Arian Jamasb comments

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                                            Arian Jamasb

Separation of core and optional dependencies

N.B. these dependencies should be added in the appropriate place: ``` pip install --no-deps rxnfp pip install --no-deps drfp pip install transformers pip install gpflow grakel ```

TypeError: construct_graph() got an unexpected keyword argument 'pdb_path'

Hi @zhaoxuetong I believe the `pdb_path` argument has been renamed to `path`.

Error occurred while constructing edges from pdb files

Hi, thanks for raising this. It looks like `'AYA'` is a modified residue we've not included. You can modify `RESI_THREE_TO_1` https://github.com/a-r-j/graphein/blob/a669516c22f73efac035ac9874ebb315132ea6ff/graphein/protein/resi_atoms.py#L630 to include: `"AYA": "A"`

`pip install` fails on fresh `python==3.11` and `python==3.10` conda environment

Thanks for flagging. I think `pip install rdkit` will do the trick for now. Looks like there are some imports that need to be caught and some better logging too.

Add `torchdrug` to project dependencies

I've tried this a few times without any success. I forget the exact dependency that caused the issues but maybe you could give it a shot in case i'm doing...

Update torch versions, CI

@amorehead I'm trying to address #70 without much luck. Any ideas?