Route requests to the correct DrugFlow API flow and execute with minimal ambiguity.

Flow Selection

• Read references/index.md first.
• Match user intent to one flow.
• Load only that flow's reference files.
• Prefer script execution from scripts// when available.

Current Flows

• Common APIs: reusable auth/workspace/balance/jobs APIs available.
• Virtual screening: complete flow available.
• Docking: complete flow available.
• ADMET: complete flow available.
• Rescoring: complete flow available.
• Structure extract: complete flow available (img2mol backend type).
• Molecular factory: complete flow available (with atom-selection helpers).

Common APIs Workflow

• Read references/flows/common-apis/call-flow.md.
• Read references/flows/common-apis/payloads.md.
• Reuse scripts/common/drugflow_api.py for:
• signin
• signup
• list_workspaces / create_workspace / ensure_workspace
• get_balance
• list_jobs
• Use scripts/common/test_common_apis.py for direct smoke tests.

Virtual Screening Workflow

• Read references/flows/virtual-screening/call-flow.md.
• Read references/flows/virtual-screening/payloads.md.
• Use scripts/virtual-screening/run_vs_flow.py for end-to-end execution.
• Always include ws_id for /api/jobs list/detail.
• For /api/jobs create, pass name, type, args (JSON string), ws_id; in non-private mode include expect_tokens and avail_tokens.

Docking Workflow

• Read references/flows/docking/call-flow.md.
• Read references/flows/docking/payloads.md.
• Use scripts/docking/run_docking_flow.py for end-to-end execution.
• Create docking jobs through POST /api/jobs with multipart fields pdb, ligands, pdb_content, and args.
• Site-driven docking box note: when --site is provided but center/size/radius are omitted, the script auto-derives the docking box from that site in local PDB.
• Always include ws_id on job list/detail requests and pass expect_tokens/avail_tokens in non-private mode.

ADMET Workflow

• Read references/flows/admet/call-flow.md.
• Read references/flows/admet/payloads.md.
• Use scripts/admet/run_admet_flow.py for end-to-end execution.
• ADMET job type is fixed to admet-dl.
• Support two input modes:
• direct smiles list
• dataset mode via dataset_id + smiles_col
• For /api/jobs create, pass name, type=admet-dl, args, ws_id, and in non-private mode expect_tokens/avail_tokens.

Rescoring Workflow

• Read references/flows/rescoring/call-flow.md.
• Read references/flows/rescoring/payloads.md.
• Use scripts/rescoring/run_rescoring_flow.py for end-to-end execution.
• Create rescoring jobs through POST /api/jobs with:
• type=rescoring
• form fields pdb, ligands, smiles_col
• args.mode=semi and args.rescoring_functions
• Script enforces input files: --pdb-file must be .pdb, --ligands-file must be .sdf.
• Always include ws_id; in non-private mode include expect_tokens and avail_tokens.

Structure Extract Workflow

• Read references/flows/structure-extract/call-flow.md.
• Read references/flows/structure-extract/payloads.md.
• Use scripts/structure-extract/run_structure_extract_flow.py for end-to-end execution.
• User-facing "结构提取" maps to backend job type=img2mol.
• For create, pass name, type=img2mol, args (dataset_id, page_list), ws_id, and in non-private mode expect_tokens/avail_tokens.
• dataset_id must be img2mol-compatible and include extras.osskey.

Molecular Factory Workflow

• Read references/flows/molecular-factory/call-flow.md.
• Read references/flows/molecular-factory/payloads.md.
• Use scripts/molecular-factory/run_molecular_factory_flow.py:
• atom-info
• extract-partial
• draw-atom-index
• create-job
• Default to non-docking molecular factory unless user explicitly asks for docking:
• args.need_docking=false
• args.pdb_use.*=false
• Default generation models:
• args.molgen_algos=["Frag-GPT","REINVENT"]
• Use helper APIs first to confirm selected_atoms/start_atoms, then submit molecular_factory job.
• Always pass ws_id; in non-private mode include expect_tokens and avail_tokens.

Output Contract

• Return method + endpoint + required parameters for each step.
• Return key ids and state: ws_id, job_id, state, result count.
• When running scripts, return command + important outputs.

Expansion Rules

• Add new flow docs under references/flows// with call-flow.md and payloads.md.
• Add runnable scripts under scripts//.
• Update references/index.md and this file's Current Flows section.

References

• references/index.md
• references/flows/common-apis/call-flow.md
• references/flows/common-apis/payloads.md
• references/flows/virtual-screening/call-flow.md
• references/flows/virtual-screening/payloads.md
• references/flows/docking/call-flow.md
• references/flows/docking/payloads.md
• references/flows/admet/call-flow.md
• references/flows/admet/payloads.md
• references/flows/molecular-factory/call-flow.md
• references/flows/molecular-factory/payloads.md
• references/flows/rescoring/call-flow.md
• references/flows/rescoring/payloads.md
• references/flows/structure-extract/call-flow.md
• references/flows/structure-extract/payloads.md