learningmatter-mit

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chem-react-ot

Generate transition state structures for chemical reactions using React-OT.

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Harga belum dikonfirmasi★ 161 Star GitHubDirektori diperbarui · 6 Sep 2026agent-skill

Ringkasan

Generate transition state structures for chemical reactions using React-OT.

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Dokumentasi sumber, bukan instruksi untuk situs ini. Periksa izin sebelum menjalankan perintah.

chem-react-ot — React-OT Transition State Generation

Goal

Generate transition state (TS) structures given reactant and product structures using the React-OT model (Optimal Transport). React-OT is a generative model that predicts TS geometries directly without requiring an initial guess path (like NEB).

Category: chemistry Environment: react-ot-agent

Key Features

  • Generative TS Prediction: Predicts 3D transition state structures from 3D reactants and products.
  • Fast Inference: Uses an ODE solver for generation, typically much faster than DFT-based NEB.
  • No Path Guess Required: Directly generates the TS structure.

Usage

1. Environment Setup

This skill requires the react-ot-agent conda environment. Ensure it is installed:

# Env: react-ot-agent
cd conda-envs/react-ot-agent
bash install.sh
2. Download Models

Before running the skill for the first time, download the pre-trained model weights:

# activate react-ot-agent first
conda activate react-ot-agent
python conda-envs/react-ot-agent/download_models.py

The checkpoint is saved to ~/.cache/react-ot/checkpoints/sb-pretrained.ckpt.

3. Generate Transition State

Run the generation script with reactant and product files (xyz, cif, pdb, etc. - anything ASE reads).

# Env: react-ot-agent
python .agents/skills/chem-react-ot/scripts/generate_ts.py \
    --reactants reactant.xyz \
    --products product.xyz \
    --output_dir results/ts_search

Arguments:

  • --reactants: Path to reactant structure file(s). Can be a single file with multiple molecules or a list of files.
  • --products: Path to product structure file(s).
  • --output_dir: Directory to save the generated TS structure (ts_generated.xyz) and trajectory (generation_traj.xyz).
  • --nfe: Number of function evaluations for the ODE solver (default: 10). Higher values might be more accurate but slower.
  • --checkpoint: Path to custom model checkpoint (optional, defaults to downloaded one).

Example

# Env: react-ot-agent
python .agents/skills/chem-react-ot/scripts/generate_ts.py \
    --reactants .agents/skills/chem-react-ot/examples/oxadiazole_isomerization/reactant.xyz \
    --products .agents/skills/chem-react-ot/examples/oxadiazole_isomerization/product.xyz \
    --output_dir .agents/skills/chem-react-ot/examples/oxadiazole_isomerization/output

Constraints

  • Environment: All scripts require the react-ot-agent conda environment.
  • Input Format: Reactant and product structures must be in any format readable by ASE (XYZ, CIF, PDB, etc.).
  • Atom Ordering: Reactant and product structures must have the same number of atoms with consistent atom ordering.
  • Model Checkpoint: The pre-trained checkpoint must be downloaded before first use (see step 2).

References

  • React-OT GitHub
  • Duan, C., Liu, G.-H., Du, Y. et al., "Optimal transport for generating transition states in chemical reactions", Nature Machine Intelligence, 2025. DOI

Author: Bowen Deng Contact: GitHub @learningmatter-mit

Metadata berkas
name: chem-react-ot
description: Generate transition state structures for chemical reactions using React-OT.
category: [chemistry]
Lihat teks asli
---
name: chem-react-ot
description: Generate transition state structures for chemical reactions using React-OT.
category: [chemistry]
---

# `chem-react-ot` — React-OT Transition State Generation

## Goal

Generate transition state (TS) structures given reactant and product structures using the React-OT model (Optimal Transport). React-OT is a generative model that predicts TS geometries directly without requiring an initial guess path (like NEB).

**Category:** `chemistry`
**Environment:** `react-ot-agent`

## Key Features

- **Generative TS Prediction:** Predicts 3D transition state structures from 3D reactants and products.
- **Fast Inference:** Uses an ODE solver for generation, typically much faster than DFT-based NEB.
- **No Path Guess Required:** Directly generates the TS structure.

## Usage

### 1. Environment Setup

This skill requires the `react-ot-agent` conda environment. Ensure it is installed:

```bash
# Env: react-ot-agent
cd conda-envs/react-ot-agent
bash install.sh
```

### 2. Download Models

Before running the skill for the first time, download the pre-trained model weights:

```bash
# activate react-ot-agent first
conda activate react-ot-agent
python conda-envs/react-ot-agent/download_models.py
```

The checkpoint is saved to `~/.cache/react-ot/checkpoints/sb-pretrained.ckpt`.

### 3. Generate Transition State

Run the generation script with reactant and product files (xyz, cif, pdb, etc. - anything ASE reads).

```bash
# Env: react-ot-agent
python .agents/skills/chem-react-ot/scripts/generate_ts.py \
    --reactants reactant.xyz \
    --products product.xyz \
    --output_dir results/ts_search
```

**Arguments:**

- `--reactants`: Path to reactant structure file(s). Can be a single file with multiple molecules or a list of files.
- `--products`: Path to product structure file(s).
- `--output_dir`: Directory to save the generated TS structure (`ts_generated.xyz`) and trajectory (`generation_traj.xyz`).
- `--nfe`: Number of function evaluations for the ODE solver (default: 10). Higher values might be more accurate but slower.
- `--checkpoint`: Path to custom model checkpoint (optional, defaults to downloaded one).

## Example

```bash
# Env: react-ot-agent
python .agents/skills/chem-react-ot/scripts/generate_ts.py \
    --reactants .agents/skills/chem-react-ot/examples/oxadiazole_isomerization/reactant.xyz \
    --products .agents/skills/chem-react-ot/examples/oxadiazole_isomerization/product.xyz \
    --output_dir .agents/skills/chem-react-ot/examples/oxadiazole_isomerization/output
```

## Constraints

- **Environment**: All scripts require the `react-ot-agent` conda environment.
- **Input Format**: Reactant and product structures must be in any format readable by ASE (XYZ, CIF, PDB, etc.).
- **Atom Ordering**: Reactant and product structures must have the same number of atoms with consistent atom ordering.
- **Model Checkpoint**: The pre-trained checkpoint must be downloaded before first use (see step 2).

## References

- [React-OT GitHub](https://github.com/deepprinciple/react-ot)
- Duan, C., Liu, G.-H., Du, Y. et al., "Optimal transport for generating transition states in chemical reactions", *Nature Machine Intelligence*, 2025. [DOI](https://doi.org/10.1038/s42256-025-01010-0)

---

**Author:** Bowen Deng
**Contact:** [GitHub @learningmatter-mit](https://github.com/learningmatter-mit)

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Lisensi: MIT

  • Dependency or permission surface needs review
  • Permission surface may require sandboxing
  • The script's handling of multiple reactant/product files is not fully documented; the example only shows single files, while the description mentions support for lists.
  • The model weight download step relies on an external URL without explicit checksum verification, which could be a supply chain risk if the source is compromised.
  • Quality score needs review
  • Permission surface needs review: secrets or environment access, shell or command execution
  • Stars/forks activity: 161 stars, 24 forks; issue activity unavailable in current metadata
  • Dependency/runtime risk: command execution surface, credential or environment access
  • Permission surface: secrets or environment access, shell or command execution
Buka audit lengkap

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Mulai dengan tugas kecil

  1. 1Baca sumber dan pastikan masukan, keluaran, dependensi, serta izin.
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  3. 3Periksa hasil dan berkas yang berubah. Laporkan hanya yang dijalankan dan simpan revisi sumber.

Periksa dependensi, kunci API, dan biaya layanan pihak ketiga pada sumber. Repositori publik tidak berarti semua layanan gratis.

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Repositori sumber
learningmatter-mit/AtomisticSkills
Lisensi
MIT
Versi
1.0.0
Push GitHub terakhir
3 Sep 2026
Direktori diperbarui
6 Sep 2026

Versi dilaporkan dalam metadata direktori; periksa rilis sumber.

Kualitas

66/100

Menjanjikan

Kepercayaan

56/100

Do not auto-install

Audit

73/100

Perlu ditinjau

  • Dependency or permission surface needs review
  • Permission surface may require sandboxing
  • The script's handling of multiple reactant/product files is not fully documented; the example only shows single files, while the description mentions support for lists.
  • The model weight download step relies on an external URL without explicit checksum verification, which could be a supply chain risk if the source is compromised.
  • Quality score needs review
  • Permission surface needs review: secrets or environment access, shell or command execution
  • Stars/forks activity: 161 stars, 24 forks; issue activity unavailable in current metadata
  • Dependency/runtime risk: command execution surface, credential or environment access
  • Permission surface: secrets or environment access, shell or command execution
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Detail lainnya
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}

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Tampilkan listing kanonis, sinyal kepercayaan dan audit saat ini, serta bukti Agent-Proven nyata di tempat pengembang mengevaluasi repositori.

[![Listed on OpenAgentSkill](https://www.openagentskill.com/api/badge/learningmatter-mit-chem-react-ot?metric=listed&label=Listed)](https://www.openagentskill.com/skills/learningmatter-mit-chem-react-ot?ref=github&utm_source=github&utm_medium=referral&utm_campaign=creator_badge)
[![OpenAgentSkill Trust](https://www.openagentskill.com/api/badge/learningmatter-mit-chem-react-ot?metric=trust&label=Trust)](https://www.openagentskill.com/skills/learningmatter-mit-chem-react-ot?ref=github&utm_source=github&utm_medium=referral&utm_campaign=creator_badge)
[![OpenAgentSkill Audit](https://www.openagentskill.com/api/badge/learningmatter-mit-chem-react-ot?metric=audit&label=Audit)](https://www.openagentskill.com/skills/learningmatter-mit-chem-react-ot/audit)
[![Agent Proven](https://www.openagentskill.com/api/badge/learningmatter-mit-chem-react-ot?metric=proven&label=Agent%20Proven)](https://www.openagentskill.com/skills/learningmatter-mit-chem-react-ot?ref=github&utm_source=github&utm_medium=referral&utm_campaign=creator_badge)

Sinyal komunitas

Bagikan apakah skill ini bermanfaat untuk alur kerja Agent Anda. Masukan gabungan meningkatkan peringkat dari waktu ke waktu.