Search Results for "chemistry data"
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Showing 303 open source projects for "chemistry data"
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Avogadro 2
Avogadro libraries provide 3D rendering, visualization, and analysis
AvogadroLibs is the core C++ library behind Avogadro 2, an open-source molecular editor and visualization platform used in chemistry, materials science, and education. It provides the essential tools for constructing, analyzing, and visualizing molecular structures in 2D and 3D. Designed for extensibility, AvogadroLibs supports plugins for quantum chemistry computations, molecular mechanics, and surface rendering. It interfaces with multiple chemistry formats and data sources, making it a versatile backbone for scientific applications and custom visualization tools. -
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TikZ
TikZ figures for concepts in physics/chemistry/ML
Collection of 111 standalone TikZ figures for illustrating concepts in physics, chemistry, and machine learning. Check out janosh.github.io to search, sort, open in Overleaf, and download figures (PDF/SVG/PNG) from this collection. -
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Fermi.jl
Fermi quantum chemistry program
Fermi.jl is a quantum chemistry framework written in pure Julia. This code is developed at the Center for Computational Quantum Chemistry at the University of Georgia under the supervision of Dr. Justin M. Turney and Prof. Henry F. Schaefer. This work is supported by the U.S. National Science Foundation under grant number CHE-1661604. Fermi focuses on post Hartree--Fock methods. Currently, only restricted references are supported. This is intended as a research code with an ever growing... -
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The Chemistry Development Kit (CDK) is a scientific, LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java. The main home page of the CDK is now at: http://cdk.github.io
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Tequila
A High-Level Abstraction Framework for Quantum Algorithms
Tequila is an abstraction framework for (variational) quantum algorithms. It operates on abstract data structures allowing the formulation, combination, automatic differentiation and optimization of generalized objectives. Tequila can execute the underlying quantum expectation values on state-of-the-art simulators as well as on real quantum devices. -
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FairChem
FAIR Chemistry's library of machine learning methods for chemistry
FAIRChem is a unified library for machine learning in chemistry and materials, consolidating data, pretrained models, demos, and application code into a single, versioned toolkit. Version 2 modernizes the stack with a cleaner core package and breaking changes relative to V1, focusing on simpler installs and a stable API surface for production and research. The centerpiece models (e.g., UMA variants) plug directly into the ASE ecosystem via a FAIRChem calculator, so users can run relaxations, molecular dynamics, spin-state energetics, and surface catalysis workflows with the same pretrained network by switching a task flag. ... -
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HomotopyContinuation.jl
A Julia package for solving systems of polynomials
HomotopyContinuation.jl is a Julia package for solving systems of polynomial equations by numerical homotopy continuation. Many models in the sciences and engineering are expressed as sets of real solutions to systems of polynomial equations. We can optimize any objective whose gradient is an algebraic function using homotopy methods by computing all critical points of the objective function. An important special case is when the objective function is the euclidean distance to a given point.... -
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Scientific Agent Skills
A set of ready to use Agent Skills for research, science, engineering
Scientific Agent Skills is an open-source collection of ready-to-use agent skills designed to turn AI coding assistants into stronger research, science, engineering, and analysis partners. It supports any AI agent compatible with the Agent Skills standard, including tools such as Cursor, Claude Code, Codex, and Gemini CLI. The repository includes 135 skills across scientific domains such as genomics, cheminformatics, clinical research, medical imaging, machine learning, physics, materials... -
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Claude Scientific Skills
A set of ready to use Agent Skills for research, science, engineering
Claude Scientific Skills is a large open source collection of ready-to-use scientific capabilities that extend AI coding agents into full research assistants. The project provides more than 170 curated skills covering domains such as genomics, drug discovery, medical imaging, physics, and advanced data analysis. Each skill bundles documentation, examples, and tool integrations so agents can reliably execute complex multi-step scientific workflows. The framework follows the open Agent Skills... -
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tm5
4DVAR data assimilation system using TM5
Model for the simulation of atmospheric tracer transport & chemistry. Allows Zooming. 4D-variational data-assimilation is possible based on the adjoint of the transport code (including zoom). -
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OpenFermion
The electronic structure package for quantum computers
OpenFermion is an open source library for compiling and analyzing quantum algorithms to simulate fermionic systems, including quantum chemistry. Among other functionalities, this version features data structures and tools for obtaining and manipulating representations of fermionic and qubit Hamiltonians. For more information, see our release paper. Currently, OpenFermion is tested on Mac, Windows, and Linux. We recommend using Mac or Linux because the electronic structure plugins are only compatible on these platforms. ... -
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Stand-alone application and Python tools for interactive and/or batch processing analysis of X-Ray Fluorescence Spectra. Graphical user interface (GUI) and batch processing capabilities provided.
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Avogadro
An intuitive molecular editor and visualization tool
Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers a flexible rendering framework and a powerful plugin architecture. -
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nmrshiftdb2 is a NMR database (web database) for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. The nmrshiftdb2 software is open source, the data is published under an open content license. The core of nmrshitdb2 are fully assigned spectra with raw data and peak lists (we have pure peak lists as well). Those datasets are peer reviewed by a...
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QSE is an application intended to help in the initial stages of data reduction of EXAFS data taken with multi-element detectors using the 'Spec' data acquisition system.
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QXRD is software for the acquisition and analysis of X-ray data taken with 2 dimensional detectors. The software can drive a Perkin Elmer XRD series flat panel detector and can be remote-controlled via a socket interface, or directly from SPEC
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SpectraViever
GUI app to view Veritas, MAX IV data
Data visualization, generate metadata log files, save spectra in .txt format for further advanced analysis. -
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Software developed for the analysis of Neutron Reflectivity data.
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MCE - Marching Cube ELD
Crystallographic software for displaying voxel maps - electron density
MCE is an crystallographic experimental program for 3D and 2D electron density map visualization. The software is mainly focused on visualization of ELD calculated from X-ray diffraction data of small molecules, but it will work for small proteins as well. Download the installation file (default download) or find in "Files" the zip-file with instant copy of the program which does not require the installation. -
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luscus
molecular editor and viewer
Luscus is the program for graphical display and editing of molecular systems. The program allows fast and easy building and/or editing different molecular structures, up to several thousands of atoms large. Luscus can also visualize dipole moments, normal modes, molecular orbitals, electron densities and electrostatic potentials. In addition, simple geometrical objects can be rendered in order to point out a geometrical feature or a physical quantity. The program is developed as a graphical... -
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GenX
X-Ray and Neutron Reflectivity Modeling
GenX is a scientific program to refine x-ray refelcetivity, neutron reflectivity and surface x-ray diffraction data using the differential evolution algorithm. GenX is very modular and highly extensible and can be used as a general fitting program. -
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Veritas RIXS Analysis
Advanced data analysis for Veritas beamline at MAX IV
You can do advanced analysis using the raw data from RIXS .h5 file. It has several tabs using which you can do different types of analysis, thereby utilizing the full potential of the Veritas beamline. Some of the features in addition to standard RIXS data analysis are: - continuous and discrete RIXS maps, - RIXS spectromicroscopy, - radiation damage analysis, - Q calibrations. -
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relax
Molecular dynamics by NMR data analysis
The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using... -
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EChem++ is a software system based on an object oriented approach to electrochemical experimentation, simulation, and data analysis. Currently, development emphasis lies on the modelling and simulation as well as the analysis modules.
