Issue with a large ligand

[idestamb]

Hey Michael,

Awesome tool! thank you for developing it. Just bumped into an issue with 1 large molecule im trying to dock. The only difference between this and other ligands ive tried before is that this is much larger. Here is the error (ignore the deprecation):
/data/anaconda3/envs/plantain/lib/python3.10/site-packages/torchmetrics/utilities/imports.py:24: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
_PYTHON_LOWER_3_8 = LooseVersion(_PYTHON_VERSION) < LooseVersion("3.8")
0%| | 0/1 [00:00<?, ?it/s]Something's wrong with compound at index 0, skipping...
100%|████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 2.79it/s]

[mixarcid]

Hey sorry I just saw this -- I realized that I don't get notifications for this repo smh.
It looks like this ligand isn't being parsed correctly by RDKit (or it failed to generate a conformer). If the embedding is the case, you can try to change the number of times it tries to embed the molecule here: https://github.com/molecularmodelinglab/bigbind/blob/7c67d75d7f4b0d0f74df5faa62372afc56d34c3d/analysis.py#L73