def testReadPDBDict(self):
test_type = ' HY1 '
test_elem = ' H'
test_dict = read_csv_dict(ELEM_DICT_FILE, pdb_dict=True)
self.assertTrue(test_type in test_dict)
self.assertEquals(test_elem, test_dict[test_type])
self.assertEquals(31, len(test_dict))
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:
chk_file_list = file_rows_to_list(cfg[CHK_FILE_LIST])
if len(cfg[REL_E_SEC]) > 0:
extracted_data = get_ene_data(cfg, chk_file_list)
ref_e_dict = read_csv_dict(cfg[REF_E_FILE], one_to_one=False, str_float=True)
find_rel_e(extracted_data, cfg, ref_e_dict)
else:
for chK_file in chk_file_list:
get_evb_atoms(cfg, chK_file)
except IOError as e:
warning("Problems reading file:", e)
return IO_ERROR
except InvalidDataError as e:
warning("Problems reading data:", e)
return INVALID_DATA
# print(psf_data_content[ATOMS_CONTENT])
return GOOD_RET # success
def testReadPDBDict(self):
test_type = ' HY1 '
test_elem = ' H'
test_dict = read_csv_dict(ELEM_DICT_FILE, pdb_dict=True)
self.assertTrue(test_type in test_dict)
self.assertEquals(test_elem, test_dict[test_type])
self.assertEquals(31, len(test_dict))
def testStringDictCheckDups(self):
# Check that fails elegantly
try:
test_dict = read_csv_dict(ELEM_DICT_FILE, ints=False, )
self.assertFalse(test_dict)
except InvalidDataError as e:
self.assertTrue("Did not find a 1:1 mapping" in e.args[0])
def testStringDictAsInt(self):
# Check that fails elegantly by passing returning value error
try:
test_dict = read_csv_dict(ELEM_DICT_FILE, one_to_one=False)
self.assertFalse(test_dict)
except ValueError as e:
self.assertTrue("invalid literal for int()" in e.message)
def testStringDictCheckDups(self):
# Check that fails elegantly
try:
test_dict = read_csv_dict(ELEM_DICT_FILE, ints=False, )
self.assertFalse(test_dict)
except InvalidDataError as e:
self.assertTrue("Did not find a 1:1 mapping" in e.message)
def testStringDictAsInt(self):
# Check that fails elegantly by passing returning value error
try:
test_dict = read_csv_dict(ELEM_DICT_FILE, one_to_one=False)
self.assertFalse(test_dict)
except ValueError as e:
self.assertTrue("invalid literal for int()" in e.message)
def main(argv=None):
# Read input
args, ret = parse_cmdline(argv)
if ret != GOOD_RET:
return ret
# Read template and data files
cfg = args.config
try:
data_tpl_content = process_data_tpl(cfg)
old_new_atom_num_dict = {}
old_new_atom_type_dict = {}
# Will return an empty dictionary for one of them if that one is not true
if cfg[MAKE_ATOM_NUM_DICT] or cfg[MAKE_ATOM_TYPE_DICT]:
make_atom_dict(cfg, data_tpl_content, old_new_atom_num_dict, old_new_atom_type_dict)
# Will return empty dicts if no file
if not cfg[MAKE_ATOM_TYPE_DICT]:
old_new_atom_type_dict = read_csv_dict(cfg[ATOM_TYPE_DICT_FILE])
process_data_files(cfg, data_tpl_content, old_new_atom_type_dict)
except IOError as e:
warning("Problems reading file:", e)
return IO_ERROR
except InvalidDataError as e:
warning("Problems reading data:", 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 dump files
cfg = args.config
try:
atom_num_dict = read_csv_dict(cfg[ATOM_REORDER_FILE])
atom_type_dict = read_csv_dict(cfg[ATOM_TYPE_FILE], one_to_one=False)
mol_num_dict = read_csv_dict(cfg[MOL_RENUM_FILE], one_to_one=False)
process_dump_files(cfg, atom_num_dict, atom_type_dict, mol_num_dict)
except IOError as e:
warning("Problems reading file:", e)
return IO_ERROR
except InvalidDataError as e:
warning("Problems reading data:", 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 dump files
cfg = args.config
try:
atom_num_dict = read_csv_dict(cfg[ATOM_REORDER_FILE])
atom_type_dict = read_csv_dict(cfg[ATOM_TYPE_FILE], one_to_one=False)
mol_num_dict = read_csv_dict(cfg[MOL_RENUM_FILE], one_to_one=False)
process_dump_files(cfg, atom_num_dict, atom_type_dict, mol_num_dict)
except IOError as e:
warning("Problems reading file:", e)
return IO_ERROR
except InvalidDataError as e:
warning("Problems reading data:", 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
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])
process_pdb(cfg, atom_num_dict, mol_num_dict, element_dict)
except IOError as e:
warning("Problems reading file:", e)
return IO_ERROR
except (InvalidDataError, ValueError) as e:
warning("Problems with input:", 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
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])
process_pdb(cfg, atom_num_dict, mol_num_dict, element_dict)
except IOError as e:
warning("Problems reading file:", e)
return IO_ERROR
except (InvalidDataError, ValueError) as e:
warning("Problems with input:", 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
if cfg[DATA_FILE] is None:
if not (os.path.isfile(cfg[DATA_FILES])):
warning(
"Did not find a list of data files at the path: {}\n"
"In the configuration file, specify a location of a single data file with the keyword {}\n"
"and/or a single data file with the keyword {}".format(
cfg[DATA_FILES], DATA_FILES, DATA_FILE))
return INVALID_DATA
type_dicts = {
SEC_ATOMS: {},
SEC_BONDS: {},
SEC_ANGLS: {},
SEC_DIHES: {},
SEC_IMPRS: {},
}
try:
atom_id_dict = read_csv_dict(cfg[ATOM_ID_DICT_FILE], one_to_one=False)
type_dicts[SEC_ATOMS] = read_csv_dict(cfg[ATOM_TYPE_DICT_FILE],
one_to_one=False)
type_dicts[SEC_BONDS] = read_csv_dict(cfg[BOND_TYPE_DICT_FILE],
one_to_one=False)
type_dicts[SEC_ANGLS] = read_csv_dict(cfg[ANGL_TYPE_DICT_FILE],
one_to_one=False)
type_dicts[SEC_DIHES] = read_csv_dict(cfg[DIHE_TYPE_DICT_FILE],
one_to_one=False)
type_dicts[SEC_IMPRS] = read_csv_dict(cfg[IMPR_TYPE_DICT_FILE],
one_to_one=False)
if cfg[DATA_COMP] is None:
process_data_files(cfg, atom_id_dict, type_dicts)
else:
comp_files(cfg, atom_id_dict, type_dicts)
except IOError as e:
warning("Problems reading file:", e)
return IO_ERROR
except InvalidDataError as e:
warning("Problems reading data:", 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:
data_tpl_content = process_data_tpl(cfg)
old_new_atom_num_dict = {}
old_new_atom_type_dict = {}
# Will return an empty dictionary for one of them if that one is not true
if cfg[MAKE_ATOM_NUM_DICT] or cfg[MAKE_ATOM_TYPE_DICT]:
make_atom_dict(cfg, data_tpl_content, old_new_atom_num_dict,
old_new_atom_type_dict)
# Will return empty dicts if no file
if not cfg[MAKE_ATOM_TYPE_DICT]:
old_new_atom_type_dict = read_csv_dict(cfg[ATOM_TYPE_DICT_FILE])
if cfg[ADJUST_ATOM] is None and len(cfg[ATOMS_DIST]) == 0:
process_data_files(cfg, data_tpl_content, old_new_atom_type_dict)
elif len(cfg[ATOMS_DIST]) == 0:
adjust_atom_xyz(cfg, data_tpl_content)
else:
adjust_atom_dist(cfg, data_tpl_content)
except IOError as e:
warning("Problems reading file:", e)
return IO_ERROR
except InvalidDataError as e:
warning("Problems reading data:", 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
cfg = args.config
try:
out_field_names = gather_out_field_names(cfg)
extracted_data = process_evb_files(cfg, out_field_names)
if len(cfg[REL_E_SEC]) > 0:
ref_e_dict = read_csv_dict(cfg[REF_E_FILE],
one_to_one=False,
str_float=True)
find_rel_e(extracted_data, cfg, out_field_names, ref_e_dict)
except IOError as e:
warning("Problems reading file:", e)
return IO_ERROR
except (InvalidDataError, ValueError) as e:
warning("Problems reading data:", 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
if cfg[DATA_FILE] is None:
if not(os.path.isfile(cfg[DATA_FILES])):
warning("Did not find a list of data files at the path: {}\n"
"In the configuration file, specify a location of a single data file with the keyword {}\n"
"and/or a single data file with the keyword {}".format(cfg[DATA_FILES], DATA_FILES, DATA_FILE))
return INVALID_DATA
type_dicts = {SEC_ATOMS: {},
SEC_BONDS: {},
SEC_ANGLS: {},
SEC_DIHES: {},
SEC_IMPRS: {}, }
try:
atom_id_dict = read_csv_dict(cfg[ATOM_ID_DICT_FILE], one_to_one=False)
type_dicts[SEC_ATOMS] = read_csv_dict(cfg[ATOM_TYPE_DICT_FILE], one_to_one=False)
type_dicts[SEC_BONDS] = read_csv_dict(cfg[BOND_TYPE_DICT_FILE], one_to_one=False)
type_dicts[SEC_ANGLS] = read_csv_dict(cfg[ANGL_TYPE_DICT_FILE], one_to_one=False)
type_dicts[SEC_DIHES] = read_csv_dict(cfg[DIHE_TYPE_DICT_FILE], one_to_one=False)
type_dicts[SEC_IMPRS] = read_csv_dict(cfg[IMPR_TYPE_DICT_FILE], one_to_one=False)
if cfg[DATA_COMP] is None:
process_data_files(cfg, atom_id_dict, type_dicts)
else:
comp_files(cfg, atom_id_dict, type_dicts)
except IOError as e:
warning("Problems reading file:", e)
return IO_ERROR
except InvalidDataError as e:
warning("Problems reading data:", e)
return INVALID_DATA
return GOOD_RET # success
def testReadAtomNumDict(self):
# Will renumber atoms and then sort them
test_dict = read_csv_dict(ATOM_DICT_FILE)
self.assertEqual(test_dict, GOOD_ATOM_DICT)
def testReadAtomNumDict(self):
# Will renumber atoms and then sort them
test_dict = read_csv_dict(ATOM_DICT_FILE)
self.assertEqual(test_dict, GOOD_ATOM_DICT)
