DeepMedChem Python SDK

The official, chemistry-thin Python client for the DeepMedChem hosted chemical-space platform. It contains no RDKit, models, databases, or proprietary search implementation.

Beta: deepmedchem 0.2 is available for early use. APIs may still change before the stable release.

Installation

pip install deepmedchem

Authenticate once, or set DEEPMEDCHEM_API_KEY in automation:

dmc login
dmc status

dmc login prints a short code and an approval URL. On a desktop it opens the URL in your browser; on a headless server, container, or SSH session it only prints the URL, which you can open on any device. Sign in or create a CHEESE account there, approve the connection, and the CLI finishes on its own. The key goes to the OS keyring when one is available, otherwise to a credentials.json file (mode 0600) next to the SDK config. Use --no-browser to force the print-only behaviour and --token-stdin to paste an existing key from a pipe.

Command line

The dmc command (also installed as deepmedchem) covers the everyday operations without writing Python:

dmc databases                        # searchable databases, delivery time, order emails
dmc usage                            # account plan and CHEESE Credits remaining today
dmc search "CC(=O)Oc1ccccc1C(=O)O" -d enamine-real-v5a -m shape -n 10
dmc search "CC(=O)Oc1ccccc1C(=O)O" -d enamine-real-v5a -o aspirin.csv
dmc substructure "[N;R0][N;R0]C(=O)" -d enamine-real-v5a -n 50 -o hydrazides.sdf
dmc sample -d freedom-space-5 -n 100 --seed 7 -o sample.smi
dmc order aspirin.csv --get-quote

databases lists every searchable space with its size, whether the vendor publishes per-compound prices, and the vendor address for orders and quotes:

$ dmc databases
database                molecules  prices  orders
----------------------  ---------  ------  ------------------------
cheminfinita-2026-02       794.2B  -       sales@otavachemicals.com
d2b-spacem1                  1.5B  -       hello@molecule.one
enamine-real-v5a           357.4B  yes     info@enamine.net
freedom-space-5            296.4B  -       sales@chem-space.com
synple-explore-2025-10       9.5T  -       sales@emolecules.com
synple-synple-2025-10        7.6T  -       sales@emolecules.com
vast-2026-h2                 6.8B  yes     contact@xtalpi.com

7 databases, made on demand and delivered in 3-6 weeks.
Order or request quotes by email, or run `dmc order results.csv`.

Searches print a table of rank, similarity score, price, and SMILES, followed by what was searched and the score range. Substructure hits show exact instead of a score, and samples have no score column. Product ids and the other API fields are kept in --json and in exports:

$ dmc search "CC(=O)Oc1ccccc1C(=O)O" -d enamine-real-v5a -n 3
rank   score  price  smiles
----  ------  -----  ----------------------
   1  0.7037   $245  O=C(O)Oc1ccccc1C(=O)O
   2  0.6667   $163  COC(=O)Oc1ccccc1C(=O)O
   3  0.5312   $245  O=C(O)COc1ccccc1C(=O)O

Searched 357.4B molecules (Enamine REAL v5a) in 380 ms.
Similarity range: 0.53-0.70 ECFP4 Tanimoto.

-o/--output saves the hits as CSV, SDF, SMILES (.smi), or JSON, inferred from the file suffix (--format overrides it). CSV and SDF carry the score, price, product id, and every other field from the response. SDF output needs RDKit (pip install "deepmedchem[sdf]"); the other formats have no extra dependencies. Every command accepts --json for the raw API response and --profile to pick a configured profile.

Requesting quotes and orders

Prepare vendor-ready requests directly from an exported result CSV:

dmc order results.csv --get-quote          # confirm prices and availability
dmc order results.csv --amount-mg 1        # initiate a 1 mg order request
dmc order results.csv --no-open             # files only; useful over SSH

The command groups molecules by vendor email, creates one directory per recipient, and then asks the operating system to open a pre-filled email draft. It never sends email or places an order. Every request remains available as email.txt plus molecules.csv if no graphical mail client is available or a draft fails to open. DeepMedChem is CCed so vendors can attribute the request.

Vendor-facing molecule files contain only the database ID, a -DMCH reference ID, and SMILES. Search scores, properties, and non-binding SDK price estimates are deliberately omitted. The message asks the vendor to confirm final pricing, availability, lead time, and order details before processing. Use --to ADDRESS for a private database without a configured procurement contact, and --database ID for older CSV files that do not carry a database column.

$ dmc usage
plan:      premium
credits:   9,999 of 10,000 remaining today (1 used)
resets:    2026-09-04T00:00:00+00:00 (in 13h 35m)

Quickstart

import deepmedchem as dmc

result = dmc.search(
    "CC(=O)OC1=CC=CC=C1C(=O)O",  # Aspirin
    database="enamine-real-v5a",
    method="shape",
    limit=3,
)

print(repr(result))
for hit in result.hits:
    price = f"${hit.price}" if hit.price is not None else "unavailable"
    print(f"{hit.rank}  score={hit.score:.4f}  price={price}  {hit.smiles}")

Example output (the database release and search results can change):

SearchResult(3 molecules, method='shape', database='enamine-real-v5a')
1  score=0.9726  price=$245  O=C(O)Oc1ccccc1C(=O)O
2  score=0.9719  price=$163  COC(=O)Oc1ccccc1C(=O)O
3  score=0.8713  price=$245  O=C(O)COc1ccccc1C(=O)O

Prices are estimates in whole US dollars for delivery to the United States. They are returned in the original search response, so both hit.price and the aligned result.prices list are available without another API request. Databases without price estimates return None; run dmc databases for the current list and the vendor address to request a binding quote.

SMILES and SMARTS substructure search

Use format="smiles" for a concrete molecular graph, including the existing junction-spanning examples. Use format="smarts" for atom lists, ring constraints, recursive expressions, and other SMARTS query features:

junction = dmc.substructure("CNC(=O)N1CCC1", format="smiles", database="enamine-real-v5a", limit=10)
hydrazides = dmc.substructure(
    "[N;R0][N;R0]C(=O)", format="smarts", database="enamine-real-v5a", limit=10
)

See the runnable substructure example for several SQC-derived SMARTS queries. Complex recursive SMARTS can require a longer timeout.

Any result writes itself with result.to_csv(path), result.to_sdf(path), or result.to_file(path) (format inferred from the suffix). dmc.usage() and Client.usage() return the account plan and the daily CHEESE Credit balance (plan, limit, used, remaining, reset_at, and an optional promo); the balance is served by the account service configured as the profile's account_url.

Module-level search, substructure, sample, catalog, and usage operations create and close a small internal client. The explicit Client remains available for connection reuse and advanced selections/runs. Search results behave as ordered SMILES sequences (result[0], result[:3], list(result)) while retaining typed hits, scores, prices, metadata, warnings, and the complete raw response locally.

The default profile calls https://api.deepmedchem.com. Keys created at https://cheese.deepmedchem.com work on both the legacy and v2 APIs. All keys for an account share one daily CHEESE Credit balance: one successful synchronous execution or durable-run item costs one credit. Synchronous work is terminated after 10 seconds; use the Runs API for longer work, where a basic item has a 60-second limit.

Credentials resolve from an explicit api_key, DEEPMEDCHEM_API_KEY, compatibility environment variables, a custom credential provider, the selected profile's OS-keyring entry, or the credentials.json fallback file. Set DEEPMEDCHEM_CREDENTIAL_STORE=file or =keyring to force one store. Use dmc login --profile dev for the development service; profiles never share credentials.

Every request identifies its source with X-DMC-Client, X-DMC-Client-Version, and X-DMC-SDK-Version. The default values attribute direct SDK use to deepmedchem-python; an application such as Navigator can override application and application_version while retaining the installed SDK version separately.

Selections and durable runs

Selection and Run are immutable, chemistry-thin builders. They produce the public molecule-selection/1 and run/1 documents; all chemistry and capability validation remains on the API.

Exact RDKit constraints and experimental predicted-property acquisition are available only through Selection. The simple search, sample, CLI, and export helpers intentionally keep their ordinary interfaces.

from deepmedchem import Client, Selection

selection = (
    Selection.from_database("enamine-real-v5a")
    .reference(
        "query",
        smiles="CCOc1ccc(C(=O)N2CCN(C)CC2)cc1",
    )
    .maximize_similarity("rdkit.ecfp4_tanimoto", reference="query")
    .require_preset("lipinski-ro5/v1")
    .where("rdkit.mol_wt", lte=450, units="Da")
    .acquire_predicted_property(
        "openadmet-herg-pchembl",
        direction="minimize",
        keep_fraction=0.25,
    )
    .include("properties", "objective_components")
    .limit(100)
)

with Client() as dmc:
    result = dmc.selections.create(selection)

Every returned RDKit value is calculated on the assembled product and enforced literally. CP16 values are predicted, experimental-acquisition-only ranking signals: they may reduce a similarity shortlist, but they are not measured assay results and do not prove that an ADMET threshold is met. The response exposes hit.acquisition.predicted_value, hit.acquisition.applicable, and one response-level result.acquisition provenance record.

Property-filtered random sampling uses the same selection contract without acquisition:

selection = (
    Selection.from_database("freedom-space-5")
    .sample(seed=42)
    .require_preset("lipinski-ro5/v1")
    .where("rdkit.mol_wt", lte=450, units="Da")
    .include("properties")
    .limit(100)
)
result = Client().selections.create(selection)

The authenticated catalog is the source of truth for each database's available properties, presets, predicted-property endpoints, and supported acquisition operation.

from deepmedchem import Client, Run, Selection

template = (
    Selection.from_database("enamine-real-v5a")
    .ranked()
    .maximize_similarity("rdkit.ecfp4_tanimoto", reference="query")
    .limit(10)
)

run_spec = Run.selection_batch(
    template=template,
    items={
        "lead-001": {"query": "CCO"},
        "lead-002": {"query": "CCN"},
    },
)

with Client() as dmc:
    run = dmc.runs.create(run_spec, idempotency_key="lead-set-v1")
    terminal = dmc.runs.wait(run.id)
    results = list(dmc.runs.iter_results(terminal.id))

AsyncClient offers matching asynchronous operations and iterators. DMCClient and AsyncDMCClient are compatibility aliases for code written against the pre-split Navigator SDK.

Navigator

The navigator terminal application is distributed separately as dmc-navigator. It depends on this SDK and adds file handling, login commands, terminal presentation, and Navigator-specific workflows.

Use with AI coding agents

The repository ships an Agent Skill in skills/deepmedchem that teaches Claude Code, Codex, Cursor, and other skill-aware agents how to search chemical space with this package and the dmc command.

# Claude Code: add the marketplace once, then install the plugin
/plugin marketplace add Deep-MedChem/deepmedchem-python
/plugin install deepmedchem@deep-medchem

# Any agent that supports the open skills format
npx skills add Deep-MedChem/deepmedchem-python

You can also copy skills/deepmedchem/ into .claude/skills/ of a project (or ~/.claude/skills/ for every project), or zip the folder and upload it as a custom skill in Claude.ai or through the Skills API.

Development

python -m venv .venv
. .venv/bin/activate
python -m pip install -e ".[test]"
ruff check .
pytest
python -m build
twine check dist/*

API documentation: https://docs.deepmedchem.com/docs/python/quickstart

Runnable authenticated examples using the established Enamine query panels are in examples/live.

For interactive RDKit visualization of similarity and SMARTS substructure queries, open the Enamine search notebook.