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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
+
+```python
+# 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
+
+```python
+# Aldehyde
+'[CH1](=O)'
+
+# Ketone
+'[C](=O)[C]'
+
+# Any carbonyl
+'[C](=O)'
+```
+
+### Carboxylic Acids and Derivatives
+
+```python
+# 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
+
+```python
+# Primary amine
+'[NH2][C]'
+
+# Secondary amine
+'[NH1]([C])[C]'
+
+# Tertiary amine
+'[N]([C])([C])[C]'
+
+# Aromatic amine (aniline)
+'c[NH2]'
+
+# Any amine
+'[NX3]'
+```
+
+### Ethers
+
+```python
+# Aliphatic ether
+'[C][O][C]'
+
+# Aromatic ether
+'c[O][C,c]'
+```
+
+### Halides
+
+```python
+# 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
+
+```python
+# Nitrile
+'C#N'
+
+# Nitro group
+'[N+](=O)[O-]'
+
+# Nitro on aromatic
+'c[N+](=O)[O-]'
+```
+
+### Thiols and Sulfides
+
+```python
+# 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
+
+```python
+# 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
+
+```python
+# 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
+
+```python
+# Pyridine
+'n1ccccc1'
+
+# Pyrrole
+'n1cccc1'
+
+# Furan
+'o1cccc1'
+
+# Thiophene
+'s1cccc1'
+
+# Imidazole
+'n1cncc1'
+
+# Pyrimidine
+'n1cnccc1'
+
+# Thiazole
+'n1ccsc1'
+
+# Oxazole
+'n1ccoc1'
+```
+
+### Fused Rings
+
+```python
+# Naphthalene
+'c1ccc2ccccc2c1'
+
+# Indole
+'c1ccc2[nH]ccc2c1'
+
+# Quinoline
+'n1cccc2ccccc12'
+
+# Benzimidazole
+'c1ccc2[nH]cnc2c1'
+
+# Purine
+'n1cnc2ncnc2c1'
+```
+
+### Macrocycles
+
+```python
+# 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
+
+```python
+# Aliphatic carbon
+'[C]'
+
+# Aromatic carbon
+'[c]'
+
+# Aliphatic carbon in ring
+'[CR]'
+
+# Aromatic carbon (alternative)
+'[cR]'
+```
+
+### Stereochemistry
+
+```python
+# 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
+
+```python
+# SP hybridization (triple bond)
+'[CX2]'
+
+# SP2 hybridization (double bond or aromatic)
+'[CX3]'
+
+# SP3 hybridization (single bonds)
+'[CX4]'
+```
+
+### Charge
+
+```python
+# 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
+
+```python
+# Hydroxyl
+'[OH]'
+
+# Amine
+'[NH,NH2]'
+
+# Amide NH
+'[N][C](=O)'
+
+# Any H-bond donor
+'[OH,NH,NH2,NH3+]'
+```
+
+### Hydrogen Bond Acceptors
+
+```python
+# 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
+
+```python
+# Alkyl chain (4+ carbons)
+'CCCC'
+
+# Branched alkyl
+'C(C)(C)C'
+
+# Aromatic rings (hydrophobic)
+'c1ccccc1'
+```
+
+### Aromatic Interactions
+
+```python
+# 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
+
+```python
+# Aromatic ring with substituents
+'c1cc(*)ccc1'
+
+# Aliphatic chain
+'CCCC'
+
+# Ether linkage
+'[C][O][C]'
+
+# Amine (basic center)
+'[N]([C])([C])'
+```
+
+### Common Scaffolds
+
+```python
+# 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
+
+```python
+# Biphenyl
+'c1ccccc1-c2ccccc2'
+
+# Benzopyran
+'c1ccc2OCCCc2c1'
+
+# Piperazine
+'N1CCNCC1'
+
+# Piperidine
+'N1CCCCC1'
+
+# Morpholine
+'N1CCOCC1'
+```
+
+## Reactive Groups
+
+### Electrophiles
+
+```python
+# Acyl chloride
+'C(=O)Cl'
+
+# Alkyl halide
+'[C][Cl,Br,I]'
+
+# Epoxide
+'C1OC1'
+
+# Michael acceptor
+'C=C[C](=O)'
+```
+
+### Nucleophiles
+
+```python
+# Primary amine
+'[NH2][C]'
+
+# Thiol
+'[SH][C]'
+
+# Alcohol
+'[OH][C]'
+```
+
+## Toxicity Alerts (PAINS)
+
+```python
+# 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
+
+```python
+# 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
+
+```python
+# 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
+
+```python
+# Any atom
+'[*]'
+
+# Heavy atom (not H)
+'[!H]'
+
+# Carbon
+'[C,c]'
+
+# Heteroatom
+'[!C;!H]'
+
+# Halogen
+'[F,Cl,Br,I]'
+```
+
+### Bond Types
+
+```python
+# Single bond
+'C-C'
+
+# Double bond
+'C=C'
+
+# Triple bond
+'C#C'
+
+# Aromatic bond
+'c:c'
+
+# Any bond
+'C~C'
+```
+
+### Ring Membership
+
+```python
+# 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
+
+```python
+# 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
+
+```python
+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
+
+1. **Be specific when needed:** Use atom properties [CX3] instead of just [C]
+2. **Use brackets for clarity:** [C] is different from C (aromatic)
+3. **Consider aromaticity:** lowercase letters (c, n, o) are aromatic
+4. **Check ring membership:** [R] for in-ring, [!R] for not in-ring
+5. **Use recursive SMARTS:** $(...) for complex patterns
+6. **Test patterns:** Always validate SMARTS on known molecules
+7. **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