from rdkit import Chem

**Writing Molecules:**

Convert molecules to text representations:

```python

**Batch Processing:**

For processing multiple molecules, use Supplier/Writer objects:

```python

**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)

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**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

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**Stereochemistry:**

```python

**Fragment Analysis:**

```python

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from rdkit.Chem import Descriptors

**Batch Descriptor Calculation:**

```python

**Lipinski's Rule of Five:**

```python

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from rdkit.Chem import rdFingerprintGenerator
from rdkit.Chem import MACCSkeys

**Similarity Calculation:**

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

**Clustering and Diversity:**

```python

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**Common SMARTS Patterns:**

```python

**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)

from rdkit.Chem import AllChem

**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

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from rdkit.Chem import AllChem

**3D Coordinate Generation and Conformers:**

```python

**Constrained Embedding:**

```python

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from rdkit.Chem import Draw

**Highlighting Substructures:**

```python

**Customizing Visualization:**

```python
from rdkit.Chem.Draw import rdMolDraw2D

**Jupyter Notebook Integration:**

```python

**Visualizing Fingerprint Bits:**

```python

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**Kekulization and Aromaticity:**

```python

**Replacing Substructures:**

```python

**Neutralizing Charges:**

```python

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from rdkit.Chem import rdMolHash

**Randomized SMILES:**

```python

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from rdkit.Chem import ChemicalFeatures
from rdkit import RDConfig
import os

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from rdkit import Chem
from rdkit.Chem import Descriptors

def analyze_druglikeness(smiles):
    mol = Chem.MolFromSmiles(smiles)
    if mol is None:
        return None

    # Calculate Lipinski descriptors
    results = {
        'MW': Descriptors.MolWt(mol),
        'LogP': Descriptors.MolLogP(mol),
        'HBD': Descriptors.NumHDonors(mol),
        'HBA': Descriptors.NumHAcceptors(mol),
        'TPSA': Descriptors.TPSA(mol),
        'RotBonds': Descriptors.NumRotatableBonds(mol)
    }

    # Check Lipinski's Rule of Five
    results['Lipinski'] = (
        results['MW'] <= 500 and
        results['LogP'] <= 5 and
        results['HBD'] <= 5 and
        results['HBA'] <= 10
    )

    return results

from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit import DataStructs

def similarity_screen(query_smiles, database_smiles, threshold=0.7):
    query_mol = Chem.MolFromSmiles(query_smiles)
    query_fp = AllChem.GetMorganFingerprintAsBitVect(query_mol, 2)

    hits = []
    for idx, smiles in enumerate(database_smiles):
        mol = Chem.MolFromSmiles(smiles)
        if mol:
            fp = AllChem.GetMorganFingerprintAsBitVect(mol, 2)
            sim = DataStructs.TanimotoSimilarity(query_fp, fp)
            if sim >= threshold:
                hits.append((idx, smiles, sim))

    return sorted(hits, key=lambda x: x[2], reverse=True)

from rdkit import Chem

def filter_by_substructure(smiles_list, pattern_smarts):
    query = Chem.MolFromSmarts(pattern_smarts)

    hits = []
    for smiles in smiles_list:
        mol = Chem.MolFromSmiles(smiles)
        if mol and mol.HasSubstructMatch(query):
            hits.append(smiles)

    return hits

mol = Chem.MolFromSmiles(smiles)
if mol is None:
    print(f"Failed to parse: {smiles}")
    continue

import pickle

**Use bulk operations:**

```python

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