martinpacesa / martinpacesa/BindCraft

Example run fails in fresh installation

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Python
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Description

Using the PDL1.pdb from the repo and default settings.

python -u ../bindcraft.py --settings '../settings_target/PDL1.json' --filters '../settings_filters/default_filters.json' --advanced '../settings_advanced/default_4stage_multimer.json'

. . . . 
lddt 0.83 ptm 0.83 i_ptm 0.81 rg 2.74
Trajectory successful, final pLDDT: 0.92
Starting trajectory took: 0 hours, 6 minutes, 49 seconds

Traceback (most recent call last):
  File "/opt/VDBSoftware/BindCraft/example2/../bindcraft.py", line 141, in <module>
    trajectory_interface_scores, trajectory_interface_AA, trajectory_interface_residues = score_interface(trajectory_relaxed, binder_chain)
  File "/opt/VDBSoftware/BindCraft/functions/pyrosetta_utils.py", line 26, in score_interface
    iam.set_interface("A_B")
TypeError: set_interface(): incompatible function arguments. The following argument types are supported:
    1. (self: pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover, interface: pyrosetta.rosetta.core.pose.DockingPartners) -> None

Invoked with: <pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover object at 0x14e563840d70>, 'A_B'

Output directory:

$ tree
.
|-- PDL1.pdb
|-- output
|   |-- Accepted
|   |   |-- Animation
|   |   |-- Pickle
|   |   |-- Plots
|   |   `-- Ranked
|   |-- MPNN
|   |   |-- Binder
|   |   |-- Relaxed
|   |   `-- Sequences
|   |-- Rejected
|   |-- Trajectory
|   |   |-- Animation
|   |   |   `-- PDL1_l147_s726978.html
|   |   |-- Clashing
|   |   |-- LowConfidence
|   |   |-- PDL1_l147_s726978.pdb
|   |   |-- Pickle
|   |   |-- Plots
|   |   |   |-- PDL1_l147_s726978_con.png
|   |   |   |-- PDL1_l147_s726978_i_con.png
|   |   |   |-- PDL1_l147_s726978_i_pae.png
|   |   |   |-- PDL1_l147_s726978_i_ptm.png
|   |   |   |-- PDL1_l147_s726978_loss.png
|   |   |   |-- PDL1_l147_s726978_pae.png
|   |   |   |-- PDL1_l147_s726978_plddt.png
|   |   |   |-- PDL1_l147_s726978_ptm.png
|   |   |   `-- PDL1_l147_s726978_rg.png
|   |   `-- Relaxed
|   |       `-- PDL1_l147_s726978.pdb
|   |-- failure_csv.csv
|   |-- final_design_stats.csv
|   |-- mpnn_design_stats.csv
|   `-- trajectory_stats.csv

Contributor guide

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start in functions/pyrosetta_utils.py at score_interface and inspect the call from bindcraft.py line 141. Reproduce the failure with the PDL1 example command and check the installed PyRosetta InterfaceAnalyzerMover API. Done means the fresh-install example completes interface scoring without the TypeError and produces the expected output statistics.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Quiet
Clarity
Clearly specified
Newbie friendliness
68/100

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