Implementation of trRosetta and trDesign for Pytorch, made into a convenient package

Related tags

Deep Learningdeep-learningartificial-intelligenceprotein-designprotein-folding
Overview

trRosetta - Pytorch (wip)

Implementation of trRosetta and trDesign for Pytorch, made into a convenient package, for protein structure prediction and design. Will also contain an experimental version of trRosetta that uses attention. The concept of trDesign will also be abstracted into a wrapper in this repository, so that it can be applied to Alphafold2 once it is replicated. Please join the efforts there if you would like to see this happen!

The original repository can be found here

Install

$ pip install tr-rosetta-pytorch

Usage

As a command-line tool, to run a structure prediction

$ tr_rosetta <input-file.a3m>

Code

import torch
from tr_rosetta_pytorch import trRosettaNetwork

model = trRosettaNetwork(
    filters = 64,
    kernel = 3,
    num_layers = 61
).cuda()

x = torch.randn(1, 526, 140, 140).cuda()

theta, phi, distance, omega = model(x)

Citations

@article {Yang1496,
    author = {Yang, Jianyi and Anishchenko, Ivan and Park, Hahnbeom and Peng, Zhenling and Ovchinnikov, Sergey and Baker, David},
    title = {Improved protein structure prediction using predicted interresidue orientations},
    URL = {https://www.pnas.org/content/117/3/1496},
    eprint = {https://www.pnas.org/content/117/3/1496.full.pdf},
    journal = {Proceedings of the National Academy of Sciences}
}
@article {Anishchenko2020.07.22.211482,
    author = {Anishchenko, Ivan and Chidyausiku, Tamuka M. and Ovchinnikov, Sergey and Pellock, Samuel J. and Baker, David},
    title = {De novo protein design by deep network hallucination},
    URL = {https://www.biorxiv.org/content/early/2020/07/23/2020.07.22.211482},
    eprint = {https://www.biorxiv.org/content/early/2020/07/23/2020.07.22.211482.full.pdf},
    journal = {bioRxiv}
}
You might also like...
PyTorch evaluation code for Delving Deep into the Generalization of Vision Transformers under Distribution Shifts.
PyTorch evaluation code for Delving Deep into the Generalization of Vision Transformers under Distribution Shifts.

Out-of-distribution Generalization Investigation on Vision Transformers This repository contains PyTorch evaluation code for Delving Deep into the Gen

Chongzhi Zhang 72 Dec 13, 2022
This package proposes simplified exporting pytorch models to ONNX and TensorRT, and also gives some base interface for model inference.

PyTorch Infer Utils This package proposes simplified exporting pytorch models to ONNX and TensorRT, and also gives some base interface for model infer

Alex Gorodnitskiy 11 Mar 20, 2022
PyTorch deep learning projects made easy.

PyTorch Template Project PyTorch deep learning project made easy. PyTorch Template Project Requirements Features Folder Structure Usage Config file fo

Victor Huang 3.8k Jan 1, 2023
Deep Learning with PyTorch made easy 馃殌 !

Deep Learning with PyTorch made easy 馃殌 ! Carefree? carefree-learn aims to provide CAREFREE usages for both users and developers. It also provides a c

null 381 Dec 22, 2022
tsai is an open-source deep learning package built on top of Pytorch & fastai focused on state-of-the-art techniques for time series classification, regression and forecasting.
tsai is an open-source deep learning package built on top of Pytorch & fastai focused on state-of-the-art techniques for time series classification, regression and forecasting.

Time series Timeseries Deep Learning Pytorch fastai - State-of-the-art Deep Learning with Time Series and Sequences in Pytorch / fastai

timeseriesAI 2.8k Jan 8, 2023
Kindle is an easy model build package for PyTorch.

Kindle is an easy model build package for PyTorch. Building a deep learning model became so simple that almost all model can be made by copy and paste from other existing model codes. So why code? when we can simply build a model with yaml markup file. Kindle builds a model with no code but yaml file which its method is inspired from YOLOv5.

Jongkuk Lim 77 Nov 11, 2022
PyTorch package for the discrete VAE used for DALL路E.

Overview [Blog] [Paper] [Model Card] [Usage] This is the official PyTorch package for the discrete VAE used for DALL路E. Installation Before running th

OpenAI 9.5k Jan 5, 2023
Python package facilitating the use of Bayesian Deep Learning methods with Variational Inference for PyTorch
Python package facilitating the use of Bayesian Deep Learning methods with Variational Inference for PyTorch

PyVarInf PyVarInf provides facilities to easily train your PyTorch neural network models using variational inference. Bayesian Deep Learning with Vari

null 342 Dec 2, 2022
quantize aware training package for NCNN on pytorch

ncnnqat ncnnqat is a quantize aware training package for NCNN on pytorch. Table of Contents ncnnqat Table of Contents Installation Usage Code Examples

null 62 Nov 23, 2022
Comments
  • Fixing a bug in sequence preprocessing

    Fixing a bug in sequence preprocessing

    When cuda is available, and a sequence of length = 1 is loaded, it is left on the cpu and not copied to the gpu. That creates an error: RuntimeError: Expected all tensors to be on the same device, but found at least two devices, cuda:0 and cpu! (when checking arugment for argument tensors in method wrapper__cat)

    opened by LiorZ 0
  • How to get a PDB file via a FASTA file?

    How to get a PDB file via a FASTA file?

    Hello, I have recently needed to make structural predictions on many small proteins, I only have their sequence, I hope to get .PDB file, can this software implement? I tried it, it seems that I can only get the .npz file. If you can, please tell me , thank you !

    opened by mooerccx 0
Releases(0.0.3)
Owner
Phil Wang
Working with Attention. It's all we need.
Phil Wang
GitHub Repository
The missing CMake project initializer

cmake-init - The missing CMake project initializer Opinionated CMake project initializer to generate CMake projects that are FetchContent ready, separ

1k Jan 01, 2023
This program was designed to detect whether someone is wearing a facemask through a live video stream.

This program was designed to detect whether someone is wearing a facemask through a live video stream. A custom lightweight CNN trained with TensorFlow on a public dataset provided by Kaggle is used

0 Apr 02, 2022
Pytorch GUI(demo) for iVOS(interactive VOS) and GIS (Guided iVOS)

GUI for iVOS(interactive VOS) and GIS (Guided iVOS) GUI Implementation of CVPR2021 paper "Guided Interactive Video Object Segmentation Using Reliabili

Yuk Heo 13 Dec 09, 2022
YOLOv4 / Scaled-YOLOv4 / YOLO - Neural Networks for Object Detection (Windows and Linux version of Darknet )

Yolo v4, v3 and v2 for Windows and Linux (neural networks for object detection) Paper YOLO v4: https://arxiv.org/abs/2004.10934 Paper Scaled YOLO v4:

Alexey 20.2k Jan 09, 2023
馃槉 Python module for face feature changing

PyWarping Python module for face feature changing Installation pip install pywarping If you get an error: No such file or directory: 'cmake': 'cmake',

Dopevog 10 Sep 10, 2021
NP DRAW paper released code

NP-DRAW: A Non-Parametric Structured Latent Variable Model for Image Generation This repo contains the official implementation for the NP-DRAW paper.

ZENG Xiaohui 22 Mar 13, 2022
[CVPRW 21] "BNN - BN = ? Training Binary Neural Networks without Batch Normalization", Tianlong Chen, Zhenyu Zhang, Xu Ouyang, Zechun Liu, Zhiqiang Shen, Zhangyang Wang

BNN - BN = ? Training Binary Neural Networks without Batch Normalization Codes for this paper BNN - BN = ? Training Binary Neural Networks without Bat

VITA 40 Dec 30, 2022
An unofficial PyTorch implementation of a federated learning algorithm, FedAvg.

Federated Averaging (FedAvg) in PyTorch An unofficial implementation of FederatedAveraging (or FedAvg) algorithm proposed in the paper Communication-E

Seok-Ju Hahn 123 Jan 06, 2023
CPU inference engine that delivers unprecedented performance for sparse models

The DeepSparse Engine is a CPU runtime that delivers unprecedented performance by taking advantage of natural sparsity within neural networks to reduce compute required as well as accelerate memory b

Neural Magic 1.2k Jan 09, 2023
SuperSDR: multiplatform KiwiSDR + CAT transceiver integrator

SuperSDR SuperSDR integrates a realtime spectrum waterfall and audio receive from any KiwiSDR around the world, together with a local (or remote) cont

Marco Cogoni 30 Nov 29, 2022
Luminous is a framework for testing the performance of Embodied AI (EAI) models in indoor tasks.

Luminous is a framework for testing the performance of Embodied AI (EAI) models in indoor tasks. Generally, we intergrete different kind of functional

28 Jan 08, 2023
A heterogeneous entity-augmented academic language model based on Open Academic Graph (OAG)

Library | Paper | Slack We released two versions of OAG-BERT in CogDL package. OAG-BERT is a heterogeneous entity-augmented academic language model wh

THUDM 58 Dec 17, 2022
Causal Imitative Model for Autonomous Driving

Causal Imitative Model for Autonomous Driving Mohammad Reza Samsami, Mohammadhossein Bahari, Saber Salehkaleybar, Alexandre Alahi. arXiv 2021. [Projec

VITA lab at EPFL 8 Oct 04, 2022
Simple-Image-Classification - Simple Image Classification Code (PyTorch)

Simple-Image-Classification Simple Image Classification Code (PyTorch) Yechan Kim This repository contains: Python3 / Pytorch code for multi-class ima

Yechan Kim 8 Oct 29, 2022
A strongly-typed genetic programming framework for Python

monkeys "If an army of monkeys were strumming on typewriters they might write all the books in the British Museum." monkeys is a framework designed to

H. Chase Stevens 115 Nov 27, 2022
This is the repository of shape matching algorithm Iterative Rotations and Assignments (IRA)

Description This is the repository of shape matching algorithm Iterative Rotations and Assignments (IRA), described in the publication [1]. Directory

MAMMASMIAS Consortium 6 Nov 14, 2022
JUSTICE: A Benchmark Dataset for Supreme Court鈥檚 Judgment Prediction

JUSTICE: A Benchmark Dataset for Supreme Court鈥檚 Judgment Prediction CSCI 544 Final Project done by: Mohammed Alsayed, Shaayan Syed, Mohammad Alali, S

Smit Patel 3 Dec 28, 2022
Detection of PCBA defect

Detection_of_PCBA_defect Detection_of_PCBA_defect Use yolov5 to train. $pip install -r requirements.txt Detect.py will detect file(jpg,mp4...) in cu

6 Nov 28, 2022
鍒╃敤Tensorflow瀹炵幇鍩轰簬CNN鐨勪腑鏂囩煭鏂囨湰鍒嗙被

Text Classification with CNN 浣跨敤鍗风Н绁炵粡缃戠粶杩涜涓枃鏂囨湰鍒嗙被 CNN鍋氬彞瀛愬垎绫荤殑璁烘枃鍙互鍙傜湅: Convolutional Neural Networks for Sentence Classification 杩樺彲浠ュ幓璇籨ennybritz澶х墰鐨勫崥瀹細Implemen

Jeremiah 4 Nov 08, 2022
Repo for parser tensorflow(.pb) and tflite(.tflite)

tfmodel_parser .pb file is the format of tensorflow model .tflite file is the format of tflite model, which usually used in mobile devices before star

1 Dec 23, 2021