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https://github.com/josiehong/3dmolms
[Bioinformatics] 3DMolMS: prediction of tandem mass spectra from 3D molecular conformations
https://github.com/josiehong/3dmolms
mass-spectrometry molecule
Last synced: 27 days ago
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[Bioinformatics] 3DMolMS: prediction of tandem mass spectra from 3D molecular conformations
- Host: GitHub
- URL: https://github.com/josiehong/3dmolms
- Owner: JosieHong
- License: other
- Created: 2022-03-03T21:14:29.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-03-10T23:04:24.000Z (8 months ago)
- Last Synced: 2024-04-14T06:21:16.237Z (7 months ago)
- Topics: mass-spectrometry, molecule
- Language: Python
- Homepage:
- Size: 116 MB
- Stars: 10
- Watchers: 6
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGE_LOG.md
- License: LICENSE
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README
# 3DMolMS
[![CC BY-NC-SA 4.0][cc-by-nc-sa-shield]][cc-by-nc-sa] (free for academic use)
**3D** **Mol**ecular Network for **M**ass **S**pectra Prediction (3DMolMS) is a deep neural network model to predict the MS/MS spectra of compounds from their 3D conformations. This model's molecular representation, learned through MS/MS prediction tasks, can be further applied to enhance performance in other molecular-related tasks, such as predicting retention times (RT) and collision cross sections (CCS).
[Read our paper in Bioinformatics](https://academic.oup.com/bioinformatics/article/39/6/btad354/7186501) | [Try our online service at GNPS](https://spectrumprediction.gnps2.org) | [Install from PyPI](https://pypi.org/project/molnetpack/)
🆕 3DMolMS v1.1.10 is now available both on PyPI and GNPS2!
The changes log can be found at [[CHANGE_LOG.md]](./CHANGE_LOG.md).
## Installation
3DMolMS is available on PyPI (`molnetpack`). You can install the latest version using `pip`:
```bash
pip install molnetpack
# PyTorch must be installed separately.
# Please check the official website of PyTorch for the proper version:
# https://pytorch.org/get-started/locally/
# e.g.
pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu124
```
3DMolMS can also be installed through source codes:
```bash
git clone https://github.com/JosieHong/3DMolMS.git
cd 3DMolMS
pip install .
```
## Usage
To get started quickly, you can instantiate a MolNet and load a CSV or MGF file for MS/MS prediction as:
```python
import torch
from molnetpack import MolNet, plot_msms
# Set the device to CPU for CPU-only usage:
device = torch.device("cpu")
# For GPU usage, set the device as follows (replace '0' with your desired GPU index):
# gpu_index = 0
# device = torch.device(f"cuda:{gpu_index}")
# Instantiate a MolNet object
molnet_engine = MolNet(device, seed=42) # The random seed can be any integer.
# Load input data (here we use a CSV file as an example)
molnet_engine.load_data(path_to_test_data='./test/input_msms.csv')
"""Load data from the specified path.
Args:
path_to_test_data (str): Path to the test data file. Supported formats are 'csv', 'mgf', and 'pkl'.
Returns:
None
"""
# Predict MS/MS
pred_spectra_df = molnet_engine.pred_msms(instrument='qtof')
"""Predict MS/MS spectra.
Args:
path_to_results (Optional[str]): Path to save the prediction results. Supports '.mgf' or '.csv' formats. If None, the results won't be saved.
path_to_checkpoint (Optional[str]): Path to the model checkpoint. If None, the model will be downloaded from a default URL.
instrument (str): Type of instrument used ('qtof' or 'orbitrap').
Returns:
pd.DataFrame: DataFrame containing the predicted MS/MS results.
"""
```
We also implement a function to plot the predicted results.
```python
# Plot the predicted MS/MS with 3D molecular conformation
plot_msms(pred_spectra_df, dir_to_img='./img/')
```
The sample input files, a CSV and an MGF, are located at `./test/demo_input.csv` and `./test/demo_input.mgf`, respectively. It's important to note that during the data loading phase, any input formats that are not supported will be automatically excluded. Below is a table outlining the types of input data that are supported:
| Item | Supported input |
|------------------|---------------------------------------------------------------|
| Atom number | <=300 |
| Atom types | 'C', 'O', 'N', 'H', 'P', 'S', 'F', 'Cl', 'B', 'Br', 'I', 'Na' |
| Precursor types | '[M+H]+', '[M-H]-', '[M+H-H2O]+', '[M+Na]+', '[M+2H]2+' |
| Collision energy | any number |
Below is an example of a predicted MS/MS spectrum plot.
A more detailed documentation for various tasks using molnetpack or source code can be found in the [docs/](docs/) directory, which includes the following:
* [./docs/](./docs/)
* [PROP_USAGE.md](./docs/PROP_USAGE.md): Guide on using `molnetpack` for RT prediction, CCS prediction, and molecular embedding.
* [MSMS_PRED.md](./docs/MSMS_PRED.md): Instructions for using 3DMolMS to predict MS/MS spectra from your own CSV files via the source code. The training details can be found in the [next section](#train-your-own-model).
* [GEN_REFER_LIB.md](./docs/GEN_REFER_LIB.md): Instructions for using 3DMolMS to generate MS/MS reference libraries from small molecule databases, such as HMDB and RefMet, via the source code.
* [PROP_PRED.md](./docs/PROP_PRED.md): Instructions for training and testing 3DMolMS on RT and CCS prediction via the source code.
* [PRETRAIN.md](./docs/PRETRAIN.md): Instructions for pretraining 3DMolMS on the QM9 dataset via the source code.
## Train your own model
**Step 0**: Clone the Repository and Set Up the Environment
Clone the 3DMolMS repository and install the required packages using the following commands:
```bash
git clone https://github.com/JosieHong/3DMolMS.git
cd 3DMolMS
# Please install the packages if you have not installed them yet.
pip install .
```
**Step 1**: Obtain the Pretrained Model
Download the pretrained model (`molnet_pre_etkdgv3.pt.zip`) from [Releases](https://github.com/JosieHong/3DMolMS/releases). You can also train the model from scratch. For details on pretraining the model on the [QM9](https://figshare.com/collections/Quantum_chemistry_structures_and_properties_of_134_kilo_molecules/978904) dataset, refer to [PRETRAIN.md](docs/PRETRAIN.md).
**Step 2**: Prepare the Datasets
Download and organize the datasets into the `./data/` directory. The current version uses four datasets:
1. Agilent DPCL, provided by [Agilent Technologies](https://www.agilent.com/).
2. [NIST20](https://www.nist.gov/programs-projects/nist23-updates-nist-tandem-and-electron-ionization-spectral-libraries), available under license for academic use.
3. [MoNA](https://mona.fiehnlab.ucdavis.edu/downloads), publicly available.
4. Waters QTOF, our own experimental dataset.
The data directory structure should look like this:
```plaintext
|- data
|- origin
|- Agilent_Combined.sdf
|- Agilent_Metlin.sdf
|- hr_msms_nist.SDF
|- MoNA-export-All_LC-MS-MS_QTOF.sdf
|- MoNA-export-All_LC-MS-MS_Orbitrap.sdf
|- waters_qtof.mgf
```
**Step 3**: Preprocess the Datasets
Run the following commands to preprocess the datasets. Specify the dataset with `--dataset` and select the instrument type as `qtof`. Use `--maxmin_pick` to apply the MaxMin algorithm for selecting training molecules; otherwise, selection will be random. The dataset configurations are in `./src/molnetpack/config/preprocess_etkdgv3.yml`.
```bash
python ./src/preprocess.py --dataset agilent nist mona waters gnps \
--instrument_type qtof orbitrap \
--data_config_path ./src/molnetpack/config/preprocess_etkdgv3.yml \
--mgf_dir ./data/mgf_debug/
```
**Step 4**: Train the Model
Use the following commands to train the model. Configuration settings for the model and training process are located in `./src/molnetpack/config/molnet.yml`.
```bash
# Train the model from pretrain:
# Q-TOF (Orbitrap is ignored here.):
python ./src/train.py --train_data ./data/qtof_etkdgv3_train.pkl \
--test_data ./data/qtof_etkdgv3_test.pkl \
--model_config_path ./src/molnetpack/config/molnet.yml \
--data_config_path ./src/molnetpack/config/preprocess_etkdgv3.yml \
--checkpoint_path ./check_point/molnet_qtof_etkdgv3.pt \
--transfer --resume_path ./check_point/molnet_pre_etkdgv3.pt \
--ex_model_path ./check_point/molnet_qtof_etkdgv3_jit.pt
# Train the model from scratch
# Q-TOF:
python ./src/train.py --train_data ./data/qtof_etkdgv3_train.pkl \
--test_data ./data/qtof_etkdgv3_test.pkl \
--model_config_path ./src/molnetpack/config/molnet.yml \
--data_config_path ./src/molnetpack/config/preprocess_etkdgv3.yml \
--checkpoint_path ./check_point/molnet_qtof_etkdgv3.pt \
--ex_model_path ./check_point/molnet_qtof_etkdgv3_jit.pt
# Orbitrap:
python ./src/train.py --train_data ./data/orbitrap_etkdgv3_train.pkl \
--test_data ./data/orbitrap_etkdgv3_test.pkl \
--model_config_path ./src/molnetpack/config/molnet.yml \
--data_config_path ./src/molnetpack/config/preprocess_etkdgv3.yml \
--checkpoint_path ./check_point/molnet_orbitrap_etkdgv3.pt \
--ex_model_path ./check_point/molnet_orbitrap_etkdgv3_jit.pt
```
**Step 5**: Evaluation
Let's evaluate the model trained above!
```bash
# Predict the spectra:
# Q-TOF:
python ./src/pred.py \
--test_data ./data/qtof_etkdgv3_test.pkl \
--model_config_path ./src/molnetpack/config/molnet.yml \
--data_config_path ./src/molnetpack/config/preprocess_etkdgv3.yml \
--resume_path ./check_point/molnet_qtof_etkdgv3.pt \
--result_path ./result/pred_qtof_etkdgv3_test.mgf
# Orbitrap:
python ./src/pred.py \
--test_data ./data/orbitrap_etkdgv3_test.pkl \
--model_config_path ./src/molnetpack/config/molnet.yml \
--data_config_path ./src/molnetpack/config/preprocess_etkdgv3.yml \
--resume_path ./check_point/molnet_orbitrap_etkdgv3.pt \
--result_path ./result/pred_orbitrap_etkdgv3_test.mgf
# Evaluate the cosine similarity between experimental spectra and predicted spectra:
# Q-TOF:
python ./src/eval.py ./data/qtof_etkdgv3_test.pkl ./result/pred_qtof_etkdgv3_test.mgf \
./eval_qtof_etkdgv3_test.csv ./eval_qtof_etkdgv3_test.png
# Orbitrap:
python ./src/eval.py ./data/orbitrap_etkdgv3_test.pkl ./result/pred_orbitrap_etkdgv3_test.mgf \
./eval_orbitrap_etkdgv3_test.csv ./eval_orbitrap_etkdgv3_test.png
```
**Additional application**
3DMolMS is also capable of predicting molecular properties and generating reference libraries for molecular identification. For more details, refer to [PROP_PRED.md](docs/PROP_PRED.md) and [GEN_REFER_LIB.md](docs/GEN_REFER_LIB.md) respectively.
## Citation
```
@article{hong20233dmolms,
title={3DMolMS: prediction of tandem mass spectra from 3D molecular conformations},
author={Hong, Yuhui and Li, Sujun and Welch, Christopher J and Tichy, Shane and Ye, Yuzhen and Tang, Haixu},
journal={Bioinformatics},
volume={39},
number={6},
pages={btad354},
year={2023},
publisher={Oxford University Press}
}
@article{hong2024enhanced,
title={Enhanced structure-based prediction of chiral stationary phases for chromatographic enantioseparation from 3D molecular conformations},
author={Hong, Yuhui and Welch, Christopher J and Piras, Patrick and Tang, Haixu},
journal={Analytical Chemistry},
volume={96},
number={6},
pages={2351--2359},
year={2024},
publisher={ACS Publications}
}
```
## License
This work is licensed under a
[Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License][cc-by-nc-sa].
[![CC BY-NC-SA 4.0][cc-by-nc-sa-image]][cc-by-nc-sa]
[cc-by-nc-sa]: http://creativecommons.org/licenses/by-nc-sa/4.0/
[cc-by-nc-sa-image]: https://licensebuttons.net/l/by-nc-sa/4.0/88x31.png
[cc-by-nc-sa-shield]: https://img.shields.io/badge/License-CC%20BY--NC--SA%204.0-lightgrey.svg