def process_custom_mcs(custom_mcs, savestate=None, verbosity=0):
""" Parses user supplied custom MCS data
:param [str, dict] custom_mcs: mcs data to be parsed
:param savestate_util.SavableState savestate: saved state data
:param int verbosity: controls verbosity level
:rtype: dict
"""
custom_mcs_result = {}
if custom_mcs:
custom_mcs = os_util.detect_type(custom_mcs, test_for_dict=True)
if isinstance(custom_mcs, str):
if rdkit.Chem.MolFromSmarts(custom_mcs) is not None:
os_util.local_print(
'Using user-supplied MCS {} for all molecules.'.format(
custom_mcs),
msg_verbosity=os_util.verbosity_level.info,
current_verbosity=verbosity)
custom_mcs_result = {'*': custom_mcs}
else:
os_util.local_print(
'Could not parse you custom MCS "{}".'.format(custom_mcs),
msg_verbosity=os_util.verbosity_level.error,
current_verbosity=verbosity)
raise SystemExit(1)
elif isinstance(custom_mcs, dict):
if all([(isinstance(key, frozenset) and len(key) == 2)
for key in custom_mcs]):
custom_mcs_result = custom_mcs
elif all([(isinstance(key, str) and key.count('-') == 1)
for key in custom_mcs]):
custom_mcs_result = {
frozenset(key.split('-')): value
for key, value in custom_mcs.items()
}
else:
os_util.local_print(
'Could not parse you custom MCS "{}". If providing a dict, make sure to follow '
'the required format (see documentation).'.format(
custom_mcs),
msg_verbosity=os_util.verbosity_level.error,
current_verbosity=verbosity)
raise SystemExit(1)
else:
os_util.local_print(
'Could not parse you custom MCS. A string or dict is required, but your data "{}" '
'was parsed as a {} (see documentation for formatting options).'
''.format(custom_mcs, type(custom_mcs)),
msg_verbosity=os_util.verbosity_level.error,
current_verbosity=verbosity)
raise SystemExit(1)
if savestate is not None:
savestate['custom_mcs'] = custom_mcs_result
savestate.setdefault('mcs_dict', {}).update(custom_mcs_result)
savestate.save_data()
return custom_mcs_result
def test_center_molecule(map_bias, all_molecules, verbosity=0):
""" Test center molecule to prepare star or wheel maps
:param [list, str] map_bias: test this bias string or list
:param list all_molecules: all molecules read com input
:param int verbosity: sets the verbosity level
:rtype: str
"""
map_bias = os_util.detect_type(map_bias, test_for_list=True)
if not map_bias:
os_util.local_print(
'A star map requires one, and only one, center molecule. You supplied none.',
msg_verbosity=os_util.verbosity_level.error,
current_verbosity=verbosity)
raise SystemExit(1)
if isinstance(map_bias, list) and len(map_bias) > 1:
os_util.local_print(
'A star map requires one, and only one, center molecule. You supplied {} ({})'
''.format(len(map_bias), map_bias),
msg_verbosity=os_util.verbosity_level.error,
current_verbosity=verbosity)
raise SystemExit(1)
if isinstance(map_bias, list):
map_bias = map_bias[0]
if map_bias not in all_molecules:
os_util.local_print(
'The center molecule you supplied ({}) not found in {}.'
''.format(map_bias, ', '.join(all_molecules)),
msg_verbosity=os_util.verbosity_level.error,
current_verbosity=verbosity)
raise ValueError('Molecule not found')
return map_bias
def test_detect_type():
assert os_util.detect_type('-1') == -1
assert os_util.detect_type('2.5') == 2.5
assert os_util.detect_type('float("inf")') == 'float("inf")'
assert os_util.detect_type('[1,2,3]') == [1, 2, 3]
assert os_util.detect_type('{1,2,3}') == {1, 2, 3}
assert os_util.detect_type('{"a": 1, "b": 2, "c": 3}') == {
"a": 1,
"b": 2,
"c": 3
}
assert os_util.detect_type('off') is False
assert os_util.detect_type('oN') is True
assert os_util.detect_type('off', test_for_boolean=False) == 'off'
assert os_util.detect_type(' a = 1, b : 2 ;c=3',
test_for_dict=True) == 'a = 1, b : 2 ;c=3'
assert os_util.detect_type(' a = 1; b : 2 ;c=3',
test_for_dict=True) == {
"a": 1,
"b": 2,
"c": 3
}
assert os_util.detect_type(' a = 1 2 3; b : 2 ;c=3',
test_for_dict=True) == {
"a": [1, 2, 3],
"b": 2,
"c": 3
}
assert os_util.detect_type('1 ; 2,3', test_for_list=True) == [1, 2, 3]
assert os_util.detect_type('1 2 3', test_for_list=True) == [1, 2, 3]
assert os_util.detect_type('1 2a 3', test_for_list=True) == '1 2a 3'
assert os_util.detect_type('1 ; "2",3', test_for_list=True) == [1, "2", 3]
assert os_util.detect_type(
'/home/user\n//\\//123',
test_for_list=True) == ['/home/user', '//\\//123']
assert os_util.detect_type('abc: 123\ndef:123\n \n\n das:abc com # comm', test_for_dict=True) == \
{'abc': 123, 'def': 123, 'das': 'abc com'}