Search Results for "light linux distribution"
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Showing 17 open source projects for "light linux distribution"
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WavePacket (C++/Python)
Time-dependent simulation of open and closed quantum systems
Note: This package has been superseded by a Python-only package. See https://github.com/ulflor/wavepacket for the follow-up project. WavePacket is a program package for numerical simulation of quantum-mechanical wavepacket dynamics of distinguishable particles. It can be used to solve single or coupled time-independent or time-dependent (linear) Schrödinger and Liouville-von Neumann-equations. Optionally accounting for the interaction with external electric fields within the semiclassical... -
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WavePacket (Matlab/Octave)
Dynamics of quantum systems, controlled by external fields
WavePacket is a program package for numerical simulation of quantum-mechanical wavepacket dynamics of distinguishable particles. It can be used to solve single or coupled time-independent or time-dependent (linear) Schrödinger and Liouville-von Neumann-equations, partly also classical or quantum-classical Liouville equations. Optionally accounting for the interaction with external electric fields within the semiclassical dipole approximation, WavePacket can be used to simulate modern... -
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ParamIT
a Toolset for Molecular Mechanical Force Field Parameterization
ParamIT is a toolkit aiding the development of molecular mechanical force field parameterization of small, drag like, molecules within CHARMM general force field (CGenFF) protocol. The developed toolkit helps the researchers in following ways: 1) automating the creation of multiple input files for quantum and molecular mechanics programs, 2) automating the output analysis and 3) substitute the use of full MM programs with a faster specialized one. The developed tools include: 1) generator of... -
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orthos
Simulation of EPR spectra of nitroxide biradicals
The program Orthos is developed to performed simulation (including nonlinear least-squares fitting) of EPR spectra of nitroxide biradicals. The program capabilities include simulation of rigid-limit and slow-motional spectra, of both isotropic and aligned samples. The spectra of multiple paramagnetic species, both bi- and monoradicals can be modeled. NB: Please note that now (as of Nov 2016) the distribution is being updated so that to improve reliability, OS-universality, and the quality... -
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DISCUS is a set of programs to simulate the atomic structure of disordered materials and calculate experimental properties such as diffuse scattering or the atomic pair distribution function.
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LOOS
Analyze molecular simulation data
LOOS is a light-weight object oriented software library for creating new tools for analyzing molecular simulation data, written in C++. The main design goal is to allow casual programmers to easily implement new analysis methods. THIS PAGE IS NO LONGER UPDATED. Please see https://github.com/GrossfieldLab/loos for all recent developments -
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WavePacket
Dynamics of quantum systems, controlled by external fields
WavePacket is a toolkit for numerical simulation of distinguishable particles. It can solve single or coupled time-independent or time-dependent (linear) Schrödinger and Liouville-von Neumann-equations, as well as classical or quantum-classical Liouville equations. External electric fields can be added within the semiclassical dipole approximation, thus WavePacket can be used to simulate modern experiments involving ultrashort light pulses in photo-induced physics or chemistry, including... -
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trj_cavity finds protein cavities throughout Molecular Dynamics (MD) simulation trajectories. The program works with files in PDB format, but it also can read/generate GROMACS compatible formats such as XTC. The same project can be compiled as a GROMACS tool or as a standalone version. Installation instructions are provided in the INSTALL file of the project and in https://sourceforge.net/p/trjcavity/wiki/Home/#ffad If you need support using this tool (or report bugs), please post it...
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RDKit
Open-Source Cheminformatics and Machine Learning
A collection of cheminformatics and machine-learning software written in C++ and Python. NOTE: the RDKit source code and downloads are now in github: https://github.com/rdkit/rdkit The core algorithms and data structures are written in C++. Wrappers are provided to use the toolkit from either Python or Java. Additionally, the RDKit distribution includes a PostgreSQL-based cartridge that allows molecules to be stored in relational database and retrieved via substructure and... -
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QUDeX-MS
Hydrogen/deuterium exchange estimation for isotopic fine structure MS
Hydrogen-deuterium exchange coupled to mass spectrometry permits analysis of structural dynamics, stability, and molecular interactions of proteins. Resolving isotopic fine structure during mass spectrometry has been recently demonstrated to allow direct detection and quantification of deuterium incorporation distinct from peaks corresponding to non-deuterium incorporated natural abundance heavy isotopomers. Here, we present a graphical tool that allows for a rapid and automated estimation... -
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Alchemy Linux
A linux distribution for chemists
Alchemy Linux is a Linux distribution (based on Fedora) for chemists (and mathematicians and physicists). This remix comes with a whole set of packages to help with experiments, simulations and publications. (This project is not maintained or endorsed by Red Hat or the Fedora project). -
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iso2l (ˈaisəutuːl, spoken isotool) is a software to calculate the isotopic distribution of a chemical formula or a amino acid chain. The development has been MOVED TO https://github.com/binfalse/iso2l
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Ion Chromatography Data Analyzer for analyzing wasted oil. Can parse data file from HW2000 workstation.
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A framework to support scientific experiments: acquiring, visualizing, analyzing, and managing experimental data. Initially developed to support the experimental process on two beamlines at the Canadian Light Source synchrotron (lightsource.ca).
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SpecMark (spectral Markov) is a method for calculating the joint probability distribution over species in a regulatory network.
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ProgPorts is an administrative and easy user interface to hundreds of proteomics, molecular dynamics, and protein crystallography programs. It is a hybrid of the prog/setup system, developed at Johns Hopkins University, and GNU-Darwin ports system.
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The ISOTOPIC PATTERN CALCULATOR is a small linux tool for mass spectrometry. It calculates the isotopic distribution for a given chemical formula or peptide sequence. GIPS is a GUI Version of the Isotopic Pattern Calculator.
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