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Common SMARTS Patterns for RDKit

This document provides a collection of commonly used SMARTS patterns for substructure searching in RDKit.

Functional Groups

Alcohols

# Primary alcohol
'[CH2][OH1]'

# Secondary alcohol
'[CH1]([OH1])[CH3,CH2]'

# Tertiary alcohol
'[C]([OH1])([C])([C])[C]'

# Any alcohol
'[OH1][C]'

# Phenol
'c[OH1]'

Aldehydes and Ketones

# Aldehyde
'[CH1](=O)'

# Ketone
'[C](=O)[C]'

# Any carbonyl
'[C](=O)'

Carboxylic Acids and Derivatives

# Carboxylic acid
'C(=O)[OH1]'
'[CX3](=O)[OX2H1]'  # More specific

# Ester
'C(=O)O[C]'
'[CX3](=O)[OX2][C]'  # More specific

# Amide
'C(=O)N'
'[CX3](=O)[NX3]'  # More specific

# Acyl chloride
'C(=O)Cl'

# Anhydride
'C(=O)OC(=O)'

Amines

# Primary amine
'[NH2][C]'

# Secondary amine
'[NH1]([C])[C]'

# Tertiary amine
'[N]([C])([C])[C]'

# Aromatic amine (aniline)
'c[NH2]'

# Any amine
'[NX3]'

Ethers

# Aliphatic ether
'[C][O][C]'

# Aromatic ether
'c[O][C,c]'

Halides

# Alkyl halide
'[C][F,Cl,Br,I]'

# Aryl halide
'c[F,Cl,Br,I]'

# Specific halides
'[C]F'  # Fluoride
'[C]Cl'  # Chloride
'[C]Br'  # Bromide
'[C]I'  # Iodide

Nitriles and Nitro Groups

# Nitrile
'C#N'

# Nitro group
'[N+](=O)[O-]'

# Nitro on aromatic
'c[N+](=O)[O-]'

Thiols and Sulfides

# Thiol
'[C][SH1]'

# Sulfide
'[C][S][C]'

# Disulfide
'[C][S][S][C]'

# Sulfoxide
'[C][S](=O)[C]'

# Sulfone
'[C][S](=O)(=O)[C]'

Ring Systems

Simple Rings

# Benzene ring
'c1ccccc1'
'[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1'  # Explicit atoms

# Cyclohexane
'C1CCCCC1'

# Cyclopentane
'C1CCCC1'

# Any 3-membered ring
'[r3]'

# Any 4-membered ring
'[r4]'

# Any 5-membered ring
'[r5]'

# Any 6-membered ring
'[r6]'

# Any 7-membered ring
'[r7]'

Aromatic Rings

# Aromatic carbon in ring
'[cR]'

# Aromatic nitrogen in ring (pyridine, etc.)
'[nR]'

# Aromatic oxygen in ring (furan, etc.)
'[oR]'

# Aromatic sulfur in ring (thiophene, etc.)
'[sR]'

# Any aromatic ring
'a1aaaaa1'

Heterocycles

# Pyridine
'n1ccccc1'

# Pyrrole
'n1cccc1'

# Furan
'o1cccc1'

# Thiophene
's1cccc1'

# Imidazole
'n1cncc1'

# Pyrimidine
'n1cnccc1'

# Thiazole
'n1ccsc1'

# Oxazole
'n1ccoc1'

Fused Rings

# Naphthalene
'c1ccc2ccccc2c1'

# Indole
'c1ccc2[nH]ccc2c1'

# Quinoline
'n1cccc2ccccc12'

# Benzimidazole
'c1ccc2[nH]cnc2c1'

# Purine
'n1cnc2ncnc2c1'

Macrocycles

# Rings with 8 or more atoms
'[r{8-}]'

# Rings with 9-15 atoms
'[r{9-15}]'

# Rings with more than 12 atoms (macrocycles)
'[r{12-}]'

Specific Structural Features

Aliphatic vs Aromatic

# Aliphatic carbon
'[C]'

# Aromatic carbon
'[c]'

# Aliphatic carbon in ring
'[CR]'

# Aromatic carbon (alternative)
'[cR]'

Stereochemistry

# Tetrahedral center with clockwise chirality
'[C@]'

# Tetrahedral center with counterclockwise chirality
'[C@@]'

# Any chiral center
'[C@,C@@]'

# E double bond
'C/C=C/C'

# Z double bond
'C/C=C\\C'

Hybridization

# SP hybridization (triple bond)
'[CX2]'

# SP2 hybridization (double bond or aromatic)
'[CX3]'

# SP3 hybridization (single bonds)
'[CX4]'

Charge

# Positive charge
'[+]'

# Negative charge
'[-]'

# Specific charge
'[+1]'
'[-1]'
'[+2]'

# Positively charged nitrogen
'[N+]'

# Negatively charged oxygen
'[O-]'

# Carboxylate anion
'C(=O)[O-]'

# Ammonium cation
'[N+]([C])([C])([C])[C]'

Pharmacophore Features

Hydrogen Bond Donors

# Hydroxyl
'[OH]'

# Amine
'[NH,NH2]'

# Amide NH
'[N][C](=O)'

# Any H-bond donor
'[OH,NH,NH2,NH3+]'

Hydrogen Bond Acceptors

# Carbonyl oxygen
'[O]=[C,S,P]'

# Ether oxygen
'[OX2]'

# Ester oxygen
'C(=O)[O]'

# Nitrogen acceptor
'[N;!H0]'

# Any H-bond acceptor
'[O,N]'

Hydrophobic Groups

# Alkyl chain (4+ carbons)
'CCCC'

# Branched alkyl
'C(C)(C)C'

# Aromatic rings (hydrophobic)
'c1ccccc1'

Aromatic Interactions

# Benzene for pi-pi stacking
'c1ccccc1'

# Heterocycle for pi-pi
'[a]1[a][a][a][a][a]1'

# Any aromatic ring
'[aR]'

Drug-like Fragments

Lipinski Fragments

# Aromatic ring with substituents
'c1cc(*)ccc1'

# Aliphatic chain
'CCCC'

# Ether linkage
'[C][O][C]'

# Amine (basic center)
'[N]([C])([C])'

Common Scaffolds

# Benzamide
'c1ccccc1C(=O)N'

# Sulfonamide
'S(=O)(=O)N'

# Urea
'[N][C](=O)[N]'

# Guanidine
'[N]C(=[N])[N]'

# Phosphate
'P(=O)([O-])([O-])[O-]'

Privileged Structures

# Biphenyl
'c1ccccc1-c2ccccc2'

# Benzopyran
'c1ccc2OCCCc2c1'

# Piperazine
'N1CCNCC1'

# Piperidine
'N1CCCCC1'

# Morpholine
'N1CCOCC1'

Reactive Groups

Electrophiles

# Acyl chloride
'C(=O)Cl'

# Alkyl halide
'[C][Cl,Br,I]'

# Epoxide
'C1OC1'

# Michael acceptor
'C=C[C](=O)'

Nucleophiles

# Primary amine
'[NH2][C]'

# Thiol
'[SH][C]'

# Alcohol
'[OH][C]'

Toxicity Alerts (PAINS)

# Rhodanine
'S1C(=O)NC(=S)C1'

# Catechol
'c1ccc(O)c(O)c1'

# Quinone
'O=C1C=CC(=O)C=C1'

# Hydroquinone
'OC1=CC=C(O)C=C1'

# Alkyl halide (reactive)
'[C][I,Br]'

# Michael acceptor (reactive)
'C=CC(=O)[C,N]'

Metal Binding

# Carboxylate (metal chelator)
'C(=O)[O-]'

# Hydroxamic acid
'C(=O)N[OH]'

# Catechol (iron chelator)
'c1c(O)c(O)ccc1'

# Thiol (metal binding)
'[SH]'

# Histidine-like (metal binding)
'c1ncnc1'

Size and Complexity Filters

# Long aliphatic chains (>6 carbons)
'CCCCCCC'

# Highly branched (quaternary carbon)
'C(C)(C)(C)C'

# Multiple rings
'[R]~[R]'  # Two rings connected

# Spiro center
'[C]12[C][C][C]1[C][C]2'

Special Patterns

Atom Counts

# Any atom
'[*]'

# Heavy atom (not H)
'[!H]'

# Carbon
'[C,c]'

# Heteroatom
'[!C;!H]'

# Halogen
'[F,Cl,Br,I]'

Bond Types

# Single bond
'C-C'

# Double bond
'C=C'

# Triple bond
'C#C'

# Aromatic bond
'c:c'

# Any bond
'C~C'

Ring Membership

# In any ring
'[R]'

# Not in ring
'[!R]'

# In exactly one ring
'[R1]'

# In exactly two rings
'[R2]'

# Ring bond
'[R]~[R]'

Degree and Connectivity

# Total degree 1 (terminal atom)
'[D1]'

# Total degree 2 (chain)
'[D2]'

# Total degree 3 (branch point)
'[D3]'

# Total degree 4 (highly branched)
'[D4]'

# Connected to exactly 2 carbons
'[C]([C])[C]'

Usage Examples

from rdkit import Chem

# Create SMARTS query
pattern = Chem.MolFromSmarts('[CH2][OH1]')  # Primary alcohol

# Search molecule
mol = Chem.MolFromSmiles('CCO')
matches = mol.GetSubstructMatches(pattern)

# Multiple patterns
patterns = {
    'alcohol': '[OH1][C]',
    'amine': '[NH2,NH1][C]',
    'carboxylic_acid': 'C(=O)[OH1]'
}

# Check for functional groups
for name, smarts in patterns.items():
    query = Chem.MolFromSmarts(smarts)
    if mol.HasSubstructMatch(query):
        print(f"Found {name}")

Tips for Writing SMARTS

Be specific when needed: Use atom properties [CX3] instead of just [C]
Use brackets for clarity: [C] is different from C (aromatic)
Consider aromaticity: lowercase letters (c, n, o) are aromatic
Check ring membership: [R] for in-ring, [!R] for not in-ring
Use recursive SMARTS: $(...) for complex patterns
Test patterns: Always validate SMARTS on known molecules
Start simple: Build complex patterns incrementally

Common SMARTS Syntax

[C] - Aliphatic carbon
[c] - Aromatic carbon
[CX4] - Carbon with 4 connections (sp3)
[CX3] - Carbon with 3 connections (sp2)
[CX2] - Carbon with 2 connections (sp)
[CH3] - Methyl group
[R] - In ring
[r6] - In 6-membered ring
[r{5-7}] - In 5, 6, or 7-membered ring
[D2] - Degree 2 (2 neighbors)
[+] - Positive charge
[-] - Negative charge
[!C] - Not carbon
[#6] - Element with atomic number 6 (carbon)
~ - Any bond type
- - Single bond
= - Double bond
# - Triple bond
: - Aromatic bond
@ - Clockwise chirality
@@ - Counter-clockwise chirality

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Common SMARTS Patterns for RDKit

Functional Groups

Alcohols

Aldehydes and Ketones

Carboxylic Acids and Derivatives

Amines

Ethers

Halides

Nitriles and Nitro Groups

Thiols and Sulfides

Ring Systems

Simple Rings

Aromatic Rings

Heterocycles

Fused Rings

Macrocycles

Specific Structural Features

Aliphatic vs Aromatic

Stereochemistry

Hybridization

Charge

Pharmacophore Features

Hydrogen Bond Donors

Hydrogen Bond Acceptors

Hydrophobic Groups

Aromatic Interactions

Drug-like Fragments

Lipinski Fragments

Common Scaffolds

Privileged Structures

Reactive Groups

Electrophiles

Nucleophiles

Toxicity Alerts (PAINS)

Metal Binding

Size and Complexity Filters

Special Patterns

Atom Counts

Bond Types

Ring Membership

Degree and Connectivity

Usage Examples

Tips for Writing SMARTS

Common SMARTS Syntax

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