DrugFlow

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name: drugflow-skills description: Multi-flow API workflow skill for this DrugFlow Django repository. Use when an agent needs executable end-to-end API procedures such as login/register, workspace and balance retrieval, job listing, virtual screening, docking, ADMET, rescoring, structure extraction, and molecular factory.

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DrugFlow Skills

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

Flow Selection

1. Read references/index.md first. 2. Match user intent to one flow. 3. Load only that flow's reference files. 4. Prefer script execution from scripts// when available.

Current Flows

1. Common APIs: reusable auth/workspace/balance/jobs APIs available. 2. Virtual screening: complete flow available. 3. Docking: complete flow available. 4. ADMET: complete flow available. 5. Rescoring: complete flow available. 6. Structure extract: complete flow available (img2mol backend type). 7. Molecular factory: complete flow available (with atom-selection helpers).

Common APIs Workflow

1. Read references/flows/common-apis/call-flow.md. 2. Read references/flows/common-apis/payloads.md. 3. Reuse scripts/common/drugflow_api.py for:

signin

signup

list_workspaces / create_workspace / ensure_workspace

get_balance

list_jobs

4. Use scripts/common/test_common_apis.py for direct smoke tests.

Virtual Screening Workflow

1. Read references/flows/virtual-screening/call-flow.md. 2. Read references/flows/virtual-screening/payloads.md. 3. Use scripts/virtual-screening/run_vs_flow.py for end-to-end execution. 4. Always include ws_id for /api/jobs list/detail. 5. For /api/jobs create, pass name, type, args (JSON string), ws_id; in non-private mode include expect_tokens and avail_tokens.

Docking Workflow

1. Read references/flows/docking/call-flow.md. 2. Read references/flows/docking/payloads.md. 3. Use scripts/docking/run_docking_flow.py for end-to-end execution. 4. Create docking jobs through POST /api/jobs with multipart fields pdb, ligands, pdb_content, and args. 5. 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. 6. Always include ws_id on job list/detail requests and pass expect_tokens/avail_tokens in non-private mode.

ADMET Workflow

1. Read references/flows/admet/call-flow.md. 2. Read references/flows/admet/payloads.md. 3. Use scripts/admet/run_admet_flow.py for end-to-end execution. 4. ADMET job type is fixed to admet-dl. 5. Support two input modes:

direct smiles list

dataset mode via dataset_id + smiles_col

6. For /api/jobs create, pass name, type=admet-dl, args, ws_id, and in non-private mode expect_tokens/avail_tokens.

Rescoring Workflow

1. Read references/flows/rescoring/call-flow.md. 2. Read references/flows/rescoring/payloads.md. 3. Use scripts/rescoring/run_rescoring_flow.py for end-to-end execution. 4. Create rescoring jobs through POST /api/jobs with:

type=rescoring

form fields pdb, ligands, smiles_col

args.mode=semi and args.rescoring_functions

5. Script enforces input files: --pdb-file must be .pdb, --ligands-file must be .sdf. 6. Always include ws_id; in non-private mode include expect_tokens and avail_tokens.

Structure Extract Workflow

1. Read references/flows/structure-extract/call-flow.md. 2. Read references/flows/structure-extract/payloads.md. 3. Use scripts/structure-extract/run_structure_extract_flow.py for end-to-end execution. 4. User-facing "结构提取" maps to backend job type=img2mol. 5. For create, pass name, type=img2mol, args (dataset_id, page_list), ws_id, and in non-private mode expect_tokens/avail_tokens. 6. dataset_id must be img2mol-compatible and include extras.osskey.

Molecular Factory Workflow

1. Read references/flows/molecular-factory/call-flow.md. 2. Read references/flows/molecular-factory/payloads.md. 3. Use scripts/molecular-factory/run_molecular_factory_flow.py:

atom-info

extract-partial

draw-atom-index

create-job

4. Default to non-docking molecular factory unless user explicitly asks for docking:

args.need_docking=false

args.pdb_use.*=false

5. Default generation models:

args.molgen_algos=["Frag-GPT","REINVENT"]

6. Use helper APIs first to confirm selected_atoms/start_atoms, then submit molecular_factory job. 7. Always pass ws_id; in non-private mode include expect_tokens and avail_tokens.

Output Contract

1. Return method + endpoint + required parameters for each step. 2. Return key ids and state: ws_id, job_id, state, result count. 3. When running scripts, return command + important outputs.

Expansion Rules

1. Add new flow docs under references/flows// with call-flow.md and payloads.md. 2. Add runnable scripts under scripts//. 3. Update references/index.md and this file's Current Flows section.

References

1. references/index.md 2. references/flows/common-apis/call-flow.md 3. references/flows/common-apis/payloads.md 4. references/flows/virtual-screening/call-flow.md 5. references/flows/virtual-screening/payloads.md 6. references/flows/docking/call-flow.md 7. references/flows/docking/payloads.md 8. references/flows/admet/call-flow.md 9. references/flows/admet/payloads.md 10. references/flows/molecular-factory/call-flow.md 11. references/flows/molecular-factory/payloads.md 12. references/flows/rescoring/call-flow.md 13. references/flows/rescoring/payloads.md 14. references/flows/structure-extract/call-flow.md 15. references/flows/structure-extract/payloads.md