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datamol

analysis

Cheminformatics with datamol, a Pythonic layer over RDKit with sensible defaults — SMILES parsing and standardization, descriptors, fingerprints, clustering, 3D conformers, and parallel processing.

Datamol Cheminformatics Skill

Overview

Datamol is a Python library that provides a lightweight, Pythonic abstraction layer over RDKit for molecular cheminformatics. Simplify complex molecular operations with sensible defaults, efficient parallelization, and modern I/O capabilities. All molecular objects are native rdkit.Chem.Mol instances, ensuring full compatibility with the RDKit ecosystem.

Version note: Examples target datamol 0.12.x. 0.12.5 (June 2024) is still the PyPI stable release as of September 2026 — over two years without a release, which is why the mismatches below are with datamol's dependencies rather than with datamol itself. Since 0.10.0, modules are lazy-loaded by default (set DATAMOL_DISABLE_LAZY_LOADING=1 to disable). Since 0.12.2, RDKit is a direct PyPI dependency of datamol. Fingerprints use RDKit's rdFingerprintGenerator API (0.12.5+).

datamol has not been released in two years, and its dependencies have moved. A fresh uv pip install datamol today pairs 0.12.5 with a current RDKit and joblib, and three calls that older tutorials still show now raise:

Call What happens Use instead
dm.to_fp(mol, n_bits=2048) Boost.Python.ArgumentError — the kwarg goes straight to RDKit's generator fpSize=2048
dm.descriptors.batch_compute_many_descriptors(mols, n_jobs=-1) ValueError: batch_size must be 'auto' or a positive integer, got: None add batch_size="auto"
dm.descriptors.compute_many_descriptors(mol)["logp"] KeyError "clogp", "n_lipinski_hbd", "n_lipinski_hba"

## Try it at the end of this file asserts all three, so you can tell in one run whether your install still behaves this way. It also pins the four return shapes and defaults that this page previously documented wrongly — apply_reaction, to_image, fuzzy_scaffolding and viz.conformers — so a future release that changes any of them fails loudly here.

Key capabilities:

  • Molecular format conversion (SMILES, SELFIES, InChI)
  • Structure standardization and sanitization
  • Molecular descriptors and fingerprints
  • 3D conformer generation and analysis
  • Clustering and diversity selection
  • Scaffold and fragment analysis
  • Chemical reaction application
  • Visualization and alignment
  • Batch processing with parallelization
  • Cloud storage support via fsspec

Installation and Setup

Guide users to install datamol:

uv pip install datamol

RDKit is installed automatically with datamol. For remote file paths (S3, GCS, HTTP), install the matching fsspec backend:

uv pip install s3fs   # AWS S3
uv pip install gcsfs  # Google Cloud Storage

Import convention:

import datamol as dm

Core Workflows

Ten workflow areas, each with worked code, are documented in references/core_workflows.md:

# Area Covers
1 Basic molecule handling to_mol, batch conversion, error handling, canonical and isomeric SMILES, sanitization and full standardization
2 Reading and writing files SDF, SMILES, CSV, Excel with rendered structures, the universal reader/writer, and cloud or HTTPS paths
3 Descriptors and properties the standard descriptor set, parallel computation, aromaticity, stereochemistry, flexibility, and filtering
4 Fingerprints and similarity ECFP4 and other types, pairwise and cross-set distances, nearest-neighbour lookup (Tanimoto distance = 1 − similarity)
5 Clustering and diversity similarity clustering, diverse subset picking, and cluster centroids
6 Scaffold analysis Bemis-Murcko scaffolds, grouping and counting, and scaffold-disjoint train/test splits
7 Fragmentation fragmenting molecules, finding common fragments across a library, and fragment-based scoring
8 3D conformers generation, access, RMSD clustering, representative selection, and SASA
9 Visualization grids, files, publication SVG, substructure alignment, atom and bond highlighting, conformer display
10 Chemical reactions reaction SMARTS, applying to a molecule or a whole library

Three end-to-end pipelines — load/filter/analyze, SAR by scaffold series, and virtual screening — are in references/workflow_patterns.md.

Parallelization

Datamol includes built-in parallelization for many operations. Use n_jobs parameter:

  • n_jobs=1: Sequential (no parallelization)
  • n_jobs=-1: Use all available CPU cores
  • n_jobs=4: Use 4 cores

Functions supporting parallelization:

  • dm.read_sdf(..., n_jobs=-1)
  • dm.descriptors.batch_compute_many_descriptors(..., n_jobs=-1, batch_size="auto") — this one needs batch_size
  • dm.cluster_mols(..., n_jobs=-1)
  • dm.pdist(..., n_jobs=-1)
  • dm.conformers.sasa(..., n_jobs=-1)

batch_compute_many_descriptors is the only one of these that defaults batch_size to None, and current joblib rejects None, so any n_jobs above 1 raises before a single descriptor is computed. Passing batch_size="auto" — joblib's own default — fixes it. The others go through dm.parallelized, which already defaults to "auto" and is unaffected.

Progress bars: Many batch operations support progress=True parameter.

Reference Documentation

For detailed API documentation, consult these reference files:

  • references/core_api.md: Core namespace functions (conversions, standardization, fingerprints, clustering)
  • references/io_module.md: File I/O operations (read/write SDF, CSV, Excel, remote files)
  • references/conformers_module.md: 3D conformer generation, clustering, SASA calculations
  • references/descriptors_viz.md: Molecular descriptors and visualization functions
  • references/fragments_scaffolds.md: Scaffold extraction, BRICS/RECAP fragmentation
  • references/reactions_data.md: Chemical reactions and toy datasets

Best Practices

  1. Always standardize molecules from external sources:

    mol = dm.standardize_mol(mol, disconnect_metals=True, normalize=True, reionize=True)

  2. Check for None values after molecule parsing:

    mol = dm.to_mol(smiles)
if mol is None:
    raise ValueError(f"could not parse SMILES: {smiles}")

  3. Use parallel processing for large datasets:

    result = dm.operation(..., n_jobs=-1, progress=True)

  4. Use cloud I/O only when requested — confirm remote write paths; install s3fs/gcsfs as needed:

    df = dm.read_sdf("s3://bucket/compounds.sdf")

  5. Use appropriate fingerprints for similarity:

    • ECFP (Morgan): General purpose, structural similarity
    • MACCS: Fast, smaller feature space
    • Atom pairs: Considers atom pairs and distances

  6. Consider scale limitations:

    • Butina clustering: ~1,000 molecules (full distance matrix)
    • For larger datasets: Use diversity selection or hierarchical methods

  7. Scaffold splitting for ML: Ensure proper train/test separation by scaffold

  8. Align molecules when visualizing SAR series

Error Handling

# Safe molecule creation
def safe_to_mol(smiles):
    try:
        mol = dm.to_mol(smiles)
        if mol is not None:
            mol = dm.standardize_mol(mol)
        return mol
    except Exception as e:
        print(f"Failed to process {smiles}: {e}")
        return None

# Safe batch processing
valid_mols = []
for smiles in smiles_list:
    mol = safe_to_mol(smiles)
    if mol is not None:
        valid_mols.append(mol)

Integration with Machine Learning

Datamol ships with scipy and scikit-learn as dependencies. Import them as normal PyPI packages — they are not scripts bundled in this skill.

import numpy as np

# Feature generation
X = np.array([dm.to_fp(mol) for mol in mols])

# Or descriptors (batch_size is required for n_jobs > 1 — see Parallelization)
desc_df = dm.descriptors.batch_compute_many_descriptors(mols, n_jobs=-1, batch_size="auto")
X = desc_df.values

# Train model (scikit-learn PyPI package)
from sklearn.ensemble import RandomForestRegressor  # third-party library
model = RandomForestRegressor()
model.fit(X, y_target)

# Predict
predictions = model.predict(X_test)

Troubleshooting

Issue: Molecule parsing fails

  • Solution: Use dm.standardize_smiles() first or try dm.fix_mol()

Issue: Memory errors with clustering

  • Solution: Use dm.pick_diverse() instead of full clustering for large sets

Issue: Slow conformer generation

  • Solution: Reduce n_confs or increase rms_cutoff to generate fewer conformers

Issue: Remote file access fails

  • Solution: Install the matching fsspec backend (uv pip install s3fs or gcsfs) and verify only the provider credentials needed for that backend are set (see Remote file support above)

Issue: Boost.Python.ArgumentError mentioning GetMorganGenerator or GetFingerprint

  • Solution: Two different causes. n_bits= is not a fingerprint kwarg — use fpSize=. And dm.to_fp takes one molecule, so featurizing a table means np.array([dm.to_fp(m) for m in df["mol"]]), not dm.to_fp(df["mol"])

Issue: ValueError: batch_size must be 'auto' or a positive integer, got: None

  • Solution: You passed n_jobs > 1 to batch_compute_many_descriptors. Add batch_size="auto"

Issue: KeyError on a descriptor you know exists

  • Solution: The keys are datamol's, not RDKit's or Lipinski's — clogp, n_lipinski_hbd, n_lipinski_hba. Print .keys() once rather than guessing. Note mw is the exact (monoisotopic) mass, not the average molecular weight

Issue: Clustering results look wrong or unpack strangely

  • Solution: dm.cluster_mols returns a 2-tuple, (index_clusters, molecule_clusters). Iterating the return value gives you those two items, not your clusters — unpack it

Issue: AttributeError: module 'rdkit.Chem' has no attribute 'rdChemReactions'

  • Solution: from rdkit import Chem does not pull in the reactions submodule. Import it directly: from rdkit.Chem import rdChemReactions

Issue: A reaction product will not sanitize, draw or convert to SMILES

  • Solution: dm.reactions.apply_reaction returns a nested list, one inner list per product group — [[Mol]] with the defaults, so the molecule is result[0][0]. A reactant that does not match returns [], never None, so if p is not None filters nothing. single_product_group=True flattens one level. And mind the argument order: product_index is the third parameter, so a positional apply_reaction(rxn, reactants, True) sets that, not as_smiles

Issue: A saved .png grid will not open, or a grid is missing molecules

  • Solution: Both are dm.viz.to_image defaults. use_svg is True, so outfile="x.png" writes SVG bytes under a .png name — pass use_svg=False, or name it .svg. And max_mols is 32, so a longer list is silently truncated — pass max_mols=len(mols)

Issue: TypeError: 'Mol' object is not iterable from dm.scaffold.fuzzy_scaffolding

  • Solution: It takes a list of molecules and returns a 3-tuple, (scaffolds, scaffold_infos, all_scaffolds). dm.to_scaffold_murcko is the per-molecule one

Try it

A self-contained check that this skill still works. No key, no account, no GPU — just uv pip install datamol.

Data — none to fetch, and datasets: is deliberately empty. The inputs are eight SMILES strings written into the block below: aspirin, salicylic acid, paracetamol, ibuprofen, caffeine, theophylline, nicotine and benzene. SMILES are the data for cheminformatics, so there is no file to download and nothing that can 404 — the pairs are chosen so that a chemically obvious relationship (aspirin is a salicylic-acid derivative; caffeine is not) becomes an assertion.

The block routes through the four traps this library actually sets, and asserts the two error paths rather than describing them — so a release that fixes n_bits fails here too, loudly, instead of leaving the note above quietly wrong.

import datamol as dm
import numpy as np
from rdkit.Chem import Descriptors

# Eight well-known drug molecules, written out here — nothing to download.
SMILES = {
    "aspirin":      "CC(=O)Oc1ccccc1C(=O)O",
    "salicylic":    "OC(=O)c1ccccc1O",
    "paracetamol":  "CC(=O)Nc1ccc(O)cc1",
    "ibuprofen":    "CC(C)Cc1ccc(cc1)C(C)C(=O)O",
    "caffeine":     "Cn1cnc2c1c(=O)n(C)c(=O)n2C",
    "theophylline": "Cn1c(=O)c2[nH]cnc2n(C)c1=O",
    "nicotine":     "CN1CCC[C@H]1c1cccnc1",
    "benzene":      "c1ccccc1",
}
names = list(SMILES)
mols = [dm.to_mol(s) for s in SMILES.values()]
assert all(m is not None for m in mols), "a SMILES failed to parse"
asp, sal, caf = (names.index(n) for n in ("aspirin", "salicylic", "caffeine"))

# 1. Descriptors. The keys are not the Lipinski names you would guess, and `mw` is the
#    EXACT (monoisotopic) mass — cross-check it against RDKit's two masses to see which.
d = dm.descriptors.compute_many_descriptors(mols[asp])
try:
    d["logp"]
    raise SystemExit("expected KeyError: the key is 'clogp'")
except KeyError:
    pass

# 2. Parallel batch descriptors. n_jobs > 1 alone raises — batch_size defaults to None,
#    which joblib rejects. Pass batch_size explicitly.
df = dm.descriptors.batch_compute_many_descriptors(mols, n_jobs=-1, batch_size="auto")

# 3. Fingerprints. The bit-count kwarg is fpSize (RDKit's generator API), not n_bits.
fp = dm.to_fp(mols[asp], fp_type="ecfp", radius=2, fpSize=2048)
maccs = dm.to_fp(mols[asp], fp_type="maccs")
try:
    dm.to_fp(mols[asp], fp_type="ecfp", radius=2, n_bits=2048)
    raise SystemExit("expected an ArgumentError: the kwarg is fpSize, not n_bits")
except Exception as e:
    assert "did not match C++ signature" in str(e), e

# 4. pdist is Tanimoto DISTANCE, not similarity: 0 = identical, 1 = nothing in common.
dist = dm.pdist(mols)

# 5. cluster_mols returns a 2-TUPLE (index clusters, molecule clusters) — not a list
#    of clusters. Iterating it directly gives you two items whatever the data says.
cluster_indices, mol_clusters = dm.cluster_mols(mols, cutoff=0.7)
flat = sorted(i for c in cluster_indices for i in c)

# 6. Reactions. rdChemReactions needs its own import — `from rdkit import Chem` alone
#    leaves Chem.rdChemReactions raising AttributeError. apply_reaction returns a NESTED
#    list (one inner list per product group), and a non-matching reactant gives [].
from rdkit.Chem import rdChemReactions
rxn = rdChemReactions.ReactionFromSmarts('[C:1][OH:2].[C:3](=[O:4])[OH:5]>>[C:1][O:2][C:3](=[O:4])')
ester = dm.reactions.apply_reaction(rxn, (dm.to_mol("CCO"), dm.to_mol("CC(=O)O")))
no_match = dm.reactions.apply_reaction(rxn, (dm.to_mol("c1ccccc1"), dm.to_mol("c1ccccc1")))

# 7. to_image defaults: SVG (a str), and only the first 32 molecules.
grid_svg = dm.viz.to_image(mols)
truncating = dm.viz.to_image([dm.to_mol("C" * (i % 8 + 1)) for i in range(40)], n_cols=4)
complete = dm.viz.to_image([dm.to_mol("C" * (i % 8 + 1)) for i in range(40)], n_cols=4,
                           max_mols=40)

# 8. fuzzy_scaffolding takes a LIST and returns a 3-tuple — to_scaffold_murcko is the
#    per-molecule one. RDKit prints hydrogen warnings to stderr here; they are not failures.
series = [dm.to_mol(s) for s in ("c1ccc2ncnc(N)c2c1", "Cc1ccc2ncnc(N)c2c1",
                                 "Clc1ccc2ncnc(N)c2c1", "COc1ccc2ncnc(N)c2c1")]
scaffolds, scaffold_infos, all_scaffolds = dm.scaffold.fuzzy_scaffolding(series)

print("datamol        :", dm.__version__)
print("descriptors    :", df.shape, "| keys include clogp/n_lipinski_hbd, not logp/hbd")
print("aspirin mw     : %.6f (exact) vs RDKit MolWt %.3f (average)"
      % (d["mw"], Descriptors.MolWt(mols[asp])))
print("aspirin clogp  : %.4f | qed %.4f | tpsa %.2f" % (d["clogp"], d["qed"], d["tpsa"]))
print("ecfp4 / maccs  :", fp.shape, fp.dtype, "on-bits", int(fp.sum()), "|", maccs.shape)
print("distance matrix:", dist.shape, "| diagonal max %.1f" % dist.diagonal().max())
print("aspirin~salicylic %.4f  <  aspirin~caffeine %.4f" % (dist[asp, sal], dist[asp, caf]))
print("clusters       :", len(cluster_indices), "sizes", [len(c) for c in cluster_indices])
print("apply_reaction :", type(ester).__name__, "of", type(ester[0]).__name__,
      "->", dm.to_smiles(ester[0][0]), "| no match ->", no_match)
print("to_image       :", type(grid_svg).__name__, "| 40 mols default vs max_mols=40:",
      len(truncating), "vs", len(complete), "chars")
print("fuzzy_scaffolds:", sorted(scaffolds))

assert d["mw"] == Descriptors.ExactMolWt(mols[asp]) != Descriptors.MolWt(mols[asp])
assert {"mw", "clogp", "n_lipinski_hbd", "n_lipinski_hba"} <= d.keys()
assert df.shape[0] == len(mols)
assert fp.shape == (2048,) and maccs.shape == (167,)
assert dist.shape == (len(mols), len(mols)) and np.allclose(dist, dist.T)
assert dist.diagonal().max() == 0.0, "distance, not similarity: a molecule is 0 from itself"
assert dist[asp, sal] < dist[asp, caf], "aspirin is closer to salicylic acid than to caffeine"
assert len(mol_clusters) == len(cluster_indices)
assert flat == list(range(len(mols))), "clusters must partition the input exactly once"

# apply_reaction: nested list, and [] rather than None when nothing matches
assert isinstance(ester, list) and isinstance(ester[0], list), "product groups nest one deep"
assert dm.to_smiles(ester[0][0]) == "CCOC(C)=O"
assert no_match == [], "a non-matching reactant returns an empty list, not None"
# to_image: SVG string by default, and max_mols=32 truncates without warning
assert isinstance(grid_svg, str) and grid_svg.lstrip().startswith("<?xml"), "use_svg is True"
assert len(complete) > len(truncating), "max_mols defaults to 32, so 40 molecules truncate"
# fuzzy_scaffolding: a list in, a 3-tuple out
assert scaffolds == {"Nc1ncnc2ccc([*:1])cc12", "Nc1ncnc2ccccc12"}
assert isinstance(scaffold_infos, type(df)) and isinstance(all_scaffolds, type(df))
try:
    dm.scaffold.fuzzy_scaffolding(mols[asp])
    raise SystemExit("expected TypeError: fuzzy_scaffolding takes a list of molecules")
except TypeError:
    pass
print("invariants OK")

Expect

Invariants — these are properties of the library and of chemistry, not of a release, and a failure means this skill is wrong:

  • mw is the exact (monoisotopic) mass. The assertion pins it to RDKit's ExactMolWt and pins it away from MolWt, so the two masses cannot be confused: 180.0423 against 180.159 for aspirin. Reading mw as average molecular weight is a quiet 0.1–0.2% error that no exception will ever raise for you.
  • The descriptor keys are clogp, n_lipinski_hbd, n_lipinski_hba. logp raises KeyError, which the block asserts rather than assumes.
  • The fingerprint width kwarg is fpSize. n_bits raises Boost.Python.ArgumentError, also asserted. ECFP4 is 2048 bits; MACCS is always 167.
  • dm.pdist returns Tanimoto distance. Symmetric, zero on the diagonal. Aspirin is closer to salicylic acid than to caffeine — a chemical fact, so it holds under any fingerprint the library might default to.
  • dm.cluster_mols returns a 2-tuple, (index_clusters, molecule_clusters), and the index clusters partition the input exactly once — every molecule in one cluster, none dropped or repeated.
  • batch_compute_many_descriptors needs batch_size when n_jobs > 1. If this line starts working without it, joblib changed, not this skill.
  • dm.reactions.apply_reaction returns a nested list, one inner list per product group, so the molecule is result[0][0]. A reactant that matches nothing returns [] — not None, and not an exception.
  • dm.viz.to_image returns an SVG str by default (use_svg=True), and shows at most max_mols=32 molecules with no warning. The block renders 40 twice, once at the default and once at max_mols=40, and asserts the second is larger.
  • dm.scaffold.fuzzy_scaffolding takes a list and returns a 3-tuple. Passing a single molecule raises TypeError, which the block asserts. The two scaffolds recovered from the 4-aminoquinazoline series are a chemical fact about that series, not a version detail.

Observed 2026-09-05 on datamol 0.12.5 / RDKit 2026.03.6 / joblib 1.6.0 / pandas 3.0.5 / NumPy 2.4.6, Python 3.11.15 — treat a mismatch here as drift to investigate, not a failure. The character counts in the to_image line are the loosest thing here; only their ordering is asserted:

datamol        : 0.12.5
descriptors    : (8, 22) | keys include clogp/n_lipinski_hbd, not logp/hbd
aspirin mw     : 180.042259 (exact) vs RDKit MolWt 180.159 (average)
aspirin clogp  : 1.3101 | qed 0.5501 | tpsa 63.60
ecfp4 / maccs  : (2048,) uint8 on-bits 24 | (167,)
distance matrix: (8, 8) | diagonal max 0.0
aspirin~salicylic 0.6410  <  aspirin~caffeine 0.9344
clusters       : 6 sizes [2, 2, 1, 1, 1, 1]
apply_reaction : list of list -> CCOC(C)=O | no match -> []
to_image       : str | 40 mols default vs max_mols=40: 42857 vs 53513 chars
fuzzy_scaffolds: ['Nc1ncnc2ccc([*:1])cc12', 'Nc1ncnc2ccccc12']
invariants OK

RDKit also writes not removing hydrogen atom without neighbors warnings to stderr during the fuzzy_scaffolding step. They come from its fuzzy-matching internals and do not indicate a failure — the block exits 0.

At cutoff=0.7 the only pairs that cluster together are aspirin with salicylic acid and caffeine with theophylline — both genuine structural pairs, which is the result worth recognising if you change the cutoff and everything collapses into one cluster.

Additional Resources