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PDJ v2.1 fixes #1

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PDJ v2.1 fixes #1

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1bfd9e3
Update PDJ version
JoshuaMHardy Jan 6, 2026
20621a5
Update gitignore
JoshuaMHardy Jan 6, 2026
8782229
Fix process workflow results directory detection
JoshuaMHardy Jan 6, 2026
ba520cb
Fix visualisation error for PDJ binder denovo
JoshuaMHardy Jan 6, 2026
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -5,3 +5,4 @@
*.pyc
test-results
/.idea
.github
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@prihoda prihoda Jan 24, 2026

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can you explain the reasoning here? typically this is not ignored because it can contain github actions

5 changes: 3 additions & 2 deletions ovo_proteindj/components/workflow_visualization_components.py
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Expand Up @@ -372,9 +372,10 @@ def visualize_binder_design_structure(design_id: str):
# TODO use target spec for this
# Note this assumes that the target chain is B in the RFdiffusion output PDB,
# and that the residue numbers are same as in the input PDB
target_chain = workflow.get_target_chain()
hotspot_selections = (
[h.replace(workflow.target_chain, "B") for h in workflow.get_hotspots().split(",")]
if workflow.get_hotspots() and workflow.target_chain
[h.replace(target_chain, "B") for h in workflow.get_hotspots().split(",")]
if workflow.get_hotspots() and target_chain
else None
)

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32 changes: 28 additions & 4 deletions ovo_proteindj/logic.py
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Expand Up @@ -32,13 +32,37 @@ def process_workflow_results(job: DesignJob, callback: Callable = None) -> list[
assert job.workflow.is_instance(models_proteindj.ProteinDJDesignWorkflow), (
"This function expects a ProteinDJDesignWorkflow instance, got: {}".format(type(job.workflow).__name__)
)

# Get source directory
source_dir = scheduler.get_output_dir(job.job_id)
run_dir = os.path.join(source_dir, "run")

# Auto-detect or use configured fold directory
fold_dir = job.workflow.params.get('fold_method', 'rfd')

# Auto-detect or use configured sequence design directory
seq_dir = job.workflow.params.get('seq_method')
if not seq_dir:
for option in ["fampnn", "mpnn"]:
if os.path.exists(os.path.join(run_dir, option)):
seq_dir = option
break

# Auto-detect or use configured structure prediction directory
pred_dir = job.workflow.params.get('pred_method')
if not pred_dir:
for option in ["af2", "boltz"]:
if os.path.exists(os.path.join(run_dir, option)):
pred_dir = option
break

return process_proteindj_output_dir(
job=job,
pool=pool,
source_dir=scheduler.get_output_dir(job.job_id),
fold_dir="rfd",
seq_dir=job.workflow.params.seq_method,
pred_dir=job.workflow.params.pred_method,
source_dir=source_dir,
fold_dir=fold_dir,
seq_dir=seq_dir,
pred_dir=pred_dir,
callback=callback,
)

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2 changes: 1 addition & 1 deletion ovo_proteindj/models_proteindj.py
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Expand Up @@ -14,7 +14,7 @@

# Pipeline version
# tag or commit ID from https://github.com/PapenfussLab/proteindj
PIPELINE_VERSION = "5db7c4e6b9507ebfdcd20090ebb3eef544abe27c"
PIPELINE_VERSION = "v2.1.1"

# Get default pipeline params from OVO config
plugin_config = config.plugins.get(__package__, {})
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