pubchem-database

1# PubChem Database
2 
3## Overview
4 
5PubChem is the world's largest freely available chemical database with 110M+ compounds and 270M+ bioactivities. Query chemical structures by name, CID, or SMILES, retrieve molecular properties, perform similarity and substructure searches, access bioactivity data using PUG-REST API and PubChemPy.
6 
7## When to Use This Skill
8 
9This skill should be used when:
10- Searching for chemical compounds by name, structure (SMILES/InChI), or molecular formula
11- Retrieving molecular properties (MW, LogP, TPSA, hydrogen bonding descriptors)
12- Performing similarity searches to find structurally related compounds
13- Conducting substructure searches for specific chemical motifs
14- Accessing bioactivity data from screening assays
15- Converting between chemical identifier formats (CID, SMILES, InChI)
16- Batch processing multiple compounds for drug-likeness screening or property analysis
17 
18## Core Capabilities
19 
20### 1. Chemical Structure Search
21 
22Search for compounds using multiple identifier types:
23 
24**By Chemical Name**:
25```python
26import pubchempy as pcp
27compounds = pcp.get_compounds('aspirin', 'name')
28compound = compounds[0]
29```
30 
31**By CID (Compound ID)**:
32```python
33compound = pcp.Compound.from_cid(2244)  # Aspirin
34```
35 
36**By SMILES**:
37```python
38compound = pcp.get_compounds('CC(=O)OC1=CC=CC=C1C(=O)O', 'smiles')[0]
39```
40 
41**By InChI**:
42```python
43compound = pcp.get_compounds('InChI=1S/C9H8O4/...', 'inchi')[0]
44```
45 
46**By Molecular Formula**:
47```python
48…