MOFFlow-2

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Implementation for Flexible MOF Generation with Torsion-Aware Flow Matching

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# Flexible MOF Generation with Torsion-Aware Flow Matching (MOFFlow-2)

[![arXiv](https://img.shields.io/badge/arXiv-2410.17270-b31b1b.svg)](https://www.arxiv.org/abs/2505.17914)

## Table of Contents
- [Installation](#installation)
  - [Clone repository](#clone-repository)
  - [Setup environment](#setup-environment)
  - [Setup .env file](#setup-env-file)
- [Preprocessing Data](#preprocessing-data)
- [Training](#training)
- [Structure Prediction Evaluation](#structure-prediction-evaluation)
  - [Match rate & RMSE](#match-rate--rmse)
- [Generation](#generation)
  - [Validity, Novelty, and Uniqueness (VNU)](#validity-novelty-and-uniqueness-vnu)
  - [Property Evaluation (with zeo++)](#property-evaluation-with-zeo)
- [📚 Citation](#-citation)

## Installation

### Clone repository
```bash
git clone https://github.com/nayoung10/MOFFlow-2.git # clone repo
cd MOFFlow-2
```

### Setup environment 
```bash
mamba env create -f env.yml
mamba activate mofflow-2
pip install git+https://github.com/microsoft/MOFDiff.git
pip install -e .
```

For **property computation**, we need to install `zeo++` from [here](https://www.zeoplusplus.org/download.html).

### Create ```.env```

Create ```.env``` file with following entries. 
```bash
export PROJECT_ROOT=<root_dir>
export ZEO_PATH=<path_to_network_binary> # (Optional) for property computation
```

## Preprocessing Data

There are two options for preparing the dataset:
1. Use our preprocessed dataset.
2. Preprocess the dataset yourself: first download the `bw_db.tar.gz` dataset from [MOFDiff](https://zenodo.org/records/10806179), then run our scripts for further processing.

**Note:** If you want to build your own dataset from raw `.cif` files, start by processing them with the scripts provided in [MOFDiff]((https://github.com/microsoft/MOFDiff)), then apply our preprocessing pipeline.

### Option 1: Use Preprocessed Data
You can download preprocessed data from either source:

1. **Zenodo**: [MOFFlow-2 preprocessed release](https://zenodo.org/records/17163237)
2. **Hugging Face (dataset repo)**: [nayoung10/mofflow2-data](https://huggingface.co/datasets/nayoung10/mofflow2-data)

If you use Hugging Face, you can download with:
```bash
hf download nayoung10/mofflow2-data --repo-type dataset --local-dir .
```

After extracting files into your project `data/` directory, the structure should look as follows:
```
data/                          <- Project dataset directory
├── lmdb/                      <- Preprocessed dataset for training structure prediction module
│   ├── csp/
│   │   ├── MetalOxo_final_train.lmdb
│   │   ├── MetalOxo_final_val.lmdb
│   │   └── MetalOxo_final_test.lmdb
│   └── gen/
│       ├── MetalOxo_final_train.lmdb
│       └── MetalOxo_final_val.lmdb
│
├── metals/                    <- Metal library (template) for generation
│   └── gen/
│       └── metal_lib_train.pkl
│
├── seqs/                      <- Preprocessed dataset for training building block generator
│   ├── mof_sequence_train.json
│   ├── mof_sequence_val.json
│   └── vocab.json
│
└── splits/                    <- (Optional) Split information for processing the dataset on your own (Option 2)
    ├── csp/
    │   ├── test_split.txt
    │   ├── train_split.txt
    │   └── val_split.txt
    └── gen/
        ├── train_split.txt
        └── val_split.txt
```

### Option 2: Preprocess Data Yourself
#### Structure dataset
1. Download `bw_db.tar.gz` from [MOFDiff](https://zenodo.org/records/10806179).
2. Extract and place `MetalOxo.lmdb` in the `data/lmdb` directory.
3. Set the task (`csp` or `gen`) in `configs.yaml` under `preprocess.task`.
4. Run the automated preprocessing script:

```bash
# Run the full preprocessing pipeline automatically
# Creates raw dataset for structure prediction module (in .lmdb)
python preprocess.py
```
*Script options:*
- `--mof-matching-repeat <N>`: Number of times to repeat the MOF matching step (default: 3).
- `--run-conversion`: Run the format conversion steps (CSV/PKL) for baselines. This is disabled by default.

#### Sequence dataset
Now, create train/validation datasets for the sequence generator module with the following script. This creates `mof_sequence_train.json` and `mof_sequence_val.json` in the `data/seqs` directory. 
```bash
# Create raw dataset for MOF sequence generator (in .json)
python preprocess/extract_sequence.py
```

## Training

### Structure Prediction
Train the structure prediction module:

```bash
python -m experiments.train experiment.task=csp experiment.name=<exp_name>
```

### Generation
For the generation task, train both the building block generator and the structure prediction module.

1. **Train the MOF sequence generator**: This model learns to generate MOF sequences. The default configuration in `configs/base_seq.yaml` trains an unconditional sequence generator; you can train it to condition on CO2 working capacity by setting `model.conditional=true`. If you encounter OOM errors, reduce `data.loader.max_tokens` and/or specify `data.loader.max_batch_size`. Note: `model.max_seq_len` is a dummy, as rotary positional embedding is used.

```bash
python -m experiments.train_seq experiment.name=<exp_name> model.conditional=false # Set to true for conditional generator
```

2. **Train the structure prediction module**: This model predicts the assembled structure given ground-truth building blocks. See `configs/base.yaml` for details. Dynamic batching is used; if you encounter OOM errors, try reducing `data.loader.dynamic.max_num_atoms` and/or specify `data.loader.dynamic.max_batch_size`.

```bash
   python -m experiments.train experiment.task=gen experiment.name=<exp_name>
   ```

## Generate MOF structures

To generate MOF structures with pretrained checkpoints, you can download from either source:

1. **Zenodo**: [MOFFlow-2 preprocessed release](https://zenodo.org/records/17163237)
2. **Hugging Face (model repo)**: [nayoung10/mofflow2-ckpt](https://huggingface.co/nayoung10/mofflow2-ckpt)

If you use Hugging Face, you can download with:
```bash
hf download nayoung10/mofflow2-ckpt --repo-type model --local-dir .
```

Place the checkpoint file (`*.pt` or `*.ckpt`) and its corresponding configuration file (`config.yaml`) in the same directory. If you downloaded archive files (`*.tar.gz`) from Hugging Face, extract them first so the checkpoint and `config.yaml` are colocated. If you trained your own model, the `config.yaml` file will have been created automatically.
```
# Example directory layout for unzipped pretrained checkpoints:
logs/
├── csp/
│   └── sp_module/
│       ├── config.yaml
│       └── ckpt.pt
└── gen/
    ├── sp_module/
    │   ├── config.yaml
    │   └── ckpt.pt
    ├── seq_module_uncond/
    │   ├── config.yaml
    │   └── ckpt.pt
    └── seq_module_cond/
        ├── config.yaml
        └── ckpt.pt
```

### Structure prediction 
To generate the MOF structures for the test set, run the following code. You may specify the number of samples to generate per test sample. For more details, look into `configs/inference.yaml`.

```bash
python -m experiments.predict \
    inference.task=csp \
    inference.ckpt_path=<path/to/ckpt.pt> \ # default to null
    inference.num_samples=<num_samples> \   # default to 1
    inference.num_devices=<num_devices> \ # default to 8 
    inference.sampler.num_timesteps=<timesteps> \ # default to 50
```

### Generation

For generation, we (1) generate MOF sequences with trained MOF sequence generator (saved as `.json`), then (2) predict MOF structures with trained MOF structure prediction module.

```bash
# 1. Generate MOF sequences (check `configs/inference_seq.yaml` for details.)
python -m experiments.predict_seq \
    inference.ckpt_path=<path/to/ckpt.pt> \ # default to null
    inference.total_samples=<num_samples> # default to 10000

# 2. Predict MOF structures (check `configs/inference.yaml` for details.)
python -m experiments.predict \
    inference.task=gen \
    inference.ckpt_path=<path/to/ckpt.pt> \ # default to null
    inference.gen.metal_lib_path=<path/to/metal_lib_train.pkl> \ # for initializing metal structures 
    inference.gen.mof_seqs_path=<path/to/seq.json> \ # path to .json file generated from Step 1
    inference.num_samples=1 
```

## Evaluation

All codes relevant to evaluation are under `evaluation/` directory.

### Structure prediction

#### Match rate & RMSE 
We compute the match rate and RMSE between the predicted and ground-truth structures. To do this, run the following script:

```bash
python -m evaluation.rmsd \
    --save_pt </path/to/predictions_*.pt> \
    --num_samples <num_samples>
```

**Arguments:**
- `--save_pt`: Glob pattern for `.pt` files generated by `experiments/predict.py` (e.g., `inference/predictions_*.pt`).
- `--num_samples`: (Optional) Number of samples to evaluate per test structure. If not specified, defaults to the value used during prediction (see `configs/inference.yaml`).

### Generation

#### Validity, Novelty, and Uniqueness (VNU)

We evaluate the generated MOFs in two stages: first at the sequence level, then at the structure level. The final VNU metric combines both results.

**Step 1: Evaluate VNU for generated sequences**

```bash
python -m evaluation.valid_seq \
    --generated_json <path/to/generated/sequence.json> \
    --train_json <data/seqs/mof_sequence_train.json> \
    --bb_lib_dir <data/bb_lib>
```
- `--generated_json`: Path to the generated sequence `.json` file (from `experiments/predict_seq.py`).
- `--train_json`: Path to the training dataset `mof_sequence_train.json` file (used for novelty evaluation).
- `--bb_lib_dir`: Path to the building block library directory. If `metals.pkl` and `organics.pkl` do not exist in this directory, they will be created automatically from the training set.

**Step 2: Evaluate VNU for generated structures**

1. **Convert predicted structures to CIF format:**
   ```bash
   python io/pt_to_cif.py \
       --save_pt </path/to/predictions_*.pt>
   ```
   - `--save_pt`: Glob pattern for `.pt` files from `experiments/predict.py`.

2. **Evaluate VNU for structures:**
   ```bash
   python -m evaluation.valid \
       --cif_path <path/to/cif/files/*.cif> \
       --csv_path <path/to/sequence/vnu/results.csv>
   ```
   - `--cif_path`: Glob pattern for CIF files generated in the previous step (Step 2-1).
   - `--csv_path`: Path to the VNU evaluation result (CSV) from Step 1.

---

#### Property Evaluation (with `zeo++`)

To compute properties of the generated structures using `zeo++`, run:

```bash
python -m evaluation.property \
    --cif_dir <path/to/cif/dir> \
    --num_cpus <num_cpus>
```
- `--cif_dir`: Directory containing the generated CIF files.
- `--num_cpus`: Number of CPUs to use for parallel computation.

## 📚 Citation

If you find our work useful, please consider citing the following:

```bibtex
@article{kim2025flexible,
  title={Flexible MOF Generation with Torsion-Aware Flow Matching},
  author={Kim, Nayoung and Kim, Seongsu and Ahn, Sungsoo},
  journal={arXiv preprint arXiv:2505.17914},
  year={2025}
}
```

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