progres | Fast protein structure searching or your money

by jgreener64 Python Version: 0.2.0 License: Non-SPDX

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kandi X-RAY | progres Summary

progres is a Python library. progres has no bugs, it has no vulnerabilities, it has build file available and it has low support. However progres has a Non-SPDX License. You can install using 'pip install progres' or download it from GitHub, PyPI.

This repository contains the method from the pre-print:. Greener JG and Jamali K. Fast protein structure searching using structure graph embeddings. bioRxiv (2022) - link. It provides the progres Python package that lets you search structures against pre-embedded structural databases and pre-embed datasets for searching against. Searching typically takes 1-2 s and is faster for multiple queries. Currently SCOPe, CATH and ECOD are provided for searching against but we aim to add others such as the AlphaFold database in future. This is work in progress software - the implementation, API and results may change. Please open issues or contact me with any feedback. Appropriate version numbers will distinguish versions. Training scripts and datasets will be made available on publication.

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Support

progres has a low active ecosystem.

It has 3 star(s) with 0 fork(s). There are 1 watchers for this library.

It had no major release in the last 12 months.

progres has no issues reported. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of progres is 0.2.0

Quality

progres has no bugs reported.

Security

progres has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

License

progres has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

progres releases are available to install and integrate.

Deployable package is available in PyPI.

Build file is available. You can build the component from source.

Installation instructions, examples and code snippets are available.

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progres Key Features

No Key Features are available at this moment for progres.

progres Examples and Code Snippets

No Code Snippets are available at this moment for progres.

Community Discussions

No Community Discussions are available at this moment for progres.Refer to stack overflow page for discussions.

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Vulnerabilities

No vulnerabilities reported

Install progres

Python 3.6 or later is required. The software is OS-independent.
Install PyTorch 1.11 or later, PyTorch Scatter and PyTorch Geometric as appropriate for your system. A GPU is not required and will only provide speedup in certain situations since multiple workers can be used on CPU. Example commands:
Run pip install progres, which will also install Biopython, mmtf-python and einops if they are not already present.
The first time you run the software the trained model and pre-embedded databases (~120 MB) will be downloaded to the package directory, which requires an internet connection.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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