I ran into a fairly new issue with running the ESM_advanced Colab with a ~120 aa sequence (that predicts well with the ESMfold Colab) that seems to happen after the prediction module has run (because I can see the message: CPU times: user 1.9 ms, sys: 988 µs, total: 2.89 ms, Wall time: 2.76 ms..). The error message I get as program crashes is the following. Thx in advance for your expert help.
length 0
IndexError Traceback (most recent call last)
in
[/usr/local/lib/python3.7/dist-packages/torch/autograd/grad_mode.py](https://localhost:8080/#) in decorate_context(*args, **kwargs)
25 def decorate_context(*args, **kwargs):
26 with self.clone():
---> 27 return func(*args, **kwargs)
28 return cast(F, decorate_context)
29
5 frames
[/usr/local/lib/python3.7/dist-packages/esm/esmfold/v1/esmfold.py](https://localhost:8080/#) in _af2_idx_to_esm_idx(self, aa, mask)
91 def _af2_idx_to_esm_idx(self, aa, mask):
92 aa = (aa + 1).masked_fill(mask != 1, 0)
---> 93 return self.af2_to_esm[aa]
94
95 def _compute_language_model_representations(self,
IndexError: tensors used as indices must be long, byte or bool tensors
and at the bottom
TypeError Traceback (most recent call last)
[](https://localhost:8080/#) in
60 return plt
61
---> 62 plot_confidence(best_output, Ls=lengths, dpi=dpi)
63 plt.show()
[](https://localhost:8080/#) in plot_confidence(output, Ls, dpi)
17
18 def plot_confidence(output, Ls=None, dpi=100):
---> 19 O = parse_output(output)
20 if "lm_contacts" in O:
21 plt.figure(figsize=(20,4), dpi=dpi)
in parse_output(output)
TypeError: 'NoneType' object is not subscriptable
I ran into a fairly new issue with running the ESM_advanced Colab with a ~120 aa sequence (that predicts well with the ESMfold Colab) that seems to happen after the prediction module has run (because I can see the message: CPU times: user 1.9 ms, sys: 988 µs, total: 2.89 ms, Wall time: 2.76 ms..). The error message I get as program crashes is the following. Thx in advance for your expert help.
length 0
IndexError Traceback (most recent call last)