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 0.4 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                        # abbreviations, sizes, prices, order emails
dmc databases --detailed             # full IDs, BioSolveIT mappings, availability, links
dmc usage                            # account plan and CHEESE Credits remaining today
dmc search "CC(=O)Oc1ccccc1C(=O)O" -d enamine -m shape -n 10
dmc search "CC(=O)Oc1ccccc1C(=O)O" -d enamine -o aspirin.csv
dmc substructure "[N;R0][N;R0]C(=O)" -d enamine -n 10 --timeout-seconds 45 -o hydrazides.sdf
dmc search "CC(=O)Oc1ccccc1C(=O)O" -d synple --subset amino-acids
dmc sample -d freedom -n 100 --seed 7 -o sample.smi
dmc order aspirin.csv --get-quote
dmc optimize run my-run -d enamine --minimize --score-cmd './dock.sh {input} {output}'
dmc optimize status                  # your optimizations; also ask, tell, results, cancel

databases lists every searchable space with its size, whether per-compound price estimates are available, and the vendor address for orders and quotes. Output captured on September 11, 2026; the catalog can change. For Enamine, the size is an estimated number of source reagent combinations, marked with ~, rather than unique molecular graphs. --detailed adds full IDs, BioSolveIT mappings, type, availability, success estimates, and vendor links. --json always returns the unmodified API catalog:

$ dmc databases
abbreviation  molecules  prices  orders
------------  ---------  ------  ------------------------
enamine          ~93.4B  yes     info@enamine.net
freedom          296.4B  yes     sales@chem-space.com
explore            9.5T  yes     sales@emolecules.com
synple             7.6T  yes     sales@emolecules.com
vast               6.8B  yes     VAST@XtalPi.com
cheminfinita     794.2B  -       sales@otavachemicals.com
spacem1            1.5B  -       hello@molecule.one

7 databases. Lead times vary by database; see --detailed.
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.

Example output from the production API (September 11, 2026):

$ dmc search "CC(=O)Oc1ccccc1C(=O)O" -d enamine -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  0.6061   $163  CC(C)(C)OC(=O)Oc1ccccc1C(=O)O

Searched ~93.4B source combinations (Enamine REAL v5a) in 396 ms.
Similarity range: 0.61-0.70 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.

Enamine filtered population

The production and development APIs use the filtered Enamine release 2026-09-06.2 by default for database="enamine", including sampling, similarity, selections, runs, and substructure search. It applies MW ≤500, logP ≤5, HBA ≤10, HBD ≤5, rotatable bonds ≤10, and TPSA ≤140 Ų on the assembled product after selecting the first valid source topology. Price estimates remain available on the returned products.

The updated estimate is 93.41B source combinations (95% interval: 93.19–93.63B), based on 18.7 million draws. This is the historical approximately 95B population, replacing the larger 336.72B normalized population as the default. The catalogue reports the estimate and its confidence interval. The CLI marks estimated counts with ~; this population counts source reagent combinations, which may produce the same molecular graph. Sampling is not uniform over unique molecular graphs. No client-side property preset is needed to select this population.

from deepmedchem import Client

with Client() as client:
    sample = client.sample(database="enamine", count=20, seed=7)
    matches = client.search_substructure("C(=O)N", database="enamine", limit=20)

DeepMedChem All Chemical Spaces

Snapshot: September 11, 2026. Use the abbreviation in database="enamine" or dmc search ... -d enamine. Full database IDs remain supported. Abbreviations resolve to the releases listed by dmc databases --detailed.

Migrating from BioSolveIT InfiniSee

Use the DeepMedChem abbreviation in Python or with -d. The BioSolveIT slugs below identify analogous collections; they are not accepted as DeepMedChem database IDs. Releases and molecule counts differ. BioSolveIT download catalog.

* No direct mapping: CHEMriya is a related Otava collection, not ChemInfinita. But it might be very similar. Contact Otava for details.

** No direct mapping: our Enamine version is built from public Enamine building blocks, so it is not identical to the BioSolveIT version. But it is very similar.

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.

Quickstart

import deepmedchem as dmc

result = dmc.search(
    "CC(=O)OC1=CC=CC=C1C(=O)O",  # Aspirin
    database="enamine",
    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 from the production API (September 11, 2026):

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=0.9551  price=$163  COC(=O)Oc1ccccc1C(C)=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.

Optimize with your own scorer

Navigator proposes molecules from a chemical space, your function scores them locally (docking, an ML model, an RDKit property), and the scores steer the next proposals until the budget is spent. Only SMILES and numbers cross the network.

import deepmedchem as dmc
from rdkit import Chem
from rdkit.Chem import QED

def score(smiles):  # one value per SMILES, None for a molecule you cannot score
    return [QED.qed(m) if (m := Chem.MolFromSmiles(s)) else None for s in smiles]

result = dmc.optimize(score, direction="maximize", database="enamine",
                      budget=500, batch_size=50, name="qed-demo")
print(result.top(10))
result.to_csv("qed_demo.csv")

direction is required and scores are never negated. name= makes the call resumable: re-run it after Ctrl-C or a crash and it continues, re-sending scores that were computed but not uploaded. A scorer may return dicts such as {"score": -9.1, "cnn_score": 0.82}; the extra keys are stored as metrics. For manual control use client.optimizations.create(...) with opt.ask() and opt.tell(batch, scores); for shell scorers and HPC queues use dmc optimize run NAME --score-cmd 'CMD {input} {output}' or dmc optimize ask/tell. Worked examples (RDKit, your own ML model, GNINA docking) are in examples/optimization.

Filters and virtual subsets

A similarity search can be restricted to a virtual subset: a definition rather than a stored catalogue, so it works on every DeepMedChem chemical space. No enumerated amino-acid version of Synple exists, yet this returns only amino acids:

dmc search "CC(C)C[C@H](NC(=O)c1ccccc1)C(=O)O" -d synple --subset amino-acids
dmc search "CC(C)C[C@H](NC(=O)c1ccccc1)C(=O)O" -d synple:amino-acids        # same search
dmc search "CC(=O)Oc1ccccc1C(=O)O" -d enamine --subset ro5 --where "tpsa=40..90"
dmc search "CC(=O)Oc1ccccc1C(=O)O" -d enamine --require "c1ccncc1" --exclude "[N+](=O)[O-]"
dmc search "CC(=O)Oc1ccccc1C(=O)O" -d enamine --require-count 1-2 "[NX3;H2]"
dmc search "CC(=O)Oc1ccccc1C(=O)O" -d enamine --max-price 200                # USD per 1 mg
dmc search "CC(=O)Oc1ccccc1C(=O)O" -d synple:amino-acids --explain           # no credit used
dmc sample -d enamine --subset druglike -n 100
dmc subsets                                                               # the registry

--subset, --where, --require, --require-count and --exclude can be repeated and are combined with AND. --where takes mw, logp, hbd, hba, rotb, tpsa, fsp3 and arom (or the rdkit.* property IDs) as mw<=450, logp<4, tpsa=40..90 or 1<=hbd<=3. --max-price USD keeps molecules whose catalogue price (whole USD, 1 mg, US delivery, the price column) is at most that amount; molecules without a price are dropped unless --keep-unpriced is given. --explain prints the selection document with the server's validation and execution estimate, and runs nothing.

amino-acids has the scope of the Mcule amino-acid catalogues: it matches 98-100% of each residue file of MCULE-AA (2026-08-01) except glycine and alanine (about 90%), whose remaining entries attach the residue through an aromatic ring nitrogen. Matching ignores stereochemistry, so natural and unnatural (D) amino acids are not told apart. dmc subsets --json prints every SMARTS.

In Python the same filters are keyword arguments of search and sample:

import deepmedchem as dmc

hits = dmc.search(query, database="synple", subset="amino-acids", limit=50)
hits = dmc.search(query, database="enamine:ro5", where=["mw<=450"], require=["c1ccncc1"])
hits = dmc.search(query, database="enamine", require=[("[NX3;H2]", 1, 2)])  # 1-2 matches
picks = dmc.sample(database="enamine", subset="druglike", count=100, seed=7)
cheap = dmc.search(query, database="enamine", max_price=200)  # price <= $200 per 1 mg

A filtered search is one molecule-selection/1 document: a similarity objective plus the filters as constraints, sent to POST /api/v2/selections and returned as a SelectionResult. Selection.subset(), .require_structure(), .exclude_structure(), .require_any_structure(), .where("mw<=450") and .max_price(200) build the same constraints by hand. The server checks every constraint on every assembled product, so each returned molecule satisfies all filters; nothing is filtered on the client. Engines that support it anchor the synthon search on synthons able to carry a required pattern instead of filtering nearest neighbours. If fewer molecules than requested pass the filters among the candidates examined, the result is shorter and carries a partial_results warning, which the CLI prints.

Limits: a filtered search returns at most 200 hits. Sampling accepts property filters only, because the API applies structure constraints to similarity searches alone. Batch search (--input) and substructure search do not take filters yet. The API does not report how many molecules a subset contains.

A price limit is enforced inside the synthon search, not by dropping expensive hits from an unfiltered list: the server skips building-block combinations priced above the limit before it ranks them, then prices every returned molecule again. It works for similarity search and sampling on databases whose catalog entry lists max_price under pricing.constraints (dmc databases --json); elsewhere the server answers capability_unavailable for constraints.price. A limit below the cheapest price of a database returns no molecules and a price_unattainable warning. Prices are planning estimates, not quotes. With RDKit installed (pip install "deepmedchem[rdkit]"), SMARTS are checked locally before any request.

SMILES and SMARTS substructure search

Enamine substructure search is enabled in production on release 2026-09-06.2. All 326 route partitions have native indexes. Returned products satisfy the filtered population rules and are checked against the original query, including bond order, recursive predicates, and chirality.

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, timeout_seconds=45, timeout=60,
)

See the runnable substructure example for several SQC-derived SMARTS queries. More demanding motifs can take tens of seconds. timeout_seconds sets the server search budget; timeout sets the SDK's HTTP timeout and should leave room for serialization and transport. A deadline can return fewer than limit hits; inspect result.raw["timed_out"], coverage, and warnings. Exact returned matches do not imply an exhaustive search of every possible product.

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 today's CHEESE Credit balance (plan, limit, used, remaining, unlimited, reset_at, seconds_to_reset) from GET /api/v2/usage. The balance is shared by all of the account's keys and the CHEESE web app, resets at midnight UTC, and reading it is free.

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. Ordinary synchronous work has a 10-second execution limit; use the Runs API for longer work, where a basic item has a 60-second limit. Substructure search uses its separate timeout_seconds budget.

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. Dev login opens https://cheese-dev.deepmedchem.com, reusing your session in that browser. If an older config.toml explicitly sets [profiles.dev].web_url to https://cheese-new-dev.deepmedchem.com, change it to https://cheese-dev.deepmedchem.com. Explicit profile URL overrides are preserved.

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, fast predicted-property acquisition, and hard assembled-product predicted ranges are available through Selection. The simple search and sample helpers and the CLI accept the common filters directly; see Filters and virtual subsets.

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. For predicted-property acquisition, factorized CP16 scores cheaply narrow the candidate pool before assembly and the pinned OpenADMET teacher predicts every unique surviving assembled product. The response exposes the two stages separately as hit.acquisition.approximate_value and hit.acquisition.predicted_value. These remain model predictions rather than assay measurements.

A hard predicted-property range is enforced only by the assembled-product teacher:

selection = (
    Selection.from_database("enamine-real-v5a")
    .reference("query", smiles="CC(=O)Oc1ccccc1C(=O)O")
    .maximize_similarity("rdkit.ecfp4_tanimoto", reference="query")
    .where_predicted_property(
        "openadmet-herg-pchembl",
        lte=5.0,
        units="pChEMBL",
    )
    .limit(20)
)

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/guides/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.

Links

• DeepMedChem website
• CHEESE UI and database overview
• API and API reference
• Documentation and Python quickstart
• Python package on PyPI
• Python SDK on GitHub

Seeded optimization and analog harvesting

client.optimizations.create(..., hit_threshold=-7, start_paused=True) initializes without proposing. After status becomes paused, use run.add_seeds(rows, mode="synthon") with measured scores and Navigator product IDs, or mode="external" with SMILES and scores. SMILES-only seeds train the surrogate; in-space product seeds also initialize analog search. Neither spends the scoring budget. If a scorer was pinned, pass the same scorer metadata with seeds.

After the seed operation finishes, run.resume() starts proposals. During an ask/tell loop, run.transition("analog_harvest_accurate", idempotency_key="harvest-1") queues a switch after scoring the current batch. analog_harvest_fast is also supported. Poll run.refresh() and inspect resource.raw["pending_operation"]; controls apply asynchronously and do not replace pending molecules. Invalid seeds pause the run with a reason and preserve its checkpoint.

dmc optimize seeds NAME seeds.json --mode synthon --idempotency-key seeds-1 and dmc optimize transition NAME analog_harvest_fast --idempotency-key harvest-1 expose the same operations. dmc optimize run and dmc.optimize() accept a hit threshold (--hit-threshold / hit_threshold). See the seed example.

Custom properties={"MolWt": (None, 350)} windows are checked on assembled products by the upgraded worker, including when combined with filters="druglike". Check the catalog's optimization property capabilities before requesting them.