Error in google colab
aaaniich opened this issue · 4 comments
Hi! I try to analyse my sequence with google colab, but i have this error. Can you help me? Thank you
IndexError Traceback (most recent call last)
in
7 with open(fasta_file, "w") as f:
8 f.write(">:H\n{}\n>:L\n{}\n".format(heavy_sequence, light_sequence))
----> 9 cst_defs = get_cst_defs(model, fasta_file, device=device)
10
11 pred_pdb = build_structure(model,
1 frames
/content/deepab/deepab/constraints/write_constraints.py in get_constraint_residue_pairs(model, fasta_file, constraint_bin_value_dict, mask_distant_orientations, use_logits, device)
94
95 if constraint_type in pairwise_constraint_types:
---> 96 if preds[pred_i][i, j].argmax().item() >= len(
97 constraint_bin_value_dict[constraint_type]):
98 continue
IndexError: index 235 is out of bounds for dimension 0 with size 235
H
QVQLKESGPGLVAPSQSLSITGTDNYIEVSGDYGVSWIRQPPGKGMVSGSGLTDGGSTYYNSALKSRLSI
SKDNSKSQVFLKMNSLDASADAMYYCAKHTYGGPGDSWGQGTSVTVSS
L
DIVMSQSPSSLAVSAGEKVTMSCRSSQSLVHSNGNTYLYRKNYLAWYQQKPGQYDATKLDSASTRESGVP
DRFTGSGSGTDFTQQSGSYPLTDLAVYYCKQSYDLPTFGAGTKLELK
It's my sequence
Hello, this may be a result of Colab updating to python3.8 in the last couple days. I am working on a fix for this currently.
Hello, this may be a result of Colab updating to python3.8 in the last couple days. I am working on a fix for this currently.
Sorry to bother you again!
Some of my sequences still end up with an error. Can you tell me what I'm doing wrong?
H
QVQLKESGPGLVAPSQSLSITGTSGSSLSKGYYGDYGVSWIRQPPGKGAISSGGGTAGGGSTYYNSALKS
RLSISKDNSKSQVFLKMNSLDDDDSAMYYCAKHTYGGPGDSWGQGTSVTVSS
L
DIVMSQSPSSLAVSAGEKVTMSCTAESQTSHVNRKNYLAWYQQKPGQRDGSSLSGASTRESGVPDRFTGS
GSGTDFTSQSKEVPLTDLAVYYCKQSYDLPTFGAGTKLELK
Hello, this may be a result of Colab updating to python3.8 in the last couple days. I am working on a fix for this currently.
I have this error every time, when I try to start step "Predict antibody structure with DeepAb"
IndexError: index 233 is out of bounds for dimension 0 with size 233