fragments_scaffolds

Scaffolds represent the core structure of molecules, useful for identifying structural families and analyzing structure-activity relationships (SAR).

Skills
Scientific
0

What it does and how to use it

A skill that teaches Claude Code to do scientific tasks well. It is packaged knowledge the model uses whenever it is relevant.

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Install (Claude Code)

mkdir -p .claude/skills/fragments-scaffolds && curl -fsSL https://doutorai.pt/data/lib/skills__fragments-scaffolds.md -o .claude/skills/fragments-scaffolds/SKILL.md

Paste this command into the terminal, in your project folder, and the component installs automatically.

Content

# Datamol Fragments and Scaffolds Reference

## Scaffolds Module (`datamol.scaffold`)

Scaffolds represent the core structure of molecules, useful for identifying structural families and analyzing structure-activity relationships (SAR).

### Murcko Scaffolds

#### `dm.to_scaffold_murcko(mol)`
Extract Bemis-Murcko scaffold (molecular framework).
- **Method**: Removes side chains, retaining ring systems and linkers
- **Returns**: Molecule object representing the scaffold
- **Use case**: Identify core structures across compound series
- **Example**:
  ```python
  mol = dm.to_mol("c1ccc(cc1)CCN") 

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