openfold

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Shape Mismatch with batch_size=2

1

Hi, When I set `batch_size: 2` in` config.py` , the following error occurs during execution: ``` File "/home/ganjh/data/openfold/openfold/model/model.py", line 568, in forward outputs, m_1_prev, z_prev, x_prev, early_stop = self.iteration( File...

jong3

setup fails, torch is not a dependency

1

When I try to install openfold from pip, it fails with the message: no module named torch. Apparently torch is required, but it's not a dependency in the setup.

cbaakman

As per https://pdbj.org/news/Deprecation_FTP_Nov2024 the old ftp link is no longer active.

davidsimon

The version of deepspeed specified in environment.yml will lead to a `module 'deepspeed' has no attribute 'comm'` error, so we need to upgrade it. The latest numpy version will lead...

etowahadams

Regarding the note from @jnwei on May 3rd, have this been addressed? "A quick note on the pytorch 2 / CUDA 12 upgrade: We've run into some technical issues with...

leiterenato

Retraining OpenFold on Cath4.2

2

Hi, i was wondering if anyone has ever retrained OpenFold on a small dataset, e.g. Cath (4.2) to see how well/bad it does at small scale. I am curious for...

OliviaViessmann

Hello! I was installing the environment using mamba for OpenFold and the required libgcc=7.2 did not work for me. ``` Could not solve for environment specs The following packages are...

pmahable

`python setup.py install` command deprecated

1

Setuptools deprecated the `setup.py install` command four years ago. By October 31st 👻, the command `python setup.py install` will stop working. At least for any version of setuptools>=80.1.0. This means...

BSchilperoort

I noticed a small inconsistency between the atom ordering described in protein.py and the actual ordering in residue_constants.py. In [protein.py](https://github.com/aqlaboratory/openfold/blob/56da08ec75d2b431232477e176fd568f7f3e1860/openfold/np/protein.py#L49C1-L50C1): ``` # Cartesian coordinates of atoms in angstroms. The atom...

Monikerton

Bumps [actions/checkout](https://github.com/actions/checkout) from 5 to 6. Release notes Sourced from actions/checkout's releases. v6.0.0 What's Changed Update README to include Node.js 24 support details and requirements by @​salmanmkc in actions/checkout#2248 Persist...

dependabot[bot]