unimol v1.0A

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---
name: unimol
description: >
  A standardized CLI wrapper for Uni-Mol molecular ML workflows that handles representation extraction (embeddings), model training (regression/classification), and property prediction with built-in RDKit SMILES validation.
  USE WHEN you need to generate molecular embeddings, train machine learning models for chemical properties, or run predictions on SMILES datasets (.csv/.smi) using the Uni-Mol framework.
compatibility: Requires uv. Dependencies (unimol-tools, rdkit, etc.) are handled automatically via inline script metadata in unimol_helper.py.
metadata:
  author: luzitian
  version: '1.0'
  repository: https://github.com/deepmodeling/Uni-Mol
---

# Uni-Mol

This skill provides practical command patterns for **Uni-Mol molecular representation / training / prediction** using the standardized CLI wrapper: `<skill_path>/scripts/unimol_helper.py`.

Key behaviors (important for Agents):

- The script prints **environment detection** (Python/Torch/CUDA) by default.
- Bad/illegal SMILES are **skipped and logged** to `*.skipped.csv` (no crash).
- Each run ends by printing **absolute output paths** like:
  - `[RESULT] repr_npy=/abs/path.npy`
  - `[RESULT] model_dir=/abs/model_dir`
  - `[RESULT] pred_csv=/abs/pred.csv`

## Quick Start

Check CLI help:

```bash
uv run python <skill_path>/scripts/unimol_helper.py --help
```

Check subcommand help:

```bash
uv run python <skill_path>/scripts/unimol_helper.py repr --help
uv run python <skill_path>/scripts/unimol_helper.py train --help
uv run python <skill_path>/scripts/unimol_helper.py predict --help
```

Disable environment printing (optional):

```bash
uv run python <skill_path>/scripts/unimol_helper.py --no-env repr --smiles "CCO" --output out.npy
```

## Core Tasks

### 1) Extract molecular representations (embedding) to .npy

Single SMILES:

```bash
uv run python <skill_path>/scripts/unimol_helper.py repr \
    --smiles "CCO" \
    --output /tmp/ccO.repr.npy
```

From CSV (default SMILES column is `smiles`):

```bash
uv run python <skill_path>/scripts/unimol_helper.py repr \
    --file data.csv \
    --smiles-col smiles \
    --output data.repr.npy
```

From SMI:

```bash
uv run python <skill_path>/scripts/unimol_helper.py repr \
    --file molecules.smi \
    --output molecules.repr.npy
```

Force CPU / GPU:

```bash
# Force CPU
uv run python <skill_path>/scripts/unimol_helper.py repr --smiles "CCO" --no-gpu --output out.npy

# Force GPU (will warn & fall back if CUDA is unavailable)
uv run python <skill_path>/scripts/unimol_helper.py repr --smiles "CCO" --use-gpu --output out.npy
```

### 2) Train a property model (classification / regression / multilabel\_\*)

Regression training (CSV must contain `smiles` and `target` columns):

```bash
uv run python <skill_path>/scripts/unimol_helper.py train \
    --task regression \
    --input train.csv \
    --smiles-col smiles \
    --target-col target \
    --epochs 50 \
    --output ./model_reg
```

Classification training:

```bash
uv run python <skill_path>/scripts/unimol_helper.py train \
    --task classification \
    --input train.csv \
    --smiles-col smiles \
    --target-col target \
    --epochs 50 \
    --output ./model_cls
```

Multilabel regression training (explicit multi-target columns):

```bash
uv run python <skill_path>/scripts/unimol_helper.py train \
    --task multilabel_regression \
    --input train.csv \
    --smiles-col smiles \
    --target-cols target_0,target_1,target_2 \
    --epochs 50 \
    --output ./model_mreg
```

Multilabel classification training:

```bash
uv run python <skill_path>/scripts/unimol_helper.py train \
    --task multilabel_classification \
    --input train.csv \
    --smiles-col smiles \
    --target-cols y_cls_0,y_cls_1,y_cls_2 \
    --epochs 50 \
    --output ./model_mcls
```

Target recognition for training:

- Single-task (`classification` / `regression`): use `--target-col` (default `target`).
- Multilabel tasks: prefer `--target-cols` (comma-separated).
- If `--target-cols` is omitted for multilabel tasks, the helper auto-detects columns named `target` or prefixed with `target_` (case-insensitive).

Force CPU:

```bash
uv run python <skill_path>/scripts/unimol_helper.py train \
    --task regression \
    --input train.csv \
    --epochs 50 \
    --output ./model_cpu \
    --no-cuda
```

### 3) Predict properties to .csv

Predict from CSV:

```bash
uv run python <skill_path>/scripts/unimol_helper.py predict \
    --model ./model_reg \
    --input test.csv \
    --smiles-col smiles \
    --output pred.csv
```

Predict from SMI:

```bash
uv run python <skill_path>/scripts/unimol_helper.py predict \
    --model ./model_reg \
    --input test.smi \
    --output pred.csv
```

Notes:

- Output CSV contains the input rows (for valid SMILES) plus `pred` / `pred_*` columns.
- If there are bad SMILES, they are skipped and saved to `pred.csv.skipped.csv` (or your `--error-log` path).

## Agent Checklist

When using this skill for users:

1. Confirm input format:
   - `.csv` requires a SMILES column (default `smiles`)
   - `.smi` uses the first token of each line as SMILES
1. Quote SMILES containing special characters (brackets/parentheses):
   - Example: `--smiles "[C]([H])([H])[H]"`
1. For CSV workflows, verify column names:
   - `repr`: `--smiles-col`
   - `train`: `--smiles-col` and `--target-col` / `--target-cols`
   - `predict`: `--smiles-col`
1. Watch for skipped SMILES:
   - Check `*.skipped.csv` and decide whether to fix or permanently drop them
1. Always capture absolute output paths:
   - Look for `[RESULT] ...=/abs/path` in stdout
1. If debugging is needed, enable full traceback:
   - `UNIMOL_HELPER_TRACE=1 uv run python <skill_path>/scripts/unimol_helper.py ...`

## References

- Uni-Mol project: https://github.com/fanxiaoyu0/Uni-Mol
- RDKit: https://www.rdkit.org/