A Multi-Resolution 3D-DenseNet for Chemical Shift Prediction in NMR Crystallography

Shuai Liu, Jie Li, Kochise C. Bennett, Brad Ganoe, Tim Stauch, Martin Head-Gordon, Alexander Hexemer, Daniela Ushizima and Teresa Head-Gordon(2019) Multiresolution 3D-DenseNet for Chemical Shift Prediction in NMR Crystallography. J. Phys. Chem. Lett. 10, 4558−4565. DOI: 10.1021/acs.jpclett.9b01570.

Dependences: requests, pytorch, tensorflow, keras

Currently we only have scripts for data preprocessing, train and test the model. We will add more interfaces to .xyz files later.

We will upload the trained model and easy-to-use interface to predict the chemical shift given xyz file (under construction).

Data Preprocessing

Under preprocessing directory cd preprocessing Please run the current script sequencially. We do not support the argparse yet (under construction).

Step 1: Download the data

Download .txt files from the data attached to original paper:

training dataset: https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-018-06972-x/MediaObjects/41467_2018_6972_MOESM3_ESM.txt

testing dataset: https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-018-06972-x/MediaObjects/41467_2018_6972_MOESM4_ESM.txt

Credit: Paruzzo F M, Hofstetter A, Musil F, et al. Chemical shifts in molecular solids by machine learning. Nature communications, 2018, 9(1): 4501.

Then the data are transformed to .xyz files into different folders

python get_data.py

Step 2: Transform the xyz files into json files

Transform the .xyz files to .json files with k nearest atoms into destination folder

python xyz_to_json.py

Step 3: Transform json files into numpy files

The xyz values, atom type and chemical shielding values are transfomed into into:

prefix_xyz.npy, prefix_points.npy and prefix_y.npy

python json_to_numpy.py

Step 4: Data augmentation

Augment xyz files with 8 fold

python data_aug.py

Step 5: Density generation

Generate the density given xyz and one-hot atom type vector numpy files

python density_gen.py

Note: for the densities other than Gaussian, we simply copy our raw script into the current script without further testing.

Models

We provide the following models in model directory:

1. MR-3D-DenseNet
2. Two baseline DenseNets
3. Regular CNN and ResNet with same number of 3x3x3 filters

Note: same as other densities, we only tested 1). 2) and 3) are not extensively tested in the current script.

Training and Testing script

We also provide the trainin gand testing script examples.

Under the default setting, please run following command sequentially:

python train.py

python test.py

IMPORTANT: these two only provide examples for oxygen. For other atom types, the file names and scale need to be changed. Also, for hydrogen, there is a filtering process to filter out the chemical shieldings < 0 or > 40 in the training dataset. All the other dataset are not filtered.

Tips: In the current setting, the atom type order is H, C, O, N and the grid size order (center to face distance): 2A, 4A, 3A, 5A, 7A. This indexing was due to that we were using 3A, 5A, 7A as a subset for ablation study. This order makes the indexing more easily. However, one can easily change the order in preprocessing/json_to_numpy.py and train/test.py, respectively.