AttributeError : Constant object has no attribute ‘kind’

[Planet-KIM]

• I used covid protein ‘nsp2.pdb’ file.(In this “ structure_utils_tests.ipynb” test file)
• In this part occured error

N_mask  = torch.tensor( prot_traj.topology.select("name == N and backbone") ).unsqueeze(0)
CA_mask = torch.tensor( prot_traj.topology.select("name == CA and backbone") ).unsqueeze(0) 
C_mask  = torch.tensor( prot_traj.topology.select("name == C and backbone")  ).unsqueeze(0)
CA_mask.shape, N_mask.shape, C_mask.shape

• Error Log

   549             self.write("...")
    550         else:
--> 551             if t.kind == "u":
    552                 self.write("u")
    553             self._write_constant(t.value)

AttributeError: 'Constant' object has no attribute 'kind'

• Please give me solutions.

[hypnopump]

can you include the complete error trace? it's difficult to see what's happening in there. Those tests worked with the deafult file

[Planet-KIM]

• I'm sorry for the late reply.
• 1. It's all error log

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-98-6b7956c78108> in <module>
      1 # select indices of backbone for angle calculation and selection
----> 2 N_mask  = torch.tensor( prot_traj.topology.select("name == N and backbone") ).unsqueeze(0)
      3 CA_mask = torch.tensor( prot_traj.topology.select("name == CA and backbone") ).unsqueeze(0)
      4 C_mask  = torch.tensor( prot_traj.topology.select("name == C and backbone")  ).unsqueeze(0)
      5 CA_mask.shape, N_mask.shape, C_mask.shape

/commons/software/anaconda3/lib/python3.8/site-packages/mdtraj/core/topology.py in select(self, selection_string)
   1054         """
   1055 
-> 1056         filter_func = parse_selection(selection_string).expr
   1057         indices = np.array([a.index for a in self.atoms if filter_func(a)])
   1058         return indices

/commons/software/anaconda3/lib/python3.8/site-packages/mdtraj/core/selection.py in __call__(self, selection)
    397 
    398         func = ast.Expression(body=ast.Lambda(signature, astnode))
--> 399         source = astunparse.unparse(astnode)
    400 
    401         expr = eval(

/commons/software/anaconda3/lib/python3.8/site-packages/astunparse/__init__.py in unparse(tree)
     11 def unparse(tree):
     12     v = cStringIO()
---> 13     Unparser(tree, file=v)
     14     return v.getvalue()
     15 

/commons/software/anaconda3/lib/python3.8/site-packages/astunparse/unparser.py in __init__(self, tree, file)
     36         self.future_imports = []
     37         self._indent = 0
---> 38         self.dispatch(tree)
     39         print("", file=self.f)
     40         self.f.flush()

/commons/software/anaconda3/lib/python3.8/site-packages/astunparse/unparser.py in dispatch(self, tree)
     64             return
     65         meth = getattr(self, "_"+tree.__class__.__name__)
---> 66         meth(tree)
     67 
     68 

/commons/software/anaconda3/lib/python3.8/site-packages/astunparse/unparser.py in _BoolOp(self, t)
    701         self.write("(")
    702         s = " %s " % self.boolops[t.op.__class__]
--> 703         interleave(lambda: self.write(s), self.dispatch, t.values)
    704         self.write(")")
    705 

/commons/software/anaconda3/lib/python3.8/site-packages/astunparse/unparser.py in interleave(inter, f, seq)
     17     seq = iter(seq)
     18     try:
---> 19         f(next(seq))
     20     except StopIteration:
     21         pass

/commons/software/anaconda3/lib/python3.8/site-packages/astunparse/unparser.py in dispatch(self, tree)
     64             return
     65         meth = getattr(self, "_"+tree.__class__.__name__)
---> 66         meth(tree)
     67 
     68 

/commons/software/anaconda3/lib/python3.8/site-packages/astunparse/unparser.py in _Compare(self, t)
    694         for o, e in zip(t.ops, t.comparators):
    695             self.write(" " + self.cmpops[o.__class__.__name__] + " ")
--> 696             self.dispatch(e)
    697         self.write(")")
    698 

/commons/software/anaconda3/lib/python3.8/site-packages/astunparse/unparser.py in dispatch(self, tree)
     64             return
     65         meth = getattr(self, "_"+tree.__class__.__name__)
---> 66         meth(tree)
     67 
     68 

/commons/software/anaconda3/lib/python3.8/site-packages/astunparse/unparser.py in _Constant(self, t)
    549             self.write("...")
    550         else:
--> 551             if t.kind == "u":
    552                 self.write("u")
    553             self._write_constant(t.value)

AttributeError: 'Constant' object has no attribute 'kind' 

• What is this problem. I want to solute this error.
• Please give me solutions.

[hypnopump]

Seems that it's a problem of the mdtraj library. May i have the pdb file you're using to debug the issue?

[Planet-KIM]

• Now i used the "data/1h22_protein_chain_1.pdb" file on this project. but occurred same error.
• Please give me solutions.

[hypnopump]

As i said, it's a problem of the mdtraj library. Try downgrading its version. Alternatively, you can share your version so that i can have a look. But keep in mind this is not essential for the AF2 working. It is just a side test/example

[Planet-KIM]

• Now i used "madtraj == 1.9.4 " (Now i try 1.9.1 version. But It's fail too)
• What version using on this project?

[hypnopump]

Please, try the fix suggested here: simonpercivall/astunparse#43 regarding the instruction to comment the if statement