from pdbfixer import PDBFixer ModuleNotFoundError: No module named 'pdbfixer'

[ChristophKnapp]

Hi, this might not be the right place to ask this but for most people it obviously works.
For some reason in my setup it can't find the module pdbfixer, which is used by esmtools. ProteusAI is installed into my python environment and I'm trying to run the code from the design_demo.py.

If you think I should ask this at esmtools, just tell me to go away.

Still any idea what might be wrong in my setup?

Regards Christoph

[enryH]

pdbfixer is not installed using pip as the package is only distributed through the conda-forge channel - probably due to certain dependencies. But you could try to see their reason not making it available through pip there.

pip installed dependencies:

ProteusAI/pyproject.toml

Lines 12 to 40 in b7065da

	dependencies = [
	"torch==2.4.1",
	"torch_geometric",
	"torch-scatter",
	"uvicorn",
	"asgiref",
	"starlette",
	#"pdbfixer",
	"shiny",
	"pandas",
	"numpy",
	"requests",
	"scipy",
	"fair-esm",
	"matplotlib",
	"biopython",
	"biotite",
	"scikit-learn",
	"optuna",
	"seaborn",
	"openpyxl",
	"py3Dmol",
	"gpytorch",
	"openmm",
	"umap-learn",
	"hdbscan",
	"proteusAI",
	#"pdbfixer @ git+https://github.com/openmm/pdbfixer@1.9"
	]

pdbfixer repo with instructions: https://github.com/openmm/pdbfixer

Well, in the end this is the reason why we have the conda environment setup.

[enryH]

OpenMM needs to be pip installable first: openmm/pdbfixer#254

They are available since this November (2024) for the latest version 8.2 and higher: https://pypi.org/project/OpenMM/

so soon this will be resolved