Skill · em Dados, IA e pesquisa

datamol

Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery: SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom…

Procedência

Antes de instalar

7 arquivos · 51 KB · só texto, nenhum script

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/datamol/.

d=".claude/skills/datamol"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/datamol"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/conformers_module.md" "$u/references/conformers_module.md" \
  -o "$d/references/core_api.md" "$u/references/core_api.md" \
  -o "$d/references/descriptors_viz.md" "$u/references/descriptors_viz.md" \
  -o "$d/references/fragments_scaffolds.md" "$u/references/fragments_scaffolds.md" \
  -o "$d/references/io_module.md" "$u/references/io_module.md" \
  -o "$d/references/reactions_data.md" "$u/references/reactions_data.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

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

d="$HOME/.claude/skills/datamol"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/datamol"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/conformers_module.md" "$u/references/conformers_module.md" \
  -o "$d/references/core_api.md" "$u/references/core_api.md" \
  -o "$d/references/descriptors_viz.md" "$u/references/descriptors_viz.md" \
  -o "$d/references/fragments_scaffolds.md" "$u/references/fragments_scaffolds.md" \
  -o "$d/references/io_module.md" "$u/references/io_module.md" \
  -o "$d/references/reactions_data.md" "$u/references/reactions_data.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Codex

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

d=".agents/skills/datamol"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/datamol"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/conformers_module.md" "$u/references/conformers_module.md" \
  -o "$d/references/core_api.md" "$u/references/core_api.md" \
  -o "$d/references/descriptors_viz.md" "$u/references/descriptors_viz.md" \
  -o "$d/references/fragments_scaffolds.md" "$u/references/fragments_scaffolds.md" \
  -o "$d/references/io_module.md" "$u/references/io_module.md" \
  -o "$d/references/reactions_data.md" "$u/references/reactions_data.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

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

d="$HOME/.agents/skills/datamol"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/datamol"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/conformers_module.md" "$u/references/conformers_module.md" \
  -o "$d/references/core_api.md" "$u/references/core_api.md" \
  -o "$d/references/descriptors_viz.md" "$u/references/descriptors_viz.md" \
  -o "$d/references/fragments_scaffolds.md" "$u/references/fragments_scaffolds.md" \
  -o "$d/references/io_module.md" "$u/references/io_module.md" \
  -o "$d/references/reactions_data.md" "$u/references/reactions_data.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Antigravity

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

d=".agents/skills/datamol"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/datamol"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/conformers_module.md" "$u/references/conformers_module.md" \
  -o "$d/references/core_api.md" "$u/references/core_api.md" \
  -o "$d/references/descriptors_viz.md" "$u/references/descriptors_viz.md" \
  -o "$d/references/fragments_scaffolds.md" "$u/references/fragments_scaffolds.md" \
  -o "$d/references/io_module.md" "$u/references/io_module.md" \
  -o "$d/references/reactions_data.md" "$u/references/reactions_data.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

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

d="$HOME/.gemini/antigravity-cli/skills/datamol"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/datamol"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/conformers_module.md" "$u/references/conformers_module.md" \
  -o "$d/references/core_api.md" "$u/references/core_api.md" \
  -o "$d/references/descriptors_viz.md" "$u/references/descriptors_viz.md" \
  -o "$d/references/fragments_scaffolds.md" "$u/references/fragments_scaffolds.md" \
  -o "$d/references/io_module.md" "$u/references/io_module.md" \
  -o "$d/references/reactions_data.md" "$u/references/reactions_data.md" \
  -o "$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.datamol

Prévia do SKILL.md

---
name: datamol
description: "Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery: SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters…
---

# Datamol Cheminformatics Skill

## Overview

Datamol is a Python library that provides a lightweight, Pythonic abstraction layer over RDKit for molecular cheminformatics. Simplify complex molecular operations with sensible defaults, efficient parallelization, and modern I/O capabilities. All molecular objects are native `rdkit.Chem.Mol` instances, ensuring full c…

**Key capabilities**:
- Molecular format conversion (SMILES, SELFIES, InChI)
- Structure standardization and sanitization
- Molecular descriptors and fingerprints
- 3D conformer generation and analysis
- Clustering and diversity selection
- Scaffold and fragment analysis
- Chemical reaction application
- Visualization and alignment
- Batch processing with parallelization
- Cloud storage support via fsspec

## Installation and Setup

Guide users to install datamol:

```bash
uv pip install datamol
```

**Import convention**:
```python
import datamol as dm
```

## Core Workflows

### 1. Basic Molecule Handling
…

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