[BUG] Unnecessary libXRender dependency introduces sudo requirement

[ddelalamo-takeda]

Currently OpenFold-3 indirectly requires libXrender, a library which must be installed with sudo. This requirement comes via pdbeccdutils.core.ccd_reader, which imports RDKit.Chem.Draw, which in turn imports rdMolDraw2D. For systems that cannot install packages with sudo (such as those running on AWS SageMaker in my case), this prevents OpenFold3 from being able to run at all. Since this module is only used for 1) parsing mmCIF files and 2) storing CCD data, I was wondering if the relevant code blocks could potentially be replaced with one of many open-source alternatives.

OS: Ubuntu 22.04.5 LTS
GPU: NVIDIA A10G, 23 GB VRAM with cuda 12.6
Python version: 3.11.14

[jnwei]

Hi @ddelalamo-takeda thanks for your report.

I wonder if there is another configuration issue at work here. While I have no experience running OpenFold3 on Sagemaker, the computer clusters on which we test OpenFold3 do not allow sudo access and there is no issue.

Would it be possible to test whether the docker image available here would be suitable for your workflow?