TypeError: can't multiply sequence by non-int of type 'Forward' in AF2_model_docking.ipynb of cell 5.

Dear Sir,

again, many thank for your work.

when I checked an example notebook execution of cell 5 gave me the following errors.

However, when I re-executed it, I was able to reproduce it.

My question is why I cannot overwrite this pair_spatial_metrics at the first execution?

Many thanks,

{
    "name": "TypeError",
    "message": "can't multiply sequence by non-int of type 'Forward'",
    "stack": "---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[8], line 7
      5 holo_chainid = 'A' # see the receptor chain ID in poseview
      6 # reverse the input as the residue is on af2 structure and crystal_ligand here is useless
----> 7 results_df = pair_spatial_metrics(
      8     str(af2), str(crystal_ligand), str(holo), 
      9     'A', holo_chainid, 
     10     bs_res_str = flexible_residues.split(','),
     11 )
     12 ca_rmsd = results_df.iloc[0].mean_ca_rmsd
     13 sc_rmsd = results_df.iloc[0].mean_sc_rmsd

File ~/software/DiffBindFR/DiffBindFR/utils/apo_holo.py:845, in pair_spatial_metrics(holo_pdb, lig_file, apo_pdb, holo_chains, apo_chains, return_bs, bs_cutoff, chi, units, debug, bs_res_str)
    843     holo_bindsite = bs_res_finder(ligand_coords, holo_prody, bs_cutoff)
    844 else:
--> 845     holo_bindsite = specific_bs_res(holo_prody, bs_res_str)
    847 # map to alignment and sequence and back to apo_binding residues
    848 apo_holo_mask, holo_bind_res, apo_bind_res = get_apo_bind_indices(
    849     holo_bindsite,
    850     holo_seq, apo_seq,
   (...)
    853     holo_crmap, apo_crmap,
    854 )

File ~/software/DiffBindFR/DiffBindFR/utils/apo_holo.py:186, in specific_bs_res(holo_prody, bs_res_str)
    183     res_sel.append(f'(chain {xs[0]} and resnum {xs[1]} and resname {xs[2]})')
    185 res_sel = ' or '.join(res_sel)
--> 186 pkt = holo_prody.select(res_sel)
    187 holo_bindsite = []
    188 if pkt is None:

File ~/miniforge-pypy3/envs/diffbindfr/lib/python3.9/site-packages/prody/atomic/atomic.py:232, in Atomic.select(self, selstr, **kwargs)
    228 def select(self, selstr, **kwargs):
    229     \"\"\"Returns atoms matching *selstr* criteria.  See :mod:`~.select` module
    230     documentation for details and usage examples.\"\"\"
--> 232     return SELECT.select(self, selstr, **kwargs)

File ~/miniforge-pypy3/envs/diffbindfr/lib/python3.9/site-packages/prody/atomic/select.py:894, in Select.select(self, atoms, selstr, **kwargs)
    891 self._replace = False
    893 self._selstr = selstr
--> 894 indices = self.getIndices(atoms, selstr, **kwargs)
    896 self._kwargs = None
    898 if len(indices) == 0:

File ~/miniforge-pypy3/envs/diffbindfr/lib/python3.9/site-packages/prody/atomic/select.py:952, in Select.getIndices(self, atoms, selstr, **kwargs)
    949         raise SelectionError(selstr, 0, 'is not a valid selection '
    950                              'string', [ss])
    951 else:
--> 952     torf = self.getBoolArray(atoms, selstr, **kwargs)
    953     return torf.nonzero()[0]

File ~/miniforge-pypy3/envs/diffbindfr/lib/python3.9/site-packages/prody/atomic/select.py:1003, in Select.getBoolArray(self, atoms, selstr, **kwargs)
   1001 selstr = replaceMacros(selstr)
   1002 try:
-> 1003     parser = self._getParser(selstr)
   1004     tokens = parser(selstr, parseAll=True)
   1005 except pp.ParseException as err:

File ~/miniforge-pypy3/envs/diffbindfr/lib/python3.9/site-packages/prody/atomic/select.py:1102, in Select._getParser(self, selstr)
   1100 parser.setParseAction(self._default)
   1101 parser.leaveWhitespace()
-> 1102 parser.enablePackrat()
   1103 self._parsers[key] = parser, expr, oplist
   1104 return parser.parseString

File ~/miniforge-pypy3/envs/diffbindfr/lib/python3.9/site-packages/pyparsing/util.py:265, in replaced_by_pep8.<locals>._inner(*args, **kwargs)
    260 @wraps(fn)
    261 def _inner(*args, **kwargs):
    262     # warnings.warn(
    263     #     f\"Deprecated - use {fn.__name__}\", DeprecationWarning, stacklevel=2
    264     # )
--> 265     return fn(*args, **kwargs)

File ~/miniforge-pypy3/envs/diffbindfr/lib/python3.9/site-packages/pyparsing/core.py:1132, in ParserElement.enable_packrat(cache_size_limit, force)
   1130     ParserElement.packrat_cache = _UnboundedCache()
   1131 else:
-> 1132     ParserElement.packrat_cache = _FifoCache(cache_size_limit)  # type: ignore[assignment]
   1133 ParserElement._parse = ParserElement._parseCache

File ~/miniforge-pypy3/envs/diffbindfr/lib/python3.9/site-packages/pyparsing/util.py:105, in _FifoCache.__init__(self, size)
    103 self.not_in_cache = not_in_cache = object()
    104 cache = {}
--> 105 keyring = [object()] * size
    106 cache_get = cache.get
    107 cache_pop = cache.pop

TypeError: can't multiply sequence by non-int of type 'Forward'"
}

HBioquant / DiffBindFR

TypeError: can't multiply sequence by non-int of type 'Forward' in AF2_model_docking.ipynb of cell 5. #13