Arne Schneuing

Hi Stratis, I think the `process_crossdock.py` file is indeed outdated and should be updated. As far as I can tell, your solution should be fine as a temporary fix because...

Hi, I would just like to add that this repository only contains checkpoints for BindingMOAD at the moment. Please keep this in mind when sampling molecules for the CrossDocked test...

Yes, the model was trained on the Binding MOAD dataset

Hi Rudramani, does the SDF file look reasonable? This error seems to occur in cases where Open Babel has trouble inferring the correct connectivity (see [here](https://community.virtual-flow.org/t/obabel-errors-unable-to-find-bonds/179))

Thanks for this suggestion! We initially tried to minimize dependencies but if `radius_graph` is much faster, we should consider using it in the future. Note that we don't remove self-loops...

The new error appears to be unrelated to the old one. Are you sure it was caused by `radius_graph`?

Hello, thanks for your questions. 1. When running the `test.py` script you have a number of post-processing options (see [here](https://github.com/arneschneuing/DiffSBDD/blob/b5511e55dd4bb3d7e9271e915b2753e822e281a1/test.py#L19)). You can for example relax the generated molecules in a...

Hello @pearl-rabbit, the diversity is usually zero when only a single molecule is generated for each protein pocket because we compute this value per target (and afterwards mean and standard...

Hi, `n_samples=100` should be fine. It means that 100 valid molecules are generated *per pocket*. How did you provide those molecules to the `evaluate()` function? Did you create a nested...

@PikaQiu520521, I'm sorry but I don't really understand the question.. What do you mean by 'discrete points'? Could you provide an example?