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ikalvet / heme_binder_diffusion

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make_maskdict_from_trb.py missing #6

Closed denizkavi closed 3 months ago

denizkavi commented 3 months ago 
### Parsing diffusion output TRB files to extract fixed motif residues
## These residues will not be redesigned with proteinMPNN
mask_json_cmd = f"{PYTHON['general']} {SCRIPT_DIR}/scripts/ligandMPNN/helper_scripts/make_maskdict_from_trb.py --out masked_pos.jsonl --trb"
for d in diffused_backbones_good:
    mask_json_cmd += " " + d.replace(".pdb", ".trb")
p = subprocess.Popen(mask_json_cmd, shell=True)
(output, err) = p.communicate()

assert os.path.exists("masked_pos.jsonl"), "Failed to create masked positions JSONL file"

In this part of the pipeline, I don't have the "ligandMPNN" directory inside my scripts. I don't think it is added when I update the submodule either. Anything I may be missing?

denizkavi commented 3 months ago

Apparently this file is in {SCRIPT_DIR}/scripts/design/make_maskdict_from_trb.py