rdkit

1# RDKit Cheminformatics Toolkit
2 
3## Overview
4 
5RDKit 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.
6 
7## Core Capabilities
8 
9### 1. Molecular I/O and Creation
10 
11**Reading Molecules:**
12 
13Read molecular structures from various formats:
14 
15```python
16from rdkit import Chem
17 
18# From SMILES strings
19mol = Chem.MolFromSmiles('Cc1ccccc1')  # Returns Mol object or None
20 
21# From MOL files
22mol = Chem.MolFromMolFile('path/to/file.mol')
23 
24# From MOL blocks (string data)
25mol = Chem.MolFromMolBlock(mol_block_string)
26 
27# From InChI
28mol = Chem.MolFromInchi('InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H')
29```
30 
31**Writing Molecules:**
32 
33Convert molecules to text representations:
34 
35```python
36# To canonical SMILES
37smiles = Chem.MolToSmiles(mol)
38 
39# To MOL block
40mol_block = Chem.MolToMolBlock(mol)
41 
42# To InChI
43inchi = Chem.MolToInchi(mol)
44```
45 
46**Batch Processing:**
47 
48For processing multiple molecules, use Supplier/Writer objects:
49 
50```python
51# Read SDF files
52suppl = Chem.SDMolSupplier('molecules.sdf')
53for mol in suppl:
54    if mol is not None:  # Check for parsing errors
55        # Process molecule
56        pass
57 
58# Read SMILES files
59…