2021-05-12 Reproducing Lim results with Season 1 components meeting notes

Data download

• LD hands-to-keyboard, using Jupyter notebook for data export

  • attempted to use openff-benchmark optimize export, targeting dataset on public QCArchive. Encountered anticipated issue where indices do not conform to <group>-<molecule>-<conformer>. Made hotfix to running code to get past this.

  • Encountered another issue further:

  • $ openff-benchmark optimize export -u https://api.qcarchive.molssi.org:443 -d 'OpenFF Full Optimization Benchmark 1' -o ./Lim_test Traceback (most recent call last): File "/users/home/ldamored/miniconda/envs/off-opt/bin/openff-benchmark", line 10, in <module> sys.exit(cli()) File "/users/home/ldamored/miniconda/envs/off-opt/lib/python3.7/site-packages/click/core.py", line 829, in __call__ return self.main(*args, **kwargs) File "/users/home/ldamored/miniconda/envs/off-opt/lib/python3.7/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/users/home/ldamored/miniconda/envs/off-opt/lib/python3.7/site-packages/click/core.py", line 1259, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/users/home/ldamored/miniconda/envs/off-opt/lib/python3.7/site-packages/click/core.py", line 1259, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/users/home/ldamored/miniconda/envs/off-opt/lib/python3.7/site-packages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, **ctx.params) File "/users/home/ldamored/miniconda/envs/off-opt/lib/python3.7/site-packages/click/core.py", line 610, in invoke return callback(*args, **kwargs) File "/users/home/ldamored/miniconda/envs/off-opt/lib/python3.7/site-packages/openff/benchmark/cli.py", line 108, in export fractal_uri, output_directory, dataset_name, delete_existing) File "/users/home/ldamored/miniconda/envs/off-opt/lib/python3.7/site-packages/openff/benchmark/geometry_optimizations/compute.py", line 209, in export_molecule_data print("... '{}' : exporting COMPLETE".format(id)) File "/users/home/ldamored/miniconda/envs/off-opt/lib/python3.7/site-packages/openff/benchmark/geometry_optimizations/compute.py", line 384, in _get_complete_optimization_result pdb.set_trace() File "/users/home/ldamored/miniconda/envs/off-opt/lib/python3.7/site-packages/qcportal/client.py", line 723, in query_results result.__dict__["client"] = self AttributeError: 'dict' object has no attribute '__dict__'