martinpacesa / martinpacesa/BindCraft
Example run fails in fresh installation
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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
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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