Skill · em Dados, IA e pesquisa

rdkit

Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced…

Procedência

Origem: davila7/claude-code-templates
Caminho: cli-tool/components/skills/scientific/rdkit
Versão fixada: 57f899e5394bb8ca166f38eacae8f0853cbfe033
Licença: MIT
Espelhado em 25/09/2026
nenhum download no Claude Code Templates (lido em 25/09/2026)

Antes de instalar

7 arquivos · 83,8 KB · inclui 3 scripts que executam: scripts/molecular_properties.py, scripts/similarity_search.py, scripts/substructure_filter.py

Instalar na sua CLI

O comando baixa a versão fixada (commit 57f899e) direto da origem, para a pasta que a CLI lê. Precisa de curl (macOS e Linux); no Windows não há comando, porque o Rook Labs é para macOS.

Claude Code

Neste projeto: instala em .claude/skills/rdkit/.

d=".claude/skills/rdkit"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/rdkit"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/references/descriptors_reference.md" "$u/references/descriptors_reference.md" \
  -o "$d/references/smarts_patterns.md" "$u/references/smarts_patterns.md" \
  -o "$d/scripts/molecular_properties.py" "$u/scripts/molecular_properties.py" \
  -o "$d/scripts/similarity_search.py" "$u/scripts/similarity_search.py" \
  -o "$d/scripts/substructure_filter.py" "$u/scripts/substructure_filter.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.claude/skills/rdkit/.

d="$HOME/.claude/skills/rdkit"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/rdkit"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/references/descriptors_reference.md" "$u/references/descriptors_reference.md" \
  -o "$d/references/smarts_patterns.md" "$u/references/smarts_patterns.md" \
  -o "$d/scripts/molecular_properties.py" "$u/scripts/molecular_properties.py" \
  -o "$d/scripts/similarity_search.py" "$u/scripts/similarity_search.py" \
  -o "$d/scripts/substructure_filter.py" "$u/scripts/substructure_filter.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Codex

Neste projeto: instala em .agents/skills/rdkit/.

d=".agents/skills/rdkit"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/rdkit"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/references/descriptors_reference.md" "$u/references/descriptors_reference.md" \
  -o "$d/references/smarts_patterns.md" "$u/references/smarts_patterns.md" \
  -o "$d/scripts/molecular_properties.py" "$u/scripts/molecular_properties.py" \
  -o "$d/scripts/similarity_search.py" "$u/scripts/similarity_search.py" \
  -o "$d/scripts/substructure_filter.py" "$u/scripts/substructure_filter.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.agents/skills/rdkit/.

d="$HOME/.agents/skills/rdkit"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/rdkit"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/references/descriptors_reference.md" "$u/references/descriptors_reference.md" \
  -o "$d/references/smarts_patterns.md" "$u/references/smarts_patterns.md" \
  -o "$d/scripts/molecular_properties.py" "$u/scripts/molecular_properties.py" \
  -o "$d/scripts/similarity_search.py" "$u/scripts/similarity_search.py" \
  -o "$d/scripts/substructure_filter.py" "$u/scripts/substructure_filter.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Antigravity

Neste projeto: instala em .agents/skills/rdkit/.

d=".agents/skills/rdkit"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/rdkit"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/references/descriptors_reference.md" "$u/references/descriptors_reference.md" \
  -o "$d/references/smarts_patterns.md" "$u/references/smarts_patterns.md" \
  -o "$d/scripts/molecular_properties.py" "$u/scripts/molecular_properties.py" \
  -o "$d/scripts/similarity_search.py" "$u/scripts/similarity_search.py" \
  -o "$d/scripts/substructure_filter.py" "$u/scripts/substructure_filter.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.gemini/antigravity-cli/skills/rdkit/.

d="$HOME/.gemini/antigravity-cli/skills/rdkit"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/rdkit"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/references/descriptors_reference.md" "$u/references/descriptors_reference.md" \
  -o "$d/references/smarts_patterns.md" "$u/references/smarts_patterns.md" \
  -o "$d/scripts/molecular_properties.py" "$u/scripts/molecular_properties.py" \
  -o "$d/scripts/similarity_search.py" "$u/scripts/similarity_search.py" \
  -o "$d/scripts/substructure_filter.py" "$u/scripts/substructure_filter.py" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Peça ao Rook

Já usa o Rook Labs? Cole no chat do Rook: instale a skill https://rooklabs.sh/marketplace/cct.rdkit

Prévia do SKILL.md

---
name: rdkit
description: "Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custo…
---

# RDKit Cheminformatics Toolkit

## Overview

RDKit 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 visualiza…

## Core Capabilities

### 1. Molecular I/O and Creation

**Reading Molecules:**

Read molecular structures from various formats:

```python
from rdkit import Chem

# From SMILES strings
mol = Chem.MolFromSmiles('Cc1ccccc1')  # Returns Mol object or None

# From MOL files
mol = Chem.MolFromMolFile('path/to/file.mol')

# From MOL blocks (string data)
mol = Chem.MolFromMolBlock(mol_block_string)

# From InChI
mol = Chem.MolFromInchi('InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H')
```

**Writing Molecules:**

Convert molecules to text representations:

```python
…

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