Open zhang-bo-lilly opened 7 hours ago
Additionally,
this line should be iloc
instead of loc
as the labels in the human_idr_boundaries_gap.tsv file are not consecutive. This seems to be also aligned with the following commented code.
Next, assume the following line is changed to iloc
https://github.com/microsoft/evodiff/blob/f696cfc0e58dcb17b31bf4110aaf11a8a612b07b/evodiff/conditional_generation_msa.py#L888
The execution will throw another error at https://github.com/microsoft/evodiff/blob/f696cfc0e58dcb17b31bf4110aaf11a8a612b07b/evodiff/conditional_generation_msa.py#L686
(Pdb) n
IndexError: index 662 is out of bounds for dimension 2 with size 201
> /home/c271831/evodiff/evodiff/conditional_generation_msa.py(686)generate_idr_msa()
-> p = preds[:, random_x, random_y, :]
(Pdb) p random_x
33
(Pdb) p random_y
662
(Pdb) p preds.shape
torch.Size([1, 64, 201, 31])
Appreciate help on getting the code running.
Hello, I am having trouble executing the example in the Generating intrinsically disordered regions of the README file.
Per #41, I downloaded the dataset needed from https://zenodo.org/records/5146063, extracted the
human_idr_homologues.zip
, and saved it ashuman_protein_alignments
directory, so the layout of the directory looks like thisFrom the root directory of the repository, I executed and observed the following
I stepped through PDB and found these
It seems to me that
https://github.com/microsoft/evodiff/blob/f696cfc0e58dcb17b31bf4110aaf11a8a612b07b/evodiff/conditional_generation_msa.py#L793
needs to be changed to
row['OMA_ID'] in name
. Is this correct?