path	# lines of code
env-setup/main.tf	26
env-setup/terraform-sample.tfvars	26
env-setup/versions.tf	53
env-setup/filestore.tf	21
env-setup/service_accounts.tf	38
env-setup/vertex-training-template.yaml	17
env-setup/pipeline_images.tf	49
env-setup/network.tf	30
env-setup/vertex-notebook.tf	23
env-setup/variables.tf	121
env-setup/outputs.tf	18
env-setup/local_provisioner.tf	34
env-setup/gcs_bucket.tf	11
1-alphafold-quick-start.ipynb	404
src/analysis/residue_constants.py	678
src/analysis/notebook_utils.py	135
src/analysis/utils.py	29
src/analysis/parsers.py	383
src/components/hhsearch.py	54
src/components/aggregate_features.py	43
src/components/hhblits.py	40
src/components/__init__.py	9
src/components/data_pipeline.py	74
src/components/alphafold_utils.py	464
src/components/relax_protein.py	43
src/components/predict_relax.py	53
src/components/configure_run.py	64
src/components/hmmsearch.py	50
src/components/jackhmmer.py	38
src/components/version.py	1
src/components/model_predict.py	48
src/pipelines/__init__.py	1
src/pipelines/alphafold_inference_pipeline.py	108
src/pipelines/alphafold_inference_pipeline_sequential.py	85
src/pipelines/alphafold_optimized_monomer.py	173
src/utils/compile_utils.py	77
src/utils/fasta_utils.py	24
src/utils/__init__.py	1
src/utils/run_utils.py	75
src/__init__.py	1
src/setup.py	7
src/config.py	32
src/frontend/index.html	13
src/frontend/src/index.css	57
src/frontend/src/components/SimpleDialog.tsx	72
src/frontend/src/components/ResponsiveAppBar.tsx	74
src/frontend/src/components/GoogleSignInButton.tsx	81
src/frontend/src/App.tsx	107
src/frontend/src/common/StringSet.ts	44
src/frontend/src/common/CommonFunctions.ts	117
src/frontend/src/main.tsx	4
src/frontend/src/NewJob.tsx	489
src/frontend/src/JobResults.tsx	227
src/frontend/vite.config.ts	5
src/backend/settings.py	3
src/backend/templates/index.html	16
src/backend/main.py	320
1.1-alphafold-quick-start-multimer.ipynb	401
env-setup-portal/main.tf	170
env-setup-portal/terraform-sample.tfvars	29
env-setup-portal/versions.tf	53
env-setup-portal/variables.tf	55
env-setup-portal/output.tf	3
2-alphafold-metadata-exploration.ipynb	570