gh-k-dense-ai-claude-scientific-skills-scientific-skills/skills/datamol/SKILL.md

name, description

name	description
datamol	Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery: SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.

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.

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

Import convention:

import datamol as dm

Core Workflows

1. Basic Molecule Handling

Creating molecules from SMILES:

import datamol as dm

# Single molecule
mol = dm.to_mol("CCO")  # Ethanol

# From list of SMILES
smiles_list = ["CCO", "c1ccccc1", "CC(=O)O"]
mols = [dm.to_mol(smi) for smi in smiles_list]

# Error handling
mol = dm.to_mol("invalid_smiles")  # Returns None
if mol is None:
    print("Failed to parse SMILES")

Converting molecules to SMILES:

# Canonical SMILES
smiles = dm.to_smiles(mol)

# Isomeric SMILES (includes stereochemistry)
smiles = dm.to_smiles(mol, isomeric=True)

# Other formats
inchi = dm.to_inchi(mol)
inchikey = dm.to_inchikey(mol)
selfies = dm.to_selfies(mol)

Standardization and sanitization (always recommend for user-provided molecules):

# Sanitize molecule
mol = dm.sanitize_mol(mol)

# Full standardization (recommended for datasets)
mol = dm.standardize_mol(
    mol,
    disconnect_metals=True,
    normalize=True,
    reionize=True
)

# For SMILES strings directly
clean_smiles = dm.standardize_smiles(smiles)

2. Reading and Writing Molecular Files

Refer to references/io_module.md for comprehensive I/O documentation.

Reading files:

# SDF files (most common in chemistry)
df = dm.read_sdf("compounds.sdf", mol_column='mol')

# SMILES files
df = dm.read_smi("molecules.smi", smiles_column='smiles', mol_column='mol')

# CSV with SMILES column
df = dm.read_csv("data.csv", smiles_column="SMILES", mol_column="mol")

# Excel files
df = dm.read_excel("compounds.xlsx", sheet_name=0, mol_column="mol")

# Universal reader (auto-detects format)
df = dm.open_df("file.sdf")  # Works with .sdf, .csv, .xlsx, .parquet, .json

Writing files:

# Save as SDF
dm.to_sdf(mols, "output.sdf")
# Or from DataFrame
dm.to_sdf(df, "output.sdf", mol_column="mol")

# Save as SMILES file
dm.to_smi(mols, "output.smi")

# Excel with rendered molecule images
dm.to_xlsx(df, "output.xlsx", mol_columns=["mol"])

Remote file support (S3, GCS, HTTP):

# Read from cloud storage
df = dm.read_sdf("s3://bucket/compounds.sdf")
df = dm.read_csv("https://example.com/data.csv")

# Write to cloud storage
dm.to_sdf(mols, "s3://bucket/output.sdf")

3. Molecular Descriptors and Properties

Refer to references/descriptors_viz.md for detailed descriptor documentation.

Computing descriptors for a single molecule:

# Get standard descriptor set
descriptors = dm.descriptors.compute_many_descriptors(mol)
# Returns: {'mw': 46.07, 'logp': -0.03, 'hbd': 1, 'hba': 1,
#           'tpsa': 20.23, 'n_aromatic_atoms': 0, ...}

Batch descriptor computation (recommended for datasets):

# Compute for all molecules in parallel
desc_df = dm.descriptors.batch_compute_many_descriptors(
    mols,
    n_jobs=-1,      # Use all CPU cores
    progress=True   # Show progress bar
)

Specific descriptors:

# Aromaticity
n_aromatic = dm.descriptors.n_aromatic_atoms(mol)
aromatic_ratio = dm.descriptors.n_aromatic_atoms_proportion(mol)

# Stereochemistry
n_stereo = dm.descriptors.n_stereo_centers(mol)
n_unspec = dm.descriptors.n_stereo_centers_unspecified(mol)

# Flexibility
n_rigid = dm.descriptors.n_rigid_bonds(mol)

Drug-likeness filtering (Lipinski's Rule of Five):

# Filter compounds
def is_druglike(mol):
    desc = dm.descriptors.compute_many_descriptors(mol)
    return (
        desc['mw'] <= 500 and
        desc['logp'] <= 5 and
        desc['hbd'] <= 5 and
        desc['hba'] <= 10
    )

druglike_mols = [mol for mol in mols if is_druglike(mol)]

4. Molecular Fingerprints and Similarity

Generating fingerprints:

# ECFP (Extended Connectivity Fingerprint, default)
fp = dm.to_fp(mol, fp_type='ecfp', radius=2, n_bits=2048)

# Other fingerprint types
fp_maccs = dm.to_fp(mol, fp_type='maccs')
fp_topological = dm.to_fp(mol, fp_type='topological')
fp_atompair = dm.to_fp(mol, fp_type='atompair')

Similarity calculations:

# Pairwise distances within a set
distance_matrix = dm.pdist(mols, n_jobs=-1)

# Distances between two sets
distances = dm.cdist(query_mols, library_mols, n_jobs=-1)

# Find most similar molecules
from scipy.spatial.distance import squareform
dist_matrix = squareform(dm.pdist(mols))
# Lower distance = higher similarity (Tanimoto distance = 1 - Tanimoto similarity)

5. Clustering and Diversity Selection

Refer to references/core_api.md for clustering details.

Butina clustering:

# Cluster molecules by structural similarity
clusters = dm.cluster_mols(
    mols,
    cutoff=0.2,    # Tanimoto distance threshold (0=identical, 1=completely different)
    n_jobs=-1      # Parallel processing
)

# Each cluster is a list of molecule indices
for i, cluster in enumerate(clusters):
    print(f"Cluster {i}: {len(cluster)} molecules")
    cluster_mols = [mols[idx] for idx in cluster]

Important: Butina clustering builds a full distance matrix - suitable for ~1000 molecules, not for 10,000+.

Diversity selection:

# Pick diverse subset
diverse_mols = dm.pick_diverse(
    mols,
    npick=100  # Select 100 diverse molecules
)

# Pick cluster centroids
centroids = dm.pick_centroids(
    mols,
    npick=50   # Select 50 representative molecules
)

6. Scaffold Analysis

Refer to references/fragments_scaffolds.md for complete scaffold documentation.

Extracting Murcko scaffolds:

# Get Bemis-Murcko scaffold (core structure)
scaffold = dm.to_scaffold_murcko(mol)
scaffold_smiles = dm.to_smiles(scaffold)

Scaffold-based analysis:

# Group compounds by scaffold
from collections import Counter

scaffolds = [dm.to_scaffold_murcko(mol) for mol in mols]
scaffold_smiles = [dm.to_smiles(s) for s in scaffolds]

# Count scaffold frequency
scaffold_counts = Counter(scaffold_smiles)
most_common = scaffold_counts.most_common(10)

# Create scaffold-to-molecules mapping
scaffold_groups = {}
for mol, scaf_smi in zip(mols, scaffold_smiles):
    if scaf_smi not in scaffold_groups:
        scaffold_groups[scaf_smi] = []
    scaffold_groups[scaf_smi].append(mol)

Scaffold-based train/test splitting (for ML):

# Ensure train and test sets have different scaffolds
scaffold_to_mols = {}
for mol, scaf in zip(mols, scaffold_smiles):
    if scaf not in scaffold_to_mols:
        scaffold_to_mols[scaf] = []
    scaffold_to_mols[scaf].append(mol)

# Split scaffolds into train/test
import random
scaffolds = list(scaffold_to_mols.keys())
random.shuffle(scaffolds)
split_idx = int(0.8 * len(scaffolds))
train_scaffolds = scaffolds[:split_idx]
test_scaffolds = scaffolds[split_idx:]

# Get molecules for each split
train_mols = [mol for scaf in train_scaffolds for mol in scaffold_to_mols[scaf]]
test_mols = [mol for scaf in test_scaffolds for mol in scaffold_to_mols[scaf]]

7. Molecular Fragmentation

Refer to references/fragments_scaffolds.md for fragmentation details.

BRICS fragmentation (16 bond types):

# Fragment molecule
fragments = dm.fragment.brics(mol)
# Returns: set of fragment SMILES with attachment points like '[1*]CCN'

RECAP fragmentation (11 bond types):

fragments = dm.fragment.recap(mol)

Fragment analysis:

# Find common fragments across compound library
from collections import Counter

all_fragments = []
for mol in mols:
    frags = dm.fragment.brics(mol)
    all_fragments.extend(frags)

fragment_counts = Counter(all_fragments)
common_frags = fragment_counts.most_common(20)

# Fragment-based scoring
def fragment_score(mol, reference_fragments):
    mol_frags = dm.fragment.brics(mol)
    overlap = mol_frags.intersection(reference_fragments)
    return len(overlap) / len(mol_frags) if mol_frags else 0

8. 3D Conformer Generation

Refer to references/conformers_module.md for detailed conformer documentation.

Generating conformers:

# Generate 3D conformers
mol_3d = dm.conformers.generate(
    mol,
    n_confs=50,           # Number to generate (auto if None)
    rms_cutoff=0.5,       # Filter similar conformers (Ångströms)
    minimize_energy=True,  # Minimize with UFF force field
    method='ETKDGv3'      # Embedding method (recommended)
)

# Access conformers
n_conformers = mol_3d.GetNumConformers()
conf = mol_3d.GetConformer(0)  # Get first conformer
positions = conf.GetPositions()  # Nx3 array of atom coordinates

Conformer clustering:

# Cluster conformers by RMSD
clusters = dm.conformers.cluster(
    mol_3d,
    rms_cutoff=1.0,
    centroids=False
)

# Get representative conformers
centroids = dm.conformers.return_centroids(mol_3d, clusters)

SASA calculation:

# Calculate solvent accessible surface area
sasa_values = dm.conformers.sasa(mol_3d, n_jobs=-1)

# Access SASA from conformer properties
conf = mol_3d.GetConformer(0)
sasa = conf.GetDoubleProp('rdkit_free_sasa')

9. Visualization

Refer to references/descriptors_viz.md for visualization documentation.

Basic molecule grid:

# Visualize molecules
dm.viz.to_image(
    mols[:20],
    legends=[dm.to_smiles(m) for m in mols[:20]],
    n_cols=5,
    mol_size=(300, 300)
)

# Save to file
dm.viz.to_image(mols, outfile="molecules.png")

# SVG for publications
dm.viz.to_image(mols, outfile="molecules.svg", use_svg=True)

Aligned visualization (for SAR analysis):

# Align molecules by common substructure
dm.viz.to_image(
    similar_mols,
    align=True,  # Enable MCS alignment
    legends=activity_labels,
    n_cols=4
)

Highlighting substructures:

# Highlight specific atoms and bonds
dm.viz.to_image(
    mol,
    highlight_atom=[0, 1, 2, 3],  # Atom indices
    highlight_bond=[0, 1, 2]      # Bond indices
)

Conformer visualization:

# Display multiple conformers
dm.viz.conformers(
    mol_3d,
    n_confs=10,
    align_conf=True,
    n_cols=3
)

10. Chemical Reactions

Refer to references/reactions_data.md for reactions documentation.

Applying reactions:

from rdkit.Chem import rdChemReactions

# Define reaction from SMARTS
rxn_smarts = '[C:1](=[O:2])[OH:3]>>[C:1](=[O:2])[Cl:3]'
rxn = rdChemReactions.ReactionFromSmarts(rxn_smarts)

# Apply to molecule
reactant = dm.to_mol("CC(=O)O")  # Acetic acid
product = dm.reactions.apply_reaction(
    rxn,
    (reactant,),
    sanitize=True
)

# Convert to SMILES
product_smiles = dm.to_smiles(product)

Batch reaction application:

# Apply reaction to library
products = []
for mol in reactant_mols:
    try:
        prod = dm.reactions.apply_reaction(rxn, (mol,))
        if prod is not None:
            products.append(prod)
    except Exception as e:
        print(f"Reaction failed: {e}")

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)
• dm.cluster_mols(..., n_jobs=-1)
• dm.pdist(..., n_jobs=-1)
• dm.conformers.sasa(..., n_jobs=-1)

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

Common Workflows and Patterns

Complete Pipeline: Data Loading → Filtering → Analysis

import datamol as dm
import pandas as pd

# 1. Load molecules
df = dm.read_sdf("compounds.sdf")

# 2. Standardize
df['mol'] = df['mol'].apply(lambda m: dm.standardize_mol(m) if m else None)
df = df[df['mol'].notna()]  # Remove failed molecules

# 3. Compute descriptors
desc_df = dm.descriptors.batch_compute_many_descriptors(
    df['mol'].tolist(),
    n_jobs=-1,
    progress=True
)

# 4. Filter by drug-likeness
druglike = (
    (desc_df['mw'] <= 500) &
    (desc_df['logp'] <= 5) &
    (desc_df['hbd'] <= 5) &
    (desc_df['hba'] <= 10)
)
filtered_df = df[druglike]

# 5. Cluster and select diverse subset
diverse_mols = dm.pick_diverse(
    filtered_df['mol'].tolist(),
    npick=100
)

# 6. Visualize results
dm.viz.to_image(
    diverse_mols,
    legends=[dm.to_smiles(m) for m in diverse_mols],
    outfile="diverse_compounds.png",
    n_cols=10
)

Structure-Activity Relationship (SAR) Analysis

# Group by scaffold
scaffolds = [dm.to_scaffold_murcko(mol) for mol in mols]
scaffold_smiles = [dm.to_smiles(s) for s in scaffolds]

# Create DataFrame with activities
sar_df = pd.DataFrame({
    'mol': mols,
    'scaffold': scaffold_smiles,
    'activity': activities  # User-provided activity data
})

# Analyze each scaffold series
for scaffold, group in sar_df.groupby('scaffold'):
    if len(group) >= 3:  # Need multiple examples
        print(f"\nScaffold: {scaffold}")
        print(f"Count: {len(group)}")
        print(f"Activity range: {group['activity'].min():.2f} - {group['activity'].max():.2f}")

        # Visualize with activities as legends
        dm.viz.to_image(
            group['mol'].tolist(),
            legends=[f"Activity: {act:.2f}" for act in group['activity']],
            align=True  # Align by common substructure
        )

Virtual Screening Pipeline

# 1. Generate fingerprints for query and library
query_fps = [dm.to_fp(mol) for mol in query_actives]
library_fps = [dm.to_fp(mol) for mol in library_mols]

# 2. Calculate similarities
from scipy.spatial.distance import cdist
import numpy as np

distances = dm.cdist(query_actives, library_mols, n_jobs=-1)

# 3. Find closest matches (min distance to any query)
min_distances = distances.min(axis=0)
similarities = 1 - min_distances  # Convert distance to similarity

# 4. Rank and select top hits
top_indices = np.argsort(similarities)[::-1][:100]  # Top 100
top_hits = [library_mols[i] for i in top_indices]
top_scores = [similarities[i] for i in top_indices]

# 5. Visualize hits
dm.viz.to_image(
    top_hits[:20],
    legends=[f"Sim: {score:.3f}" for score in top_scores[:20]],
    outfile="screening_hits.png"
)

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:
       # Handle invalid SMILES
   

3. Use parallel processing for large datasets:

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

4. Leverage fsspec for cloud storage:

   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

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

# Or descriptors
desc_df = dm.descriptors.batch_compute_many_descriptors(mols, n_jobs=-1)
X = desc_df.values

# Train model
from sklearn.ensemble import RandomForestRegressor
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: Ensure fsspec and appropriate cloud provider libraries are installed (s3fs, gcsfs, etc.)

Additional Resources

• Datamol Documentation: https://docs.datamol.io/
• RDKit Documentation: https://www.rdkit.org/docs/
• GitHub Repository: https://github.com/datamol-io/datamol