data_headers = [INDEX, RMSD] + read_csv_header(data_file)
num_vals = len(base_dict.values())
for data_id, data_dict in enumerate(data_dict_list):
rmsd = 0.0
for key, val in base_dict.items():
try:
rmsd += (data_dict[key] - val)**2
except KeyError:
raise InvalidDataError(
"Could not find key '{}' from base file in compared data file."
.format(key))
data_dict[INDEX] = data_id
data_dict[RMSD] = round((rmsd / num_vals)**0.5, 2)
out_name = create_out_fname(data_file, prefix=RMSD + '_')
write_csv(data_dict_list, out_name, data_headers)
def testEmptyFile(self):
self.assertIsNone(read_csv_header(EMPTY_CSV))
def testFirstRow(self):
self.assertListEqual(CSV_HEADER, read_csv_header(CSV_FILE))
def process_dump_files(cfg):
"""
@param cfg: configuration data read from ini file
"""
dump_file_list = []
if os.path.isfile(cfg[DUMP_FILE_LIST]):
dump_file_list += file_rows_to_list(cfg[DUMP_FILE_LIST])
if cfg[DUMP_FILE] is not None:
dump_file_list.append(cfg[DUMP_FILE])
if len(dump_file_list) == 0:
raise InvalidDataError(
"Found no dump files to process. Use the configuration ('ini') file to specify the name "
"of a single dump file with the keyword '{}' or a file listing dump files with the "
"keyword '{}'.".format(DUMP_FILE, DUMP_FILE_LIST))
gofr_data = {}
evb_dict = {}
out_fieldnames = None
# If RDFs are to be calculated, initialize empty data structures
if cfg[GOFR_OUTPUT]:
g_dr = cfg[GOFR_DR]
g_max = cfg[GOFR_MAX]
gofr_data[GOFR_BINS] = np.arange(0.0, g_max + g_dr, g_dr)
if len(gofr_data[GOFR_BINS]) < 2:
raise InvalidDataError(
"Insufficient number of bins to calculate RDFs. Check input: "
"{}: {}, {}: {},".format(GOFR_DR, cfg[GOFR_DR], GOFR_MAX,
cfg[GOFR_MAX]))
if cfg[CALC_HO_GOFR]:
ini_gofr_data(gofr_data, HO_BIN_COUNT, GOFR_BINS, HO_STEPS_COUNTED)
if cfg[CALC_OO_GOFR]:
ini_gofr_data(gofr_data, OO_BIN_COUNT, GOFR_BINS, OO_STEPS_COUNTED)
if cfg[CALC_HH_GOFR]:
ini_gofr_data(gofr_data, HH_BIN_COUNT, GOFR_BINS, HH_STEPS_COUNTED)
if cfg[CALC_OH_GOFR]:
ini_gofr_data(gofr_data, OH_BIN_COUNT, GOFR_BINS, OH_STEPS_COUNTED)
if cfg[CALC_TYPE_GOFR]:
ini_gofr_data(gofr_data, TYPE_BIN_COUNT, GOFR_BINS,
TYPE_STEPS_COUNTED)
if cfg[PER_FRAME_OUTPUT]:
out_fieldnames = setup_per_frame_output(cfg)
if cfg[EVB_SUM_FILE] is not None:
evb_dict = read_csv_to_dict(cfg[EVB_SUM_FILE], cfg[ALIGN_COL])
evb_headers = read_csv_header(cfg[EVB_SUM_FILE])
cfg[EVB_SUM_HEADERS] = []
for header in evb_headers:
if header not in out_fieldnames:
cfg[EVB_SUM_HEADERS].append(header)
if cfg[CALC_CEC_DIST]:
for header in [CEC_X, CEC_Y, CEC_Z]:
if header not in cfg[EVB_SUM_HEADERS]:
raise InvalidDataError(
"If '{}' is set to True, these headers must be found in the '{}': {}."
"".format(CALC_CEC_DIST, EVB_SUM_FILE,
[CEC_X, CEC_Y, CEC_Z]))
out_fieldnames += cfg[EVB_SUM_HEADERS]
per_frame_write_mode = 'w'
base_out_file_name = cfg[DUMP_FILE_LIST]
for dump_file in dump_file_list:
data_to_print = []
# output file base name to change at each iteration if not combining output
if cfg[COMBINE_OUTPUT] is False:
base_out_file_name = dump_file
read_dump_file(dump_file, cfg, data_to_print, gofr_data,
out_fieldnames, per_frame_write_mode, evb_dict)
if cfg[PER_FRAME_OUTPUT]:
print_per_frame(base_out_file_name, cfg, data_to_print,
out_fieldnames, per_frame_write_mode)
# if combining files, after first loop, always append to file
if cfg[COMBINE_OUTPUT]:
per_frame_write_mode = 'a'
if cfg[GOFR_OUTPUT]:
print_gofr(cfg, gofr_data)
def testEmptyFile(self):
self.assertIsNone(read_csv_header(EMPTY_CSV))
def testFirstRow(self):
self.assertListEqual(CSV_HEADER, read_csv_header(CSV_FILE))
