> ## Documentation Index
> Fetch the complete documentation index at: https://docs.openbio.tech/llms.txt
> Use this file to discover all available pages before exploring further.

# Molecular Chemistry Tools

> Chemical analysis and molecular property calculations

OpenBio provides computational chemistry tools for analyzing molecules, calculating properties, and assessing drug-likeness.

## RDKit - Chemical Informatics

**Purpose**: Comprehensive molecular analysis and property calculation

**Available analyses**:

* Calculate molecular properties (MW, logP, HBD/HBA, TPSA)
* Assess drug-likeness (Lipinski, Veber rules)
* Generate 2D structure visualizations
* Convert between formats (SMILES, InChI)
* Find substructures and functional groups
* Calculate molecular similarity
* Generate chemical fingerprints

**Example**: "Calculate properties for this SMILES: CC(=O)Oc1ccccc1C(=O)O"

## SA Score - Synthetic Accessibility

**Purpose**: Predict ease of chemical synthesis

**Features**:

* Scale: 1-10 (1 = easy, 10 = very difficult)
* Prioritizes synthesizable compounds
* Filters virtual libraries
* Guides medicinal chemistry design

**Interpretation**:

* **1-3**: Easy, routine synthesis
* **4-6**: Moderate difficulty, feasible
* **7-8**: Difficult, requires expertise
* **9-10**: Very difficult or impractical

## Quick Examples

* "Calculate properties for this SMILES: CC(=O)Oc1ccccc1C(=O)O"
* "Check if this compound is drug-like"
* "Show the structure of aspirin"
* "Calculate synthetic accessibility for this compound"
* "How similar are compound A and B?"

## Common Workflows

**Compound Characterization**: Calculate properties → Check drug-likeness → Assess synthesis → Generate report

**Library Filtering**: Filter by MW → Filter by logP → Check Lipinski → Calculate SA score → Rank results

**Similarity Search**: Generate fingerprint → Calculate similarity → Rank by Tanimoto → Compare structures