def main(argv=None):
# Read input
args, ret = parse_cmdline(argv)
if ret != GOOD_RET:
return ret
cfg = args.config
# Read and process pdb files
try:
atom_num_dict = read_csv_dict(cfg[ATOM_REORDER_FILE])
mol_num_dict = read_csv_dict(cfg[MOL_RENUM_FILE], one_to_one=False)
element_dict = create_element_dict(cfg[ELEMENT_DICT_FILE], pdb_dict=False)
radii_dict = create_element_dict(cfg[RADII_DICT_FILE], pdb_dict=False)
process_psf(cfg, atom_num_dict, mol_num_dict, element_dict, radii_dict)
except IOError as e:
warning("Problems reading file:", e)
return IO_ERROR
except InvalidDataError as e:
warning(e)
return INVALID_DATA
return GOOD_RET # success
def main(argv=None):
# Read input
args, ret = parse_cmdline(argv)
if ret != GOOD_RET:
return ret
cfg = args.config
# Read and process pdb files
try:
atom_num_dict = read_csv_dict(cfg[ATOM_REORDER_FILE])
mol_num_dict = read_csv_dict(cfg[MOL_RENUM_FILE], one_to_one=False)
element_dict = create_element_dict(cfg[ELEMENT_DICT_FILE],
pdb_dict=False)
radii_dict = create_element_dict(cfg[RADII_DICT_FILE], pdb_dict=False)
process_psf(cfg, atom_num_dict, mol_num_dict, element_dict, radii_dict)
except IOError as e:
warning("Problems reading file:", e)
return IO_ERROR
except InvalidDataError as e:
warning(e)
return INVALID_DATA
return GOOD_RET # success
def main(argv=None):
# Read input
args, ret = parse_cmdline(argv)
if ret != GOOD_RET or args is None:
return ret
# Read template and data files
cfg = args.config
try:
if cfg[PDB_TPL_FILE] is None:
pdb_tpl_content = None
else:
pdb_tpl_content = process_pdb_tpl(cfg[PDB_TPL_FILE])
# add new row at the beginning for remark
pdb_tpl_content[HEAD_CONTENT] = [
"REMARK 450 "
] * 3 + pdb_tpl_content[HEAD_CONTENT]
if cfg[DATA_TPL_FILE] is None:
data_tpl_content = None
else:
data_tpl_content = process_data_tpl(cfg)
element_dict = create_element_dict(ELEMENT_DICT_FILE, pdb_dict=False)
print('"file_name","qmmm_energy","opt_complete","job_complete"')
for cp2k_file in cfg[CP2K_FILES]:
process_cp2k_file(cfg, cp2k_file, data_tpl_content,
pdb_tpl_content, element_dict)
except IOError as e:
warning("Problems reading file:", e)
return IO_ERROR
except (InvalidDataError, KeyError, ValueError) as e:
warning("Problems reading data:", e)
return INVALID_DATA
return GOOD_RET # success