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https://github.com/MinkaiXu/GeoDiff

Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022).
https://github.com/MinkaiXu/GeoDiff

computational-biology computational-chemistry conformation diffusion-models generative-models graph-neural-networks iclr iclr2022 molecule score-matching

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Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022).

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# GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation



[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://github.com/MinkaiXu/GeoDiff/blob/main/LICENSE)



[[OpenReview](https://openreview.net/forum?id=PzcvxEMzvQC)] [[arXiv](https://arxiv.org/abs/2203.02923)] [[Code](https://github.com/MinkaiXu/GeoDiff)]



The official implementation of GeoDiff: A Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022 **Oral Presentation [54/3391]**).



![cover](assets/geodiff_framework.png)



## Environments



### Install via Conda (Recommended)



```bash

# Clone the environment

conda env create -f env.yml

# Activate the environment

conda activate geodiff

# Install PyG

conda install pytorch-geometric=1.7.2=py37_torch_1.8.0_cu102 -c rusty1s -c conda-forge

```



## Dataset



### Offical Dataset

The offical raw GEOM dataset is avaiable [[here]](https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/JNGTDF).



### Preprocessed dataset

We provide the preprocessed datasets (GEOM) in this [[google drive folder]](https://drive.google.com/drive/folders/1b0kNBtck9VNrLRZxg6mckyVUpJA5rBHh?usp=sharing). After downleading the dataset, it should be put into the folder path as specified in the `dataset` variable of config files `./configs/*.yml`.



### Prepare your own GEOM dataset from scratch (optional)



You can also download origianl GEOM full dataset and prepare your own data split. A guide is available at previous work ConfGF's [[github page]](https://github.com/DeepGraphLearning/ConfGF#prepare-your-own-geom-dataset-from-scratch-optional).



## Training



All hyper-parameters and training details are provided in config files (`./configs/*.yml`), and free feel to tune these parameters.



You can train the model with the following commands:



```bash

# Default settings

python train.py ./config/qm9_default.yml

python train.py ./config/drugs_default.yml

# An ablation setting with fewer timesteps, as described in Appendix D.2.

python train.py ./config/drugs_1k_default.yml

```



The model checkpoints, configuration yaml file as well as training log will be saved into a directory specified by `--logdir` in `train.py`.



## Generation



We provide the checkpoints of two trained models, i.e., `qm9_default` and `drugs_default` in the [[google drive folder]](https://drive.google.com/drive/folders/1b0kNBtck9VNrLRZxg6mckyVUpJA5rBHh?usp=sharing). Note that, please put the checkpoints `*.pt` into paths like `${log}/${model}/checkpoints/`, and also put corresponding configuration file `*.yml` into the upper level directory `${log}/${model}/`.



Attention: if you want to use pretrained models, please use the code at the [`pretrain`](https://github.com/MinkaiXu/GeoDiff/tree/pretrain) branch, which is the vanilla codebase for reproducing the results with our pretrained models. We recently notice some issue of the codebase and update it, making the `main` branch not compatible well with the previous checkpoints.



You can generate conformations for entire or part of test sets by:



```bash

python test.py ${log}/${model}/checkpoints/${iter}.pt \

    --start_idx 800 --end_idx 1000

```

Here `start_idx` and `end_idx` indicate the range of the test set that we want to use. All hyper-parameters related to sampling can be set in `test.py` files. Specifically, for testing qm9 model, you could add the additional arg `--w_global 0.3`, which empirically shows slightly better results.



Conformations of some drug-like molecules generated by GeoDiff are provided below.





   




## Evaluation



After generating conformations following the obove commands, the results of all benchmark tasks can be calculated based on the generated data.



### Task 1. Conformation Generation



The `COV` and `MAT` scores on the GEOM datasets can be calculated using the following commands:



```bash

python eval_covmat.py ${log}/${model}/${sample}/sample_all.pkl

```



### Task 2. Property Prediction



For the property prediction, we use a small split of qm9 different from the `Conformation Generation` task. This split is also provided in the [[google drive folder]](https://drive.google.com/drive/folders/1b0kNBtck9VNrLRZxg6mckyVUpJA5rBHh?usp=sharing). Generating conformations and evaluate `mean  absolute errors (MAR)` metric on this split can be done by the following commands:



```bash

python ${log}/${model}/checkpoints/${iter}.pt --num_confs 50 \

      --start_idx 0 --test_set data/GEOM/QM9/qm9_property.pkl

python eval_prop.py --generated ${log}/${model}/${sample}/sample_all.pkl

```



## Visualizing molecules with PyMol



Here we also provide a guideline for visualizing molecules with PyMol. The guideline is borrowed from previous work ConfGF's [[github page]](https://github.com/DeepGraphLearning/ConfGF#prepare-your-own-geom-dataset-from-scratch-optional).



### Start Setup



1. `pymol -R`

2. `Display - Background - White`

3. `Display - Color Space - CMYK`

4. `Display - Quality - Maximal Quality`

5. `Display Grid`

   1. by object:  use `set grid_slot, int, mol_name` to put the molecule into the corresponding slot

   2. by state: align all conformations in a single slot

   3. by object-state: align all conformations and put them in separate slots. (`grid_slot` dont work!)

6. `Setting - Line and Sticks - Ball and Stick on - Ball and Stick ratio: 1.5`

7. `Setting - Line and Sticks - Stick radius: 0.2 - Stick Hydrogen Scale: 1.0`



### Show Molecule



1. To show molecules



   1. `hide everything`

   2. `show sticks`



2. To align molecules: `align name1, name2`



3. Convert RDKit mol to Pymol



   ```python

   from rdkit.Chem import PyMol

   v= PyMol.MolViewer()

   rdmol = Chem.MolFromSmiles('C')

   v.ShowMol(rdmol, name='mol')

   v.SaveFile('mol.pkl')

   ```



## Citation

Please consider citing the our paper if you find it helpful. Thank you!

```

@inproceedings{

xu2022geodiff,

title={GeoDiff: A Geometric Diffusion Model for Molecular Conformation Generation},

author={Minkai Xu and Lantao Yu and Yang Song and Chence Shi and Stefano Ermon and Jian Tang},

booktitle={International Conference on Learning Representations},

year={2022},

url={https://openreview.net/forum?id=PzcvxEMzvQC}

}

```



## Acknowledgement



This repo is built upon the previous work ConfGF's [[codebase]](https://github.com/DeepGraphLearning/ConfGF#prepare-your-own-geom-dataset-from-scratch-optional). Thanks Chence and Shitong!



## Contact



If you have any question, please contact me at [email protected] or [email protected].



## Known issues



1. The current codebase is not compatible with more recent torch-geometric versions.

2. The current processed dataset (with PyD data object) is not compatible with more recent torch-geometric versions.