Example run fails in fresh installation

[averagehat]

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

[ykcor8902]

Same question met.

After asking chatgpt, it says that the pyrosetta version is not compatible with the usage in pyrosetta_utils.py.

I personally tried to uninstall the environment and reinstall it using the following script, which specifies the version of pyrosetta to be 2025.29.

install_bindcraft_202529.sh

After reconfiguring the environment, it works. But personally I don't know if the pyrosetta version is the most suitable one.

And I use cuda 12.6, but the version of cuda may not influence the settings, it should be tried.

May it help.

[ykcor8902]

Same question met.

After asking chatgpt, it says that the pyrosetta version is not compatible with the usage in pyrosetta_utils.py.

I personally tried to uninstall the environment and reinstall it using the following script, which specifies the version of pyrosetta to be 2025.29.

install_bindcraft_202529.sh

After reconfiguring the environment, it works. But personally I don't know if the pyrosetta version is the most suitable one.

And I use cuda 12.6, but the version of cuda may not influence the settings, it should be tried.

May it help.

After a personal test, the 2026.3 version (which could be installed by

pip install \
'pyrosetta==2026.3+releasequarterly.5e498f1409' \
--find-links https://west.rosettacommons.org/pyrosetta/quarterly/release.cxx11thread.serialization \
--no-deps

could also work, which is newer than 2025.29 version.

By the way, the default install script installed 2026.29 version on 20260808, which doesn't work.

[averagehat]

Neither suggestion worked for me. Also--what python version are you on?

Using the install_bindcraft_202529.sh install script:

Installing ColabDesign

Collecting git+https://github.com/sokrypton/ColabDesign.git
  Cloning https://github.com/sokrypton/ColabDesign.git to /tmp/pip-req-build-45mlgzp2
  Running command git clone --filter=blob:none --quiet https://github.com/sokrypton/ColabDesign.git /tmp/pip-req-build-45mlgzp2
  Resolved https://github.com/sokrypton/ColabDesign.git to commit e31a56fe1d9b4de25c8697f3a28b75892941cc72
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Building wheels for collected packages: colabdesign
  Building wheel for colabdesign (pyproject.toml) ... done
  Created wheel for colabdesign: filename=colabdesign-1.1.3-py3-none-any.whl size=49868252 sha256=f0dc4d9a1d1498cdfc6340facfc937c66fe65e6b1846aa77cb425aa3ab55321f
  Stored in directory: /tmp/pip-ephem-wheel-cache-be0bndnq/wheels/17/cf/49/c29de6f205fc51717698726bf695a5f1e02c8aaeaac9ad1797
Successfully built colabdesign
Installing collected packages: colabdesign
Successfully installed colabdesign-1.1.3
Error: colabdesign module not found after installation

And attempting to run gives the error:

Traceback (most recent call last):
  File "/opt/VDBSoftware/BindCraft/./bindcraft.py", line 5, in <module>
    from functions import *
  File "/opt/VDBSoftware/BindCraft/functions/__init__.py", line 11, in <module>
    from .pyrosetta_utils import *
  File "/opt/VDBSoftware/BindCraft/functions/pyrosetta_utils.py", line 6, in <module>
    import pyrosetta as pr
ModuleNotFoundError: No module named 'pyrosetta'

[martinpacesa]

Should be fixed with this #373

[ykcor8902]

Neither suggestion worked for me. Also--what python version are you on?

Using the install_bindcraft_202529.sh install script:

Installing ColabDesign

Collecting git+https://github.com/sokrypton/ColabDesign.git
  Cloning https://github.com/sokrypton/ColabDesign.git to /tmp/pip-req-build-45mlgzp2
  Running command git clone --filter=blob:none --quiet https://github.com/sokrypton/ColabDesign.git /tmp/pip-req-build-45mlgzp2
  Resolved https://github.com/sokrypton/ColabDesign.git to commit e31a56fe1d9b4de25c8697f3a28b75892941cc72
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Building wheels for collected packages: colabdesign
  Building wheel for colabdesign (pyproject.toml) ... done
  Created wheel for colabdesign: filename=colabdesign-1.1.3-py3-none-any.whl size=49868252 sha256=f0dc4d9a1d1498cdfc6340facfc937c66fe65e6b1846aa77cb425aa3ab55321f
  Stored in directory: /tmp/pip-ephem-wheel-cache-be0bndnq/wheels/17/cf/49/c29de6f205fc51717698726bf695a5f1e02c8aaeaac9ad1797
Successfully built colabdesign
Installing collected packages: colabdesign
Successfully installed colabdesign-1.1.3
Error: colabdesign module not found after installation

And attempting to run gives the error:

Traceback (most recent call last):
File "/opt/VDBSoftware/BindCraft/./bindcraft.py", line 5, in
from functions import *
File "/opt/VDBSoftware/BindCraft/functions/init.py", line 11, in
from .pyrosetta_utils import *
File "/opt/VDBSoftware/BindCraft/functions/pyrosetta_utils.py", line 6, in
import pyrosetta as pr
ModuleNotFoundError: No module named 'pyrosetta'

Sorry, but I worked fluently with my script, having no idea about the possible cause for this error, I have python 3.10 by the way...

However, after the mend of pyrosetta_utils.py by a kind contributor just now, now the default install_bindcraft.sh should work, I guess.

[averagehat]

The default install script still leads to the same error:

ModuleNotFoundError: No module named 'pyrosetta'

Manually installing pyrosetta with

$ pip install pyrosetta --find-links https://west.rosettacommons.org/pyrosetta/quarterly/release.cxx11thread.serialization

And then running with

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

Leads to:

Traceback (most recent call last):
  File "/opt/VDBSoftware/bindcraft/BindCraft/./bindcraft.py", line 5, in <module>
    from functions import *
  File "/opt/VDBSoftware/bindcraft/BindCraft/functions/__init__.py", line 12, in <module>
    from .colabdesign_utils import *
  File "/opt/VDBSoftware/bindcraft/BindCraft/functions/colabdesign_utils.py", line 11, in <module>
    from colabdesign import mk_afdesign_model, clear_mem
  File "/opt/VDBSoftware/envs/bindcraft/lib/python3.10/site-packages/colabdesign/__init__.py", line 10, in <module>
    from colabdesign.af.model import mk_af_model
  File "/opt/VDBSoftware/envs/bindcraft/lib/python3.10/site-packages/colabdesign/af/__init__.py", line 10, in <module>
    from colabdesign.af.model import mk_af_model
  File "/opt/VDBSoftware/envs/bindcraft/lib/python3.10/site-packages/colabdesign/af/model.py", line 7, in <module>
    from colabdesign.af.alphafold.model import data, config, model, all_atom
  File "/opt/VDBSoftware/envs/bindcraft/lib/python3.10/site-packages/colabdesign/af/alphafold/model/data.py", line 20, in <module>
    from colabdesign.af.alphafold.model import utils
  File "/opt/VDBSoftware/envs/bindcraft/lib/python3.10/site-packages/colabdesign/af/alphafold/model/utils.py", line 23, in <module>
    import haiku as hk
  File "/opt/VDBSoftware/envs/bindcraft/lib/python3.10/site-packages/haiku/__init__.py", line 20, in <module>
    from haiku import experimental
  File "/opt/VDBSoftware/envs/bindcraft/lib/python3.10/site-packages/haiku/experimental/__init__.py", line 21, in <module>
    from haiku._src.base import current_name
  File "/opt/VDBSoftware/envs/bindcraft/lib/python3.10/site-packages/haiku/_src/base.py", line 39, in <module>
    import jax.extend.core as jex_core
ModuleNotFoundError: No module named 'jax.extend.core'

[martinpacesa]

Did you try the latest version from today? I just tested it and ran fine for me

[ykcor8902]

The default install script still leads to the same error:

ModuleNotFoundError: No module named 'pyrosetta'
Manually installing pyrosetta with

$ pip install pyrosetta --find-links https://west.rosettacommons.org/pyrosetta/quarterly/release.cxx11thread.serialization

And then running with

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

Traceback (most recent call last):
File "/opt/VDBSoftware/bindcraft/BindCraft/./bindcraft.py", line 5, in
from functions import *
File "/opt/VDBSoftware/bindcraft/BindCraft/functions/init.py", line 12, in
from .colabdesign_utils import *
File "/opt/VDBSoftware/bindcraft/BindCraft/functions/colabdesign_utils.py", line 11, in
from colabdesign import mk_afdesign_model, clear_mem
File "/opt/VDBSoftware/envs/bindcraft/lib/python3.10/site-packages/colabdesign/init.py", line 10, in
from colabdesign.af.model import mk_af_model
File "/opt/VDBSoftware/envs/bindcraft/lib/python3.10/site-packages/colabdesign/af/init.py", line 10, in
from colabdesign.af.model import mk_af_model
File "/opt/VDBSoftware/envs/bindcraft/lib/python3.10/site-packages/colabdesign/af/model.py", line 7, in
from colabdesign.af.alphafold.model import data, config, model, all_atom
File "/opt/VDBSoftware/envs/bindcraft/lib/python3.10/site-packages/colabdesign/af/alphafold/model/data.py", line 20, in
from colabdesign.af.alphafold.model import utils
File "/opt/VDBSoftware/envs/bindcraft/lib/python3.10/site-packages/colabdesign/af/alphafold/model/utils.py", line 23, in
import haiku as hk
File "/opt/VDBSoftware/envs/bindcraft/lib/python3.10/site-packages/haiku/init.py", line 20, in
from haiku import experimental
File "/opt/VDBSoftware/envs/bindcraft/lib/python3.10/site-packages/haiku/experimental/init.py", line 21, in
from haiku._src.base import current_name
File "/opt/VDBSoftware/envs/bindcraft/lib/python3.10/site-packages/haiku/_src/base.py", line 39, in
import jax.extend.core as jex_core
ModuleNotFoundError: No module named 'jax.extend.core'

Have you ever completely removed the BindCraft environment, and then reinstall it again using the default installation script?

If you want, you may try the below command which ChatGPT gives me, and don't forget to change the cuda version in the command bash install_bindcraft.sh --cuda '12.6' --pkg_manager 'conda' to your own version, and then you can just copy all the things down and try it in your linux shell.

# Leave any currently active environment
conda deactivate 2>/dev/null || true

# Completely remove the previous BindCraft environment
conda env remove -n BindCraft -y 2>/dev/null || true

# Go to your software directory
cd /opt/VDBSoftware

# Keep the old repository as a backup
if [ -d BindCraft ]; then
    mv BindCraft "BindCraft_backup_$(date +%Y%m%d_%H%M%S)"
fi

# Clone the latest BindCraft main branch
git clone https://github.com/martinpacesa/BindCraft.git
cd BindCraft

# Show the exact commit being used
git log -1 --oneline

# Verify that the current PyRosetta compatibility fix is present
echo
echo "Checking current InterfaceAnalyzerMover implementation:"
grep -n -A15 -B3 "iam = InterfaceAnalyzerMover" functions/pyrosetta_utils.py

echo
echo "Checking DockingPartners compatibility code:"
grep -n "DockingPartners" functions/pyrosetta_utils.py

# Fresh install
# Replace 12.6 with the CUDA version appropriate for your system
bash install_bindcraft.sh --cuda '12.6' --pkg_manager 'conda'

# Activate the freshly created environment
source "$(conda info --base)/etc/profile.d/conda.sh"
conda activate BindCraft

# Check which environment is actually being used
echo
echo "Python:"
which python

echo
echo "Pip:"
which pip

echo
echo "Conda prefix:"
echo "$CONDA_PREFIX"

# Verify PyRosetta installation and test the same compatibility
# mechanism currently used by BindCraft
python - <<'PY'
import sys
import pyrosetta as pr

print()
print("Python:", sys.executable)
print("PyRosetta:", pr.__version__)
print("PyRosetta path:", pr.__file__)

InterfaceAnalyzerMover = pr.rosetta.protocols.analysis.InterfaceAnalyzerMover

iam = InterfaceAnalyzerMover()

interface = "A_B"

docking_partners_type = getattr(
    pr.rosetta.core.pose,
    "DockingPartners",
    None
)

if docking_partners_type is not None:
    print("DockingPartners API detected.")
    interface = docking_partners_type.docking_partners_from_string(interface)
else:
    print("Legacy string interface API detected.")

iam.set_interface(interface)

print("InterfaceAnalyzerMover compatibility test: PASSED")
PY