matteoferla/Fragmenstein

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:pencil: pyrosetta has a new way of installation #286
matteoferla authored 52545fb8
complete00:00:15
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codeclimate prepare
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I, [2024-10-29T12:43:46.062278 #1]  INFO -- : Skipping file ./fragmenstein/monster/mcs_mapping/types.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 17
    atomCompare: rdFMCS.AtomCompare
               ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.064686 #1]  INFO -- : Skipping file ./fragmenstein/monster/_util_compare.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 41
    def get_color_origins(self) -> Dict[str, Dict[int, str]]:
                                ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.073826 #1]  INFO -- : Skipping file ./fragmenstein/monster/mcs_mapping/compare_atom.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 22
    def __init__(self, comparison: rdFMCS.AtomCompare = rdFMCS.AtomCompare.CompareAnyHeavyAtom):
                                 ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.085636 #1]  INFO -- : Skipping file ./fragmenstein/monster/mcs_mapping/utils.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 10
    def flip_mapping(mapping: Sequence[Tuple[int, int]]) -> Sequence[Tuple[int, int]]:
                            ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.091896 #1]  INFO -- : Skipping file ./fragmenstein/monster/_place.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 34
    mol: Chem.Mol,
       ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.097109 #1]  INFO -- : Skipping file ./fragmenstein/monster/_join_neighboring.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 20
    def join_neighboring_mols(self, mol_A: Chem.Mol, mol_B: Chem.Mol): # noqa uppercase is fine.
                                         ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.103300 #1]  INFO -- : Skipping file ./fragmenstein/monster/_place_modes/_no_blending.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 15
    def no_blending(self, broad=False) -> None:
                                       ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.108544 #1]  INFO -- : Skipping file ./fragmenstein/monster/_place_modes/_expand.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 17
    def by_expansion(self, primary_name: Optional[str] = None, min_mode_index: int = 0) -> Chem.Mol:
                                       ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.114876 #1]  INFO -- : Skipping file ./fragmenstein/monster/_place_modes/_make_chimera.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 12
    def make_chimera(self, template: Chem.Mol, min_mode_index=0) -> Chem.Mol:
                                   ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.119979 #1]  INFO -- : Skipping file ./fragmenstein/monster/_place_modes/_refine.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 20
    scaffold: Chem.Mol,
            ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.126171 #1]  INFO -- : Skipping file ./fragmenstein/monster/_place_modes/_full.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 12
    def full_blending(self) -> None:
                            ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.131396 #1]  INFO -- : Skipping file ./fragmenstein/monster/_place_modes/_mappings.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 13
    hit: Chem.Mol,
       ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.137540 #1]  INFO -- : Skipping file ./fragmenstein/monster/_place_modes/_partial.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 29
    def partial_blending(self) -> None:
                               ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.148954 #1]  INFO -- : Skipping file ./fragmenstein/monster/_combine.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 25
    def combine(self, keep_all: bool = True, collapse_rings: bool = True, joining_cutoff: int = 5):
                              ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.154529 #1]  INFO -- : Skipping file ./fragmenstein/monster/_modification_logging.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 21
    def keep_copy(self, mol: Chem.Mol, label=None):
                           ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.160362 #1]  INFO -- : Skipping file ./fragmenstein/monster/_communal.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 59
    def _find_closest(self, mol_A: Chem.Mol, mol_B: Chem.Mol) -> Tuple[Chem.RWMol, int, int, float]:
                                 ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.167902 #1]  INFO -- : Skipping file ./fragmenstein/monster/_base.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 66
    hits: List[Chem.Mol],
        ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.172016 #1]  INFO -- : Skipping file ./fragmenstein/monster/_collapse_ring.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 34
    def collapse_mols(self, mols: List[Chem.Mol]):
                                ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.179461 #1]  INFO -- : Skipping file ./fragmenstein/monster/_merge.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 29
    hits: Optional[List[Chem.Mol]] = None,
        ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.183474 #1]  INFO -- : Skipping file ./fragmenstein/monster/bond_provenance.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 18
    def set_all_bonds(cls, mol: Chem.Mol, provenance_name:str) -> None:
                              ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.190801 #1]  INFO -- : Skipping file ./fragmenstein/monster/_utility.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 21
    SVG = lambda *args, **kwargs: print('Install IPython...')
                                      ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.202002 #1]  INFO -- : Skipping file ./fragmenstein/monster/positional_mapping.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 27
    def get_positional_mapping(cls, mol_A: Chem.Mol, mol_B: Chem.Mol, dummy_w_dummy=True) -> Dict[int, int]:
                                         ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.207476 #1]  INFO -- : Skipping file ./fragmenstein/monster/unmerge_mapper.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 53
    followup: Chem.Mol,
            ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.213269 #1]  INFO -- : Skipping file ./fragmenstein/monster/_ff.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 14
    success: bool
           ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.224520 #1]  INFO -- : Skipping file ./fragmenstein/multivictor/multivictor.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 22
    def place(self,  smiles: str, number_runs: int= 10,
                           ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.230176 #1]  INFO -- : Skipping file ./fragmenstein/display.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 31
    def color_in(mols: List[Chem.Mol], color_scale=None, skip_feija=False):
                     ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.235907 #1]  INFO -- : Skipping file ./fragmenstein/mol3d_display.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 39
    def _add_mol(self, mol, name=None, carbon_color: Optional[str] = None, opacity=1., **kwargs):
                                                   ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.241388 #1]  INFO -- : Skipping file ./fragmenstein/branding.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 40
    divergent_colors:Dict[int, List[str]] = {int(k): v for k, v in json.loads(json_str).items()}
                    ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.247256 #1]  INFO -- : Skipping file ./fragmenstein/igor/pyrosetta_import.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 24
    def __getattr__(self, attr: str):
                              ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.252710 #1]  INFO -- : Skipping file ./fragmenstein/igor/_igor_min.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 25
    def pose2str(self, pose: Optional[pyrosetta.Pose] = None) -> str:
                           ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.258499 #1]  INFO -- : Skipping file ./fragmenstein/igor/_igor_utils.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 22
    def dock(self) -> pyrosetta.Pose:
                   ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.263995 #1]  INFO -- : Skipping file ./fragmenstein/igor/_igor_base.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 11
    self.ligand_residue: List[int] = []
                       ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.270047 #1]  INFO -- : Skipping file ./fragmenstein/igor/__init__.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 50
    def residues_in_selector(self, pose: pyrosetta.Pose, selector) -> List[str]:
                                       ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.275557 #1]  INFO -- : Skipping file ./fragmenstein/igor/_igor_init.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 28
    pose: pyrosetta.Pose,
        ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.281386 #1]  INFO -- : Skipping file ./fragmenstein/version.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 4
    def get_versions() -> Dict[str, str]:
                       ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.286990 #1]  INFO -- : Skipping file ./fragmenstein/victor/_victor_igor.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 10
    def _fix_minimized(self, ligand: Optional[Chem.Mol]=None, add_dummy:bool=True) -> Chem.Mol:
                                   ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.293506 #1]  INFO -- : Skipping file ./fragmenstein/victor/_victor_validate.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 11
    def validate(self, reference_mol: Chem.Mol) -> Dict[str, float]:
                                    ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.298438 #1]  INFO -- : Skipping file ./fragmenstein/victor/_victor_show.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 19
    def to_nglview(self, print_legend: bool = False) -> MolNGLWidget:
                                     ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.311411 #1]  INFO -- : Skipping file ./fragmenstein/victor/_victor_combine.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 21
    long_name: Optional[str] = None,
             ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.321566 #1]  INFO -- : Skipping file ./fragmenstein/victor/_victor_base.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 106
    hits: List[Chem.Mol],
        ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.322839 #1]  INFO -- : Skipping file ./fragmenstein/victor/_victor_common.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 19
    self.journal.warning(f'{self.long_name} - Folder {path} exists.')
                                                                   ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.332958 #1]  INFO -- : Skipping file ./fragmenstein/victor/_victor_store.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 25
    name = f'hit{h}'
                   ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.334105 #1]  INFO -- : Skipping file ./fragmenstein/victor/plip.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 52
    def __init__(self, pdb_block: str, resn='LIG', resi=1, chain='B'):
                                ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.344318 #1]  INFO -- : Skipping file ./fragmenstein/victor/_victor_safety.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 10
    execute: Optional[Callable] = None,
           ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.356172 #1]  INFO -- : Skipping file ./fragmenstein/victor/_victor_plonk.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 32
    return f'LINK         SG  {self.covalent_resn} {p_chain} {p_resi: >3}                ' + \
                                                                                         ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.372414 #1]  INFO -- : Skipping file ./fragmenstein/victor/minimalPDB.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 32
    def __init__(self, block: str, remove_water=False, remove_other_hetatms=False, ligname="LIG"):
                            ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.380360 #1]  INFO -- : Skipping file ./fragmenstein/victor/_victor_utils.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 45
    def dock(self) -> Chem.Mol:
                   ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.383952 #1]  INFO -- : Skipping file ./fragmenstein/victor/_victor_place.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 14
    smiles: str,
          ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.392225 #1]  INFO -- : Skipping file ./fragmenstein/victor/_victor_journal.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 16
    self.journal.warning(f'{self.long_name} - {w.message} ({w.category})')
                                                                        ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.404713 #1]  INFO -- : Skipping file ./fragmenstein/faux_victors/quick.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 37
    def preminimized_undummied_mol(self) -> Chem.Mol:
                                         ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.411131 #1]  INFO -- : Skipping file ./fragmenstein/faux_victors/mcs_monster.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 21
    def __init__(self, hits: Chem.Mol, mcs_parameters=rdFMCS.MCSParameters()):
                           ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.415975 #1]  INFO -- : Skipping file ./fragmenstein/faux_victors/brics.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 38
    def __init__(self, hits: List[Chem.Mol]):
                           ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.422583 #1]  INFO -- : Skipping file ./fragmenstein/faux_victors/others.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 17
    def make_coordinate_constraints_for_placement(self, *args, **kwargs) -> str:
                                                                         ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.433803 #1]  INFO -- : Skipping file ./fragmenstein/faux_victors/no_pyrosetta.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 47
    self.journal.debug(f'{self.long_name} - saving pose collage')
                                                               ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.438920 #1]  INFO -- : Skipping file ./fragmenstein/laboratory/_place.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 24
    smiles: str
          ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.445219 #1]  INFO -- : Skipping file ./fragmenstein/laboratory/_combine.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 14
    def combine_subprocess(self, binary_hits: List[bytes]) -> dict:
                                            ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.450279 #1]  INFO -- : Skipping file ./fragmenstein/laboratory/_base.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 15
    def binarize(mol:Chem.Mol, ignore_errors:bool=True) -> bytes:
                    ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.456655 #1]  INFO -- : Skipping file ./fragmenstein/laboratory/_score.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 22
    def get_pains(mol) -> List[str]:
                       ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.461696 #1]  INFO -- : Skipping file ./fragmenstein/laboratory/_extras.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 53
    df: pd.DataFrame,
      ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.467978 #1]  INFO -- : Skipping file ./fragmenstein/laboratory/__init__.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 11
    warn(f'Supressed {error.__class__.__name__}: {error}')
                                                        ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.472775 #1]  INFO -- : Skipping file ./fragmenstein/laboratory/validator.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 26
    def hits_check(mols_col: pd.Series) -> bool:
                           ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.479260 #1]  INFO -- : Skipping file ./fragmenstein/demo/_base_dataset_holder.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 17
    dataset_package: ModuleType = '__main__'
                   ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.495630 #1]  INFO -- : Skipping file ./fragmenstein/demo/__init__.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 25
    def get_5SB7_mols(cls) -> List[Chem.Mol]:
                           ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.506886 #1]  INFO -- : Skipping file ./fragmenstein/ngl_display.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 39
    def add_mol(self, mol: Chem.Mol, carbon_color: str = '', colorValue:str='') -> ComponentViewer:
                         ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.513628 #1]  INFO -- : Skipping file ./fragmenstein/extraction_funs.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 12
    def add_dummy_to_mol(ligand: Chem.Mol,
                               ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.518438 #1]  INFO -- : Skipping file ./fragmenstein/walton/_advmoves.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 11
    def atom_on_plane(self, mol_idx: int, atom_idx: Union[int, Geometry.Point3D], plane: str):
                                   ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.525002 #1]  INFO -- : Skipping file ./fragmenstein/walton/_base.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 17
    mols: List[Chem.Mol],
        ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.529699 #1]  INFO -- : Skipping file ./fragmenstein/walton/_polygon.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 11
    bond_type: Chem.BondType = Chem.BondType.SINGLE,
             ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.541206 #1]  INFO -- : Skipping file ./fragmenstein/walton/_art.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 15
    def _mol2svg(self, mol: Chem.Mol) -> str:  # noqa it is static, but I dont care.
                          ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.548390 #1]  INFO -- : Skipping file ./fragmenstein/walton/_movements.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 13
    def get_point(self, atom_idx: Union[int, Geometry.Point3D], mol_idx: int = -1) -> Geometry.Point3D:
                                ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.552660 #1]  INFO -- : Skipping file ./fragmenstein/openmm/openvictor.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 21
    self.journal.debug(f'{self.long_name} - Starting system setup')
                                                                 ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.564260 #1]  INFO -- : Skipping file ./fragmenstein/openmm/fritz.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 52
    prepped_mol: Chem.Mol,
               ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.571170 #1]  INFO -- : Skipping file ./fragmenstein/__init__.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 22
    warn(f'Igor (minimizer) unavailable —{err}.', category=ImportWarning)
                                                 ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.582462 #1]  INFO -- : Skipping file ./fragmenstein/cli/victor.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 9
    def _define_victor(self, parser: argparse.ArgumentParser):
                                   ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.587819 #1]  INFO -- : Skipping file ./fragmenstein/cli/pipeline.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 32
    def _define_pipeline(self, parser: argparse.ArgumentParser):
                                     ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.593621 #1]  INFO -- : Skipping file ./fragmenstein/cli/laboratory.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 12
    def common(self, parser: argparse.ArgumentParser):
                           ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.599291 #1]  INFO -- : Skipping file ./fragmenstein/cli/base.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 37
    def __call__(self, cli_override: Optional[List[str]] = None):
                                   ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.605168 #1]  INFO -- : Skipping file ./fragmenstein/cli/monster.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 8
    def _define_monster(self, parser: argparse.ArgumentParser):
                                    ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.616498 #1]  INFO -- : Skipping file ./fragmenstein/cli/utils.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 9
    def _define_utils(self, parser: argparse.ArgumentParser):
                                  ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.622969 #1]  INFO -- : Skipping file ./fragmenstein/error.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 6
    def fix_name(self, mol: Union[Chem.Mol, str]):
                          ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.627984 #1]  INFO -- : Skipping file ./fragmenstein/m_rmsd.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 61
    followup: Chem.Mol,
            ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.634551 #1]  INFO -- : Skipping file ./fragmenstein/mpro/dataframe.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 10
    def fetch_postera() -> pd.DataFrame:
                        ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.639344 #1]  INFO -- : Skipping file ./fragmenstein/mpro/__init__.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 27
    def from_hit_codes(cls, hit_codes: List[str], **options):
                                     ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.665243 #1]  INFO -- : Skipping file ./fragmenstein/settings.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 50
    raise ValueError(f'FRAGMENSTEIN_SETTINGS={os.environ["FRAGMENSTEIN_SETTINGS"]} does not exist as a file')
                                                                                                           ^
SyntaxError: invalid syntax


I, [2024-10-29T12:43:46.677317 #1]  INFO -- : Skipping file ./.readthedocs/source/conf.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
  File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
    print(json.dumps(to_json(ast.parse(source))))
  File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
    return compile(source, filename, mode, PyCF_ONLY_AST)
  File "<unknown>", line 40
    os.system(f'cp ../../images/{filename} _static/{filename}')
                                                             ^
SyntaxError: invalid syntax