rdkit — quality + safety report

---
name: rdkit
description: Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.
license: BSD-3-Clause license
metadata:
  version: "1.0"
  skill-author: K-Dense Inc.
---

# RDKit Cheminformatics Toolkit

## Overview

RDKit is a comprehensive cheminformatics library providing Python APIs for molecular analysis and manipulation. This skill provides guidance for reading/writing molecular structures, calculating descriptors, fingerprinting, substructure searching, chemical reactions, 2D/3D coordinate generation, and molecular visualization. Use this skill for drug discovery, computational chemistry, and cheminformatics research tasks.

## Core Capabilities

### 1. Molecular I/O and Creation

**Reading Molecules:**

Read molecular structures from various formats:

```python
from rdkit import Chem

# From SMILES strings
mol = Chem.MolFromSmiles('Cc1ccccc1')  # Returns Mol object or None

# From MOL files
mol = Chem.MolFromMolFile('path/to/file.mol')

# From MOL blocks (string data)
mol = Chem.MolFromMolBlock(mol_block_string)

# From InChI
mol = Chem.MolFromInchi('InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H')
```

**Writing Molecules:**

Convert molecules to text representations:

```python
# To canonical SMILES
smiles = Chem.MolToSmiles(mol)

# To MOL block
mol_block = Chem.MolToMolBlock(mol)

# To InChI
inchi = Chem.MolToInchi(mol)
```

**Batch Processing:**

For processing multiple molecules, use Supplier/Writer objects:

```python
# Read SDF files
suppl = Chem.SDMolSupplier('molecules.sdf')
for mol in suppl:
    if mol is not None:  # Check for parsing errors
        # Process molecule
        pass

# Read SMILES files
suppl = Chem.SmilesMolSupplier('molecules.smi', titleLine=False)

# For large files or compressed data
import gzip

with gzip.open('molecules.sdf.gz') as f:
    suppl = Chem.ForwardSDMolSupplier(f)
    for mol in suppl:
        # Process molecule
        pass

# Multithreaded processing for large datasets
suppl = Chem.MultithreadedSDMolSupplier('molecules.sdf')

# Write molecules to SDF
writer = Chem.SDWriter('output.sdf')
for mol in molecules:
    writer.write(mol)
writer.close()
```

**Important Notes:**
- All `MolFrom*` functions return `None` on failure with error messages
- Always check for `None` before processing molecules
- Molecules are automatically sanitized on import (validates valence, perceives aromaticity)

### 2. Molecular Sanitization and Validation

RDKit automatically sanitizes molecules during parsing, executing 13 steps including valence checking, aromaticity perception, and chirality assignment.

**Sanitization Control:**

```python
# Disable automatic sanitization
mol = Chem.MolFromSmiles('C1=CC=CC=C1', sanitize=False)

# Manual sanitization
Chem.SanitizeMol(mol)

# Detect problems before sanitization
problems = Chem.DetectChemistryProblems(mol)
for problem in problems:
    print(problem.GetType(), problem.Message())

# Partial sanitization (skip specific steps)
from rdkit.Chem import rdMolStandardize
Chem.SanitizeMol(mol, sanitizeOps=Chem.SANITIZE_ALL ^ Chem.SANITIZE_PROPERTIES)
```

**Common Sanitization Issues:**
- Atoms with explicit valence exceeding maximum allowed will raise exceptions
- Invalid aromatic rings will cause kekulization errors
- Radical electrons may not be properly assigned without explicit specification

### 3. Molecular Analysis and Properties

**Accessing Molecular Structure:**

```python
# Iterate atoms and bonds
for atom in mol.GetAtoms():
    print(atom.GetSymbol(), atom.GetIdx(), atom.GetDegree())

for bond in mol.GetBonds():
    print(bond.GetBeginAtomIdx(), bond.GetEndAtomIdx(), bond.GetBondType())

# Ring information
ring_info = mol.GetRingInfo()
ring_info.NumRings()
ring_info.AtomRings()  # Returns tuples of atom indices

# Check if atom is in ring
atom = mol.GetAtomWithIdx(0)
atom.IsInRing()
atom.IsInRingSize(6)  # Check for 6-membered rings

# Find smallest set of smallest rings (SSSR)
from rdkit.Chem import GetSymmSSSR
rings = GetSymmSSSR(mol)
```

**Stereochemistry:**

```python
# Find chiral centers
from rdkit.Chem import FindMolChiralCenters
chiral_centers = FindMolChiralCenters(mol, includeUnassigned=True)
# Returns list of (atom_idx, chirality) tuples

# Assign stereochemistry from 3D coordinates
from rdkit.Chem import AssignStereochemistryFrom3D
AssignStereochemistryFrom3D(mol)

# Check bond stereochemistry
bond = mol.GetBondWithIdx(0)
stereo = bond.GetStereo()  # STEREONONE, STEREOZ, STEREOE, etc.
```

**Fragment Analysis:**

```python
# Get disconnected fragments
frags = Chem.GetMolFrags(mol, asMols=True)

# Fragment on specific bonds
from rdkit.Chem import FragmentOnBonds
frag_mol = FragmentOnBonds(mol, [bond_idx1, bond_idx2])

# Count ring systems
from rdkit.Chem.Scaffolds import MurckoScaffold
scaffold = MurckoScaffold.GetScaffoldForMol(mol)
```

### 4. Molecular Descriptors and Properties

**Basic Descriptors:**

```python
from rdkit.Chem import Descriptors

# Molecular weight
mw = Descriptors.MolWt(mol)
exact_mw = Descriptors.ExactMolWt(mol)

# LogP (lipophilicity)
logp = Descriptors.MolLogP(mol)

# Topological polar surface area
tpsa = Descriptors.TPSA(mol)

# Number of hydrogen bond donors/acceptors
hbd = Descriptors.NumHDonors(mol)
hba = Descriptors.NumHAcceptors(mol)

# Number of rotatable bonds
rot_bonds = Descriptors.NumRotatableBonds(mol)

# Number of aromatic rings
aromatic_rings = Descriptors.NumAromaticRings(mol)
```

**Batch Descriptor Calculation:**

```python
# Calculate all descriptors at once
all_descriptors = Descriptors.CalcMolDescriptors(mol)
# Returns dictionary: {'MolWt': 180.16, 'MolLogP': 1.23, ...}

# Get list of available descriptor names
descriptor_names = [desc[0] for desc in Descriptors._descList]
```

**Lipinski's Rule of Five:**

```python
# Check drug-likeness
mw = Descriptors.MolWt(mol) <= 500
logp = Descriptors.MolLogP(mol) <= 5
hbd = Descriptors.NumHDonors(mol) <= 5
hba = Descriptors.NumHAcceptors(mol) <= 10

is_drug_like = mw and logp and hbd and hba
```

### 5. Fingerprints and Molecular Similarity

**Fingerprint Types:**

```python
from rdkit.Chem import rdFingerprintGenerator
from rdkit.Chem import MACCSkeys

# RDKit topological fingerprint
rdk_gen = rdFingerprintGenerator.GetRDKitFPGenerator(minPath=1, maxPath=7, fpSize=2048)
fp = rdk_gen.GetFingerprint(mol)

# Morgan fingerprints (circular fingerprints, similar to ECFP)
# Modern API using rdFingerprintGenerator
morgan_gen = rdFingerprintGenerator.GetMorganGenerator(radius=2, fpSize=2048)
fp = morgan_gen.GetFingerprint(mol)
# Count-based fingerprint
fp_count = morgan_gen.GetCountFingerprint(mol)

# MACCS keys (166-bit structural key)
fp = MACCSkeys.GenMACCSKeys(mol)

# Atom pair fingerprints
ap_gen = rdFingerprintGenerator.GetAtomPairGenerator()
fp = ap_gen.GetFingerprint(mol)

# Topological torsion fingerprints
tt_gen = rdFingerprintGenerator.GetTopologicalTorsionGenerator()
fp = tt_gen.GetFingerprint(mol)

# Avalon fingerprints (if available)
from rdkit.Avalon import pyAvalonTools
fp = pyAvalonTools.GetAvalonFP(mol)
```

**Similarity Calculation:**

```python
from rdkit import DataStructs
from rdkit.Chem import rdFingerprintGenerator

# Generate fingerprints using generator
mfpgen = rdFingerprintGenerator.GetMorganGenerator(radius=2, fpSize=2048)
fp1 = mfpgen.GetFingerprint(mol1)
fp2 = mfpgen.GetFingerprint(mol2)

# Calculate Tanimoto similarity
similarity = DataStructs.TanimotoSimilarity(fp1, fp2)

# Calculate similarity for multiple molecules
fps = [mfpgen.GetFingerprint(m) for m in [mol2, mol3, mol4]]
similarities = DataStructs.BulkTanimotoSimilarity(fp1, fps)

# Other similarity metrics
dice = DataStructs.DiceSimilarity(fp1, fp2)
cosine = DataStructs.CosineSimilarity(fp1, fp2)
```

**Clustering and Diversity:**

```python
# Butina clustering based on fingerprint similarity
from rdkit.ML.Cluster import Butina

# Calculate distance matrix
dists = []
mfpgen = rdFingerprintGenerator.GetMorganGenerator(radius=2, fpSize=2048)
fps = [mfpgen.GetFingerprint(mol) for mol in mols]
for i in range(len(fps)):
    sims = DataStructs.BulkTanimotoSimilarity(fps[i], fps[:i])
    dists.extend([1-sim for sim in sims])

# Cluster with distance cutoff
clusters = Butina.ClusterData(dists, len(fps), distThresh=0.3, isDistData=True)
```

### 6. Substructure Searching and SMARTS

**Basic Substructure Matching:**

```python
# Define query using SMARTS
query = Chem.MolFromSmarts('[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1')  # Benzene ring

# Check if molecule contains substructure
has_match = mol.HasSubstructMatch(query)

# Get all matches (returns tuple of tuples with atom indices)
matches = mol.GetSubstructMatches(query)

# Get only first match
match = mol.GetSubstructMatch(query)
```

**Common SMARTS Patterns:**

```python
# Primary alcohols
primary_alcohol = Chem.MolFromSmarts('[CH2][OH1]')

# Carboxylic acids
carboxylic_acid = Chem.MolFromSmarts('C(=O)[OH]')

# Amides
amide = Chem.MolFromSmarts('C(=O)N')

# Aromatic heterocycles
aromatic_n = Chem.MolFromSmarts('[nR]')  # Aromatic nitrogen in ring

# Macrocycles (rings > 12 atoms)
macrocycle = Chem.MolFromSmarts('[r{12-}]')
```

**Matching Rules:**
- Unspecified properties in query match any value in target
- Hydrogens are ignored unless explicitly specified
- Charged query atom won't match uncharged target atom
- Aromatic query atom won't match aliphatic target atom (unless query is generic)

### 7. Chemical Reactions

**Reaction SMARTS:**

```python
from rdkit.Chem import AllChem

# Define reaction using SMARTS: reactants >> products
rxn = AllChem.ReactionFromSmarts('[C:1]=[O:2]>>[C:1][O:2]')  # Ketone reduction

# Apply reaction to molecules
reactants = (mol1,)
products = rxn.RunReactants(reactants)

# Products is tuple of tuples (one tuple per product set)
for product_set in products:
    for product in product_set:
        # Sanitize product
        Chem.SanitizeMol(product)
```

**Reaction Features:**
- Atom mapping preserves specific atoms between reactants and products
- Dummy atoms in products are replaced by corresponding reactant atoms
- "Any" bonds inherit bond order from reactants
- Chirality preserved unless explicitly changed

**Reaction Similarity:**

```python
# Generate reaction fingerprints
fp = AllChem.CreateDifferenceFingerprintForReaction(rxn)

# Compare reactions
similarity = DataStructs.TanimotoSimilarity(fp1, fp2)
```

### 8. 2D and 3D Coordinate Generation

**2D Coordinate Generation:**

```python
from rdkit.Chem import AllChem

# Generate 2D coordinates for depiction
AllChem.Compute2DCoords(mol)

# Align molecule to template structure
template = Chem.MolFromSmiles('c1ccccc1')
AllChem.Compute2DCoords(template)
AllChem.GenerateDepictionMatching2DStructure(mol, template)
```

**3D Coordinate Generation and Conformers:**

```python
# Generate single 3D conformer using ETKDG
AllChem.EmbedMolecule(mol, randomSeed=42)

# Generate multiple conformers
conf_ids = AllChem.EmbedMultipleConfs(mol, numConfs=10, randomSeed=42)

# Optimize geometry with force field
AllChem.UFFOptimizeMolecule(mol)  # UFF force field
AllChem.MMFFOptimizeMolecule(mol)  # MMFF94 force field

# Optimize all conformers
for conf_id in conf_ids:
    AllChem.MMFFOptimizeMolecule(mol, confId=conf_id)

# Calculate RMSD between conformers
from rdkit.Chem import AllChem
rms = AllChem.GetConformerRMS(mol, conf_id1, conf_id2)

# Align molecules
AllChem.AlignMol(probe_mol, ref_mol)
```

**Constrained Embedding:**

```python
# Embed with part of molecule constrained to specific coordinates
AllChem.ConstrainedEmbed(mol, core_mol)
```

### 9. Molecular Visualization

**Basic Drawing:**

```python
from rdkit.Chem import Draw

# Draw single molecule to PIL image
img = Draw.MolToImage(mol, size=(300, 300))
img.save('molec

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