Error while running the tutorial walkthrough

[sli259]

I am trying to run the walkthrough tutorial on Chignoline and got the following error at initial step to generate the psf file, can you tell me what I missed?

---------------------------------------------------------------------------
InvalidIndexError                         Traceback (most recent call last)
Input In [29], in <cell line: 6>()
      3 PDB_file = 'data/chignolin_cln025.pdb'
      4 PSF_file = 'data/chignolin_ca_top.psf'
----> 6 pdb2psf_CA(PDB_file, PSF_file, bonds = True, angles = False)

File ~/miniconda3/envs/torchmd_cg/lib/python3.9/site-packages/torchmd_cg/utils/psfwriter.py:7, in pdb2psf_CA(pdb_name_in, psf_name_out, bonds, angles)
      6 def pdb2psf_CA(pdb_name_in, psf_name_out, bonds=True, angles=True):
----> 7     mol = Molecule(pdb_name_in)
      8     mol.filter("name CA")
     10     n = mol.numAtoms

File ~/miniconda3/envs/torchmd_cg/lib/python3.9/site-packages/moleculekit/molecule.py:299, in Molecule.__init__(self, filename, name, **kwargs)
    296 self.viewname = name
    298 if filename is not None:
--> 299     self.read(filename, **kwargs)

File ~/miniconda3/envs/torchmd_cg/lib/python3.9/site-packages/moleculekit/molecule.py:1147, in Molecule.read(self, filename, type, skip, frames, append, overwrite, keepaltloc, guess, guessNE, _logger, **kwargs)
   1145 for rr in readers:
   1146     try:
-> 1147         mol = rr(fname, frame=frame, topoloc=tmppdb, **kwargs)
   1148     except FormatError:
   1149         continue

File ~/miniconda3/envs/torchmd_cg/lib/python3.9/site-packages/moleculekit/readers.py:1100, in PDBread(filename, mode, frame, topoloc, validateElements, uniqueBonds)
   1098 if "element" in parsedtopo:
   1099     idx, newelem = pdbGuessElementByName(parsedtopo.element, parsedtopo.name)
-> 1100     parsedtopo.at[idx, "element"] = newelem
   1102 for field in topodtypes:
   1103     if (
   1104         field in parsedtopo
   1105         and topodtypes[field] == str
   1106         and parsedtopo[field].dtype == object
   1107     ):

File ~/miniconda3/envs/torchmd_cg/lib/python3.9/site-packages/pandas/core/indexing.py:2274, in _AtIndexer.__setitem__(self, key, value)
   2271     self.obj.loc[key] = value
   2272     return
-> 2274 return super().__setitem__(key, value)

File ~/miniconda3/envs/torchmd_cg/lib/python3.9/site-packages/pandas/core/indexing.py:2229, in _ScalarAccessIndexer.__setitem__(self, key, value)
   2226 if len(key) != self.ndim:
   2227     raise ValueError("Not enough indexers for scalar access (setting)!")
-> 2229 self.obj._set_value(*key, value=value, takeable=self._takeable)

File ~/miniconda3/envs/torchmd_cg/lib/python3.9/site-packages/pandas/core/frame.py:3869, in DataFrame._set_value(self, index, col, value, takeable)
   3867 else:
   3868     series = self._get_item_cache(col)
-> 3869     loc = self.index.get_loc(index)
   3871 # setitem_inplace will do validation that may raise TypeError
   3872 #  or ValueError
   3873 series._mgr.setitem_inplace(loc, value)

File ~/miniconda3/envs/torchmd_cg/lib/python3.9/site-packages/pandas/core/indexes/range.py:388, in RangeIndex.get_loc(self, key, method, tolerance)
    386         except ValueError as err:
    387             raise KeyError(key) from err
--> 388     self._check_indexing_error(key)
    389     raise KeyError(key)
    390 return super().get_loc(key, method=method, tolerance=tolerance)

File ~/miniconda3/envs/torchmd_cg/lib/python3.9/site-packages/pandas/core/indexes/base.py:5637, in Index._check_indexing_error(self, key)
   5633 def _check_indexing_error(self, key):
   5634     if not is_scalar(key):
   5635         # if key is not a scalar, directly raise an error (the code below
   5636         # would convert to numpy arrays and raise later any way) - GH29926
-> 5637         raise InvalidIndexError(key)
InvalidIndexError: []

[MaciejMajew]

Hi! There might be some issue with your moleculekit installation. Please check this issue: #23