can't multiply sequencce by non-int of type 'Forward'

[tonyageall]

I can not reproduce your example from the tutorial. My error is:

Traceback (most recent call last):
File "/home/afarina/SIM_ENV/bin/lightdock3_setup.py", line 93, in
calculate_anm(receptor, args.anm_rec, args.anm_rec_rmsd, args.anm_seed, DEFAULT_REC_NM_FILE)
File "/home/afarina/SIM_ENV/lib/python3.10/site-packages/lightdock/prep/simulation.py", line 136, in calculate_anm
modes = calculate_nmodes(parsed_lightdock_structure, num_nmodes, rmsd, seed, structure)
File "/home/afarina/SIM_ENV/lib/python3.10/site-packages/lightdock/structure/nm.py", line 42, in calculate_nmodes
num_atoms_prody = prody_molecule.select("protein or nucleic").numAtoms()
File "/home/afarina/SIM_ENV/lib/python3.10/site-packages/prody/atomic/atomic.py", line 232, in select
return SELECT.select(self, selstr, **kwargs)
File "/home/afarina/SIM_ENV/lib/python3.10/site-packages/prody/atomic/select.py", line 895, in select
indices = self.getIndices(atoms, selstr, **kwargs)
File "/home/afarina/SIM_ENV/lib/python3.10/site-packages/prody/atomic/select.py", line 953, in getIndices
torf = self.getBoolArray(atoms, selstr, **kwargs)
File "/home/afarina/SIM_ENV/lib/python3.10/site-packages/prody/atomic/select.py", line 1004, in getBoolArray
parser = self._getParser(selstr)
File "/home/afarina/SIM_ENV/lib/python3.10/site-packages/prody/atomic/select.py", line 1103, in _getParser
parser.enablePackrat()
File "/home/afarina/SIM_ENV/lib/python3.10/site-packages/pyparsing/util.py", line 265, in _inner
return fn(*args, **kwargs)
File "/home/afarina/SIM_ENV/lib/python3.10/site-packages/pyparsing/core.py", line 1132, in enable_packrat
ParserElement.packrat_cache = _FifoCache(cache_size_limit) # type: ignore[assignment]
File "/home/afarina/SIM_ENV/lib/python3.10/site-packages/pyparsing/util.py", line 105, in init
keyring = [object()] * size
TypeError: can't multiply sequence by non-int of type 'Forward'

I am not sure where this is coming from. I installed from pip.

[brianjimenez]

Please @tonyageall , could you specify which example and version of LightDock did you install (I assume it's the last, but just to double check). If you could also share the exact prompt it would be great.

[tonyageall]

release Release 0.9.4 and I was trying to walk through your examples here https://lightdock.org/tutorials/0.9.3/simple_docking fails on lightdock3_setup.py 2UUY_rec.pdb 2UUY_lig.pdb --noxt --noh --now -anm

[brianjimenez]

Problem comes from pyparsing version 3.1.2, a dependency by ProDy library which is a dependency for LightDock (sorry, no control over it until ProDy nor pyparsing teams fix it). In the meantime, a workaround consists in downgrading the version to 3.1.1. Just type: pip install pyparsing==3.1.1

Please, could you confirm this solves the issue?

[tonyageall]

works know thank you so much