john-bradshaw/synthesis-dags

Code for our paper "Barking up the right tree: an approach to search over molecule synthesis DAGs"

synthesis-dags's Issues

Google Drive for Molecule Transformer doesn't exist

Hi John, the link of Google Drive for the pertrained Molecule Transformer is invalid. Could you please update the link?
Thanks a lot.

Molecular Transformer failed to run

Hi John, thanks for updating the Readme. I really appreciate it!

I have encountered a new issue and I'm wondering whether you could help me with it. When I'm running the functional_tests/reaction_predictor_server_checker.py, there is an error occurred. The return value of the request is: {'error': 'Runtime Error: cublas runtime error : the GPU program failed to execute at /opt/conda/conda-bld/pytorch_1533672544752/work/aten/src/THC/THCBlas.cu:249', 'status': 'error'}
The error is: Traceback (most recent call last):
File "functional_tests/reaction_predictor_server_checker.py", line 48, in
main()
File "functional_tests/reaction_predictor_server_checker.py", line 42, in main
print(rp(reactants))
File "/rds/user/yo279/hpc-work/project/synthesis-dags/syn_dags/model/reaction_predictors.py", line 55, in call
self._run_list_of_reactant_sets(reactant_sets_new_needed)))
File "/rds/user/yo279/hpc-work/project/synthesis-dags/syn_dags/model/reaction_predictors.py", line 134, in _run_list_of_reactant_sets
raise ex
File "/rds/user/yo279/hpc-work/project/synthesis-dags/syn_dags/model/reaction_predictors.py", line 131, in _run_list_of_reactant_sets
op_back = return_list[0]
KeyError: 0
Besides, the training code for synthesis-dags can run successfully, while the sampling code also has the error above.
Thanks for your assistance!

Breaking changes to protobuf

Hi, I just installed this on a new machine and found one issue regarding the conda_dogae_gpu.yml environment setup. Namely, it seems like Google recently introduced backwards-incompatible changes to protobuf:

https://developers.google.com/protocol-buffers/docs/news/2022-05-06#python-updates

I'm not exactly clear on what changed, but the suggested option of downgrading to protobuf==3.20 (via pip) worked for me. There may be a better option (… regenerating some _pb2 files?), but otherwise would suggest updating the environment to pin version on protobuf.