Using pretrained GROVER to extract the atomic fingerprints from molecule

Overview

Extract atomic fingerprints from molecules using pretrained GROVER

Using pretrained GROVER to extract the atomic fingerprints from molecule. The fingerprints can be used for further tasks.

GROVER is short for Graph Representation frOm self-superVised mEssage passing tRansformer which is a Transformer-based self-supervised message-passing neural network by Rong and colleagues as in the paper: Self-Supervised Graph Transformer on Large-Scale Molecular Data.

Install requirements

  1. Create and activate a conda environment:
conda create --name grover python=3.6.8
conda activate grover
  1. Install requirements from requirements.txt file. Additionally, install torchinfo:
conda install -c conda-forge -c pytorch -c acellera -c RMG --file=requirements.txt
pip install torchinfo

Download the pretrained models

There are two pretrained models provided by the original authors. Download, extract and save the .pt file in models_pretrained/.

Inference figerprints

Run the main.py file:

python main.py

Details about the arguments can be viewed in the setup_parser() function found in the main.py, or by running:

python main.py -h

If no arguments are specified, then the default arguments will be used.

By default, the outputs are saved in extracted_fingerprint. The outputs include 3 files:

  • atom_fp.npy: contains the atomic fingerprints.
  • distance.npy: contains the pair-wise shortest relative distance matrices between nodes of the molecular graphs.
  • smiles.txt: contains the SMILES strings of the molecules.

In order to read the .npy files, please refer to this part in the numpy.save documentation

Owner
Xuan Vu Nguyen
Chemistry graduate at Vietnam-France University | Machine learning practicer.
Xuan Vu Nguyen
[NeurIPS 2021] Code for Unsupervised Learning of Compositional Energy Concepts

Unsupervised Learning of Compositional Energy Concepts This is the pytorch code for the paper Unsupervised Learning of Compositional Energy Concepts.

45 Nov 30, 2022
ADB-IP-ROTATION - Use your mobile phone to gain a temporary IP address using ADB and data tethering

ADB IP ROTATE This an Python script based on Android Debug Bridge (adb) shell sc

Dor Bismuth 2 Jul 12, 2022
Oscar and VinVL

Oscar: Object-Semantics Aligned Pre-training for Vision-and-Language Tasks VinVL: Revisiting Visual Representations in Vision-Language Models Updates

Microsoft 938 Dec 26, 2022
Full-featured Decision Trees and Random Forests learner.

CID3 This is a full-featured Decision Trees and Random Forests learner. It can save trees or forests to disk for later use. It is possible to query tr

Alejandro Penate-Diaz 3 Aug 15, 2022
A pure PyTorch batched computation implementation of "CIF: Continuous Integrate-and-Fire for End-to-End Speech Recognition"

A pure PyTorch batched computation implementation of "CIF: Continuous Integrate-and-Fire for End-to-End Speech Recognition"

張致強 14 Dec 02, 2022
The code for 'Deep Residual Fourier Transformation for Single Image Deblurring'

Deep Residual Fourier Transformation for Single Image Deblurring Xintian Mao, Yiming Liu, Wei Shen, Qingli Li and Yan Wang News 2021.12.5 Release Deep

145 Jan 05, 2023
Pytorch and Torch testing code of CartoonGAN

CartoonGAN-Test-Pytorch-Torch Pytorch and Torch testing code of CartoonGAN [Chen et al., CVPR18]. With the released pretrained models by the authors,

Yijun Li 642 Dec 27, 2022
Kaggle | 9th place (part of) solution for the Bristol-Myers Squibb – Molecular Translation challenge

Part of the 9th place solution for the Bristol-Myers Squibb – Molecular Translation challenge translating images containing chemical structures into I

Erdene-Ochir Tuguldur 22 Nov 30, 2022
Project page for End-to-end Recovery of Human Shape and Pose

End-to-end Recovery of Human Shape and Pose Angjoo Kanazawa, Michael J. Black, David W. Jacobs, Jitendra Malik CVPR 2018 Project Page Requirements Pyt

1.4k Dec 29, 2022
A python toolbox for predictive uncertainty quantification, calibration, metrics, and visualization

Website, Tutorials, and Docs    Uncertainty Toolbox A python toolbox for predictive uncertainty quantification, calibration, metrics, and visualizatio

Uncertainty Toolbox 1.4k Dec 28, 2022
Neural Style and MSG-Net

PyTorch-Style-Transfer This repo provides PyTorch Implementation of MSG-Net (ours) and Neural Style (Gatys et al. CVPR 2016), which has been included

Hang Zhang 904 Dec 21, 2022
PointRCNN: 3D Object Proposal Generation and Detection from Point Cloud, CVPR 2019.

PointRCNN PointRCNN: 3D Object Proposal Generation and Detection from Point Cloud Code release for the paper PointRCNN:3D Object Proposal Generation a

Shaoshuai Shi 1.5k Dec 27, 2022
Scale-aware Automatic Augmentation for Object Detection (CVPR 2021)

SA-AutoAug Scale-aware Automatic Augmentation for Object Detection Yukang Chen, Yanwei Li, Tao Kong, Lu Qi, Ruihang Chu, Lei Li, Jiaya Jia [Paper] [Bi

DV Lab 182 Dec 29, 2022
A repository for generating stylized talking 3D and 3D face

style_avatar A repository for generating stylized talking 3D faces and 2D videos. This is the repository for paper Imitating Arbitrary Talking Style f

Haozhe Wu 191 Dec 22, 2022
An adaptive hierarchical energy management strategy for hybrid electric vehicles

An adaptive hierarchical energy management strategy This project contains the source code of an adaptive hierarchical EMS combining heuristic equivale

19 Dec 13, 2022
BRNet - code for Automated assessment of BI-RADS categories for ultrasound images using multi-scale neural networks with an order-constrained loss function

BRNet code for "Automated assessment of BI-RADS categories for ultrasound images using multi-scale neural networks with an order-constrained loss func

Yong Pi 2 Mar 09, 2022
Deep universal probabilistic programming with Python and PyTorch

Getting Started | Documentation | Community | Contributing Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch. Notab

7.7k Dec 30, 2022
make ASCII Art by Deep Learning

DeepAA This is convolutional neural networks generating ASCII art. This repository is under construction. This work is accepted by NIPS 2017 Workshop,

OsciiArt 1.4k Dec 28, 2022
This is the dataset and code release of the OpenRooms Dataset.

This is the dataset and code release of the OpenRooms Dataset.

Visual Intelligence Lab of UCSD 95 Jan 08, 2023
Look Closer: Bridging Egocentric and Third-Person Views with Transformers for Robotic Manipulation

Look Closer: Bridging Egocentric and Third-Person Views with Transformers for Robotic Manipulation Official PyTorch implementation for the paper Look

Rishabh Jangir 20 Nov 24, 2022