Search Results for "atom"
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Showing 32 open source projects for "atom"
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Protenix
A trainable PyTorch reproduction of AlphaFold 3
...It supports both āfullā models and lightweight variants such as āProtenix-Mini,ā offering a trade-off between speed/compute cost and predictive accuracy ā making structure prediction accessible even in resource-constrained environments. The project also includes support for constraints (e.g., specifying residue- or atom-level contact constraints, or pocket constraints) to guide predictions toward biologically or experimentally relevant conformations, which enhances its utility for tasks like modeling complexes, ligands, or antibodyāantigen interactions. -
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Materials Discovery: GNoME
AI discovers 520000 stable inorganic crystal structures for research
...The project centers on Graph Networks for Materials Exploration (GNoME), a message-passing neural network architecture trained on density functional theory (DFT) data to predict material stability and energy formation. Using GNoME, DeepMind identified 381,000 new stable materials, later expanding the dataset to include over 520,000 materials within 1 meV/atom of the convex hull as of August 2024. The repository provides datasets, model definitions, and interactive Colabs for exploring these materials, computing decomposition energies, and visualizing chemical families. Additionally, it includes JAX-based implementations of GNoME and Nequipāthe latter being used to train interatomic potentials for dynamic simulations. -
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granary
The social web translator
The social web translator. Fetches and converts data between social networks, HTML and JSON with microformats2, ActivityStreams/ActivityPub, Atom, JSON Feed, and more. Granary is a library and REST API that fetches and converts between a wide variety of social data sources and formats. Free yourself from silo API chaff and expose the sweet social data foodstuff inside in standard formats and protocols. -
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Pelican
Static site generator that supports Markdown and reST syntax
...Chronological content (e.g., articles, blog posts) as well as static pages. Integration with external services. Site themes (created using Jinja2 templates). Publication of articles in multiple languages. Generation of Atom and RSS feeds. Code syntax highlighting via Pygments. Import existing content from WordPress, Dotclear, or RSS feeds. Fast rebuild times due to content caching and selective output writing. Extensible via a rich plugin ecosystem, Pelican Plugins. Pelican considers āarticlesā to be chronological content, such as posts on a blog, and thus associated with a date. ... -
MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhereāacross AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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AtomAI
Deep and Machine Learning for Microscopy
AtomAI is a Pytorch-based package for deep and machine-learning analysis of microscopy data that doesn't require any advanced knowledge of Python or machine learning. The intended audience is domain scientists with a basic understanding of how to use NumPy and Matplotlib. It was developed by Maxim Ziatdinov at Oak Ridge National Lab. The purpose of the AtomAI is to provide an environment that bridges the instrument-specific libraries and general physical analysis by enabling the seamless... -
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discord_feedbot
Moved to https://gitlab.com/ffreiheit/discord_feedbot
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tootbot.py
A small python 3.x script to replicate tweets on a mastodon account
...Forked from https://github.com/cquest/tootbot Specialized in RSS feed, in particular from Nitter (https://nitter.net - https://github.com/zedeus/nitter) It gets the tweets from RSS available at https://nitter.net, then does some cleanup on the content: twitter tracking links (t.co) are dereferenced twitter hosted pictures are retrieved and uploaded to mastodon the tweets from RSS source's are joined based on the domain name to avoid duplicates It can also toot RSS/atom feeds (see cron-example.sh). A sqlite database is used to keep track of tweets than have been tooted. The script is simply called by a cron job and can run on any server. -
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PyTracking
Visual tracking library based on PyTorch
...Official implementation of the RTS (ECCV 2022), ToMP (CVPR 2022), KeepTrack (ICCV 2021), LWL (ECCV 2020), KYS (ECCV 2020), PrDiMP (CVPR 2020), DiMP (ICCV 2019), and ATOM (CVPR 2019) trackers, including complete training code and trained models. -
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Open Drug Discovery Toolkit (ODDT)
Modular and comprehensive toolkit for use in cheminformatics
...Most important and handy property of Molecule in ODDT are Numpy dictionaries containing most properties of supplied molecule. Some of them are straightforward, other require some calculation, ie. atom features. Dictionaries are provided for major entities of molecules. -
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Molecular Dynamics Studio
Molecular Dynamics Cell Construction
...PACKMOL can generate a random collection of molecules using the molecule templates from NanoEngineer-1 thus providing the initial MD cell. Modifications to PACKMOL allow the atom type data to be passed through to the MSI2LMP software. MSI2LMP creates a LAMMPS input file based on class I or class II force fields. MSI2LMP was modified to use numerically coded force field data generated by NanoEngineer-1. The MMP file format was extended and integrated into all three software applications. http://www.nanoengineer-1.net http://www.ime.unicamp.br/~martinez/packmol/ http://lammps.sandia.gov/ -
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FeedAgregator
RSS and Atom feed agregator in desktop widgets + notifications
FeedAgregator periodically looks for RSS/Atom feed updates. If an update is found, a notification is sent. In addition, desktop widgets display either all the entries of one feed or the latest entry of each feed of a given category. FeedAgregator is designed for Linux. It is written in Python 3 and relies mostly upon Tk GUI toolkit. The application is in the system tray, so it might not work with all desktop environments (see Troubleshooting). -
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Phaistos is a framework for all-atom Monte Carlo simulations of proteins. It incorporates several advanced probabilistic models of protein structure for conformational sampling, efficient move-algorithms and the OPLS and PROFASI forcefields.
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orbkit (Moved to Github)
A Modular Python Toolbox for Cross-Platform Post-Processing of Quantum
PLEASE NOTE ORBKIT HAS BEEN MOVED TO https://github.com/orbkit/orbkit orbkit is a parallel Python program package for post-processing wave function data extracted from output files of MOLPRO (Molden File Format), TURBOMOLE (AOMix file format), GAMESS-US, PROAIMS/AIMPAC (wfn/wfx file format), and Gaussian (Output File and Formatted Checkpoint File) output files. Futhermore, an interface to cclib, a parser for quantum chemical logfiles, is provided. If you use orbkit in your work,... -
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eSBMTools
python tools for enhanced native structure-based modeling
eSBMTools: python tools that assist the setup and evaluation of native structure-based simulations of proteins and nucleic acids, both at the CĪ± and all-atom level. The tools interface with GROMACS and support its standard output formats. Information from other sources like bioinformatics or experimental data can be added to the standard native structure-based model (SBM). Publication to be cited: Benjamin Lutz, Claude Sinner, Geertje Heuermann, Abhinav Verma, and Alexander Schug. eSBMTools 1.0: enhanced native structure-based modeling tools. ... -
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**(9 march 2016) this project is continued on github : http://jaapkroe.github.io/polypy ** Python script to analyze (shortest-path) rings in structures read from xyz-files. It can be useful for example to identify defects in crystal structures or molecules.
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LeechCraft is a cross-platform modular "internet-client" application. It has plugins that allow one to browse the web, chat via instant messaging (like Jabber or IRC), read RSS/Atom feeds, download files via BitTorrent, Direct Connect and other protocols, play media files and much more.
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Charm is a full-featured, cross-platfom blogging client for LiveJournal, Atom (Movable Type, Blogger), and MetaWeb (WordPress). It is console-based, all-text, and can be used entirely from the command line. It is written in Python.
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This is a simple gmail atom reader, it uses PyQt4. Gmail Atom Reader will show an icon on your tray, and will populate it's menu with all your unread messages. A notification window will show up with details of your unread messages.
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MIPGen
Simple Molecular Interaction Potential Generator in Python
Molecular Interaction Potential Generator MIPGEN is a python program that will calculate Molecular Interaction Potential grids over a given molecule, that could be either a protein or a small organic compound (drug). The output will be a series of grids with DX format (*.dx) that the user will be able to visualize using any Molecular visualization program like VMD, PyMol, Chimera... For more information on dependencies and usage, please read the Documentation. Users are welcome... -
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pyRssReader
A rss reader
pyRssReader is on open source and free program. pyRssReader is used to read the rss feeds from the websites. At this moment pyRssReader supports the follow feed types: RSS 0.90, Netscape RSS 0.91, Atom 0.3, Atom 1.0, CDF feeds and more types. -
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Cortez, for create new news service model for RSS and blogging. Cortez will just offer the environment to create post, read news thru RSS(ATOM) and syndicate within the multiple blogs.
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lylina is a river-of-news style web-based RSS/Atom feed aggregator loosely based on it's predicessor, lilina. It features a dynamic multi-user system and a scalable database backend, providing the best way to get all your news in one place.
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Fasafiso is a blogging system written in PHP using a MySQL database backend. It supports multi-user blogging, themes, multilanguage, a Blogger-like API to post entries remotely, commenting on posts, rss and atom feeds.
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WikiGateway is a library which allows you to act as a client to a wiki website, executing operations like getPage, putPage, and getRecentChanges. It can be used from the command line, from Perl or Python, as an Atom web service, or as a WikiXmlRpc server
