Metadata-Version: 2.4
Name: deepmedchem
Version: 0.3.0b1
Summary: Official Python client for the DeepMedChem chemical-space platform
Project-URL: Homepage, https://deepmedchem.com
Project-URL: Documentation, https://docs.deepmedchem.com/docs/python/quickstart
Project-URL: Repository, https://github.com/Deep-MedChem/deepmedchem-python
Project-URL: Issues, https://github.com/Deep-MedChem/deepmedchem-python/issues
Author: Deep MedChem
License-Expression: MIT
License-File: LICENSE
Keywords: api-client,chemical-space,cheminformatics,drug-discovery
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Typing :: Typed
Requires-Python: >=3.9
Requires-Dist: eval-type-backport<1,>=0.2; python_version < '3.10'
Requires-Dist: httpx<1,>=0.27
Requires-Dist: keyring<27,>=24
Requires-Dist: platformdirs<5,>=3.10
Requires-Dist: pydantic<3,>=2.8
Requires-Dist: pyyaml<7,>=6
Requires-Dist: tomli<3,>=2; python_version < '3.11'
Provides-Extra: auth
Provides-Extra: sdf
Requires-Dist: rdkit>=2023.9; extra == 'sdf'
Provides-Extra: test
Requires-Dist: build<2,>=1.2; extra == 'test'
Requires-Dist: pytest<10,>=8.2; extra == 'test'
Requires-Dist: ruff>=0.6; extra == 'test'
Requires-Dist: twine<7,>=5; extra == 'test'
Description-Content-Type: text/markdown

# DeepMedChem Python SDK

[![PyPI](https://img.shields.io/pypi/v/deepmedchem?style=flat-square&logo=pypi&logoColor=white)](https://pypi.org/project/deepmedchem/)
[![Python](https://img.shields.io/pypi/pyversions/deepmedchem?style=flat-square&logo=python&logoColor=white)](https://pypi.org/project/deepmedchem/)
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[![License: MIT](https://img.shields.io/badge/license-MIT-blue?style=flat-square)](LICENSE)
[![Production API](https://img.shields.io/badge/API-api.deepmedchem.com-0A7EA4?style=flat-square)](https://api.deepmedchem.com/api/v2/docs)
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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

```bash
pip install deepmedchem
```

Authenticate once, or set `DEEPMEDCHEM_API_KEY` in automation:

```bash
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:

```bash
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:

```text
$ 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:

```text
$ 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:

```bash
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.

```text
$ 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

```python
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):

```text
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:

```python
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](examples/docs/substructure_search.py) 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, fast predicted-property acquisition, and hard assembled-product predicted
ranges are available through `Selection`. The simple `search`, `sample`, CLI, and export helpers
keep their ordinary interfaces.

```python
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:

```python
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:

```python
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.

```python
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](https://agentskills.io) in
[`skills/deepmedchem`](skills/deepmedchem/SKILL.md) that teaches Claude Code, Codex, Cursor, and
other skill-aware agents how to search chemical space with this package and the `dmc` command.

```bash
# 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

```bash
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`](examples/live/README.md).

For interactive RDKit visualization of similarity and SMARTS substructure queries, open the
[`Enamine search notebook`](examples/notebooks/enamine_search.ipynb).
