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Showing 35 open source projects for "https"
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KherveFitting
Fit X-ray Photoelectron Spectroscopy (XPS) and XAS data
...Several intensity calibration available:TPP-2M, Scoffield, Wagner. Atomic concentration acurately calculated and matching with Thermo Avantage software. YouTube Channel: https://www.youtube.com/@xpsexamples-imperialcolleg6571 -
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...Those datasets are peer reviewed by a board of reviewers. The project is supported by a scientific advisory board. nmrshiftdb2 is part of the NFDI4Chem initiative (https://nfdi4chem.de/) and will provide a component for a curated repository there. Please consult the documentation for more detailed information.
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Hydrogen Bond Analysis Tool (HBAT)
HBAT 2 is migrated from PERL to Python.
HBAT(Hydrogen Bond Analysis Tool) is a tool to automate the analysis of hydrogen bonds present in a PDB Structure file. HBAT 2 is migrated from PERL to Python. Latest Documentation: https://hbat.abhishek-tiwari.com/ Web Server Version: http://hbat-web.abhishek-tiwari.com Latest Github Release: http://github.com/abhishektiwari/hbat Citation: Tiwari, A., & Panigrahi, S. K. (2007). HBAT: A Complete Package for Analysing Strong and Weak Hydrogen Bonds in Macromolecular Crystal Structures. In Silico Biology, 7(6). https://doi.org/10.3233/ISI-2007-00337 -
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OSRA is a utility designed to convert graphical representations of chemical structures and reactions, as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES or SD file format- a computer recognizable molecular structure You can find links to the binary executables here: https://sourceforge.net/p/osra/wiki/Download/
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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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Software and codes created in "Laboratorio de Química Computacional" of "Facultad de Ciencias y Tecnología" of "Universidad de Carabobo"
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Chemical Trajectory Analyzer
A software package for processing and analyzing chemical trajectories
ChemTraYzer creates reaction models from molecular dynamics simulations. It's available as open software (MIT license). Please find a full description @ https://www.ltt.rwth-aachen.de/cms/LTT/Forschung/Forschung-am-LTT/Model-Based-Fuel-Design/Aktuelle-Projekte/~kqbf/ChemTraYzer/lidx/1 M.Döntgen, M.-D.Przybylski-Freund, L.C.Kröger, W.A.Kopp, A.E.Ismail, K.Leonhard, "Automated Discovery of Reaction Pathways, Rate Constants, and Transition States Using Reactive Molecular Dynamics Simulations", J. ... -
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CVSim
Cyclic Voltammetry Simulation Program for Research and Education
This a cyclic voltammetry (CV) program created for teaching CV undergraduate chemistry students. For research, download the version from https://sourceforge.net/projects/cvsimplus/ . CVSim uses the implicit method to simulate diffusion. Development of new methods for more accurate simulation of the diffusion is under way. For more details and discussion contact me at akeramid@ucy.ac.cy. -
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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 dipole approximation, WavePacket can be used to simulate modern experiments involving ultrashort light pulses in photo-induced physics or chemistry. ... -
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WavePacket (Matlab/Octave)
Dynamics of quantum systems, controlled by external fields
...First established in 2004, the present Matlab version is in a stable, mature state. Further development mainly by Burkhard Schmidt at WIAS and FU Berlin. See also our articles at https://doi.org/10.1016/j.cpc.2016.12.007 https://doi.org/10.1016/j.cpc.2018.02.022 https://doi.org/10.1002/JCC.26045 -
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Jljp
Calculates the voltage across a liquid junction between two solutions
An analogous project written in C# can be found here: https://github.com/swharden/JLJP Liquid junction potential calculator. It's a tool for scientists and engineers who have to do with electrochemistry and electrokinetics. When two solutions containing ions are put into contact, possibly through a porous diaphragm, a voltage develops across them. The calculation of the voltage is not trivial. -
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WaveTrain (Python)
Quantum dynamics of chain-like systems using tensor train formats
WaveTrain is an open-source software for numerical simulations of chain-like quantum systems with nearest-neighbor (NN) interactions only (with or without periodic boundary conditions). This Python package is centered around tensor train (TT, or matrix product) representations of quantum-mechanical Hamiltonian operators and (stationary or time-evolving) state vectors. WaveTrain builds on the Python tensor train toolbox scikit_tt, which provides efficient construction methods, storage... -
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CoolingPower
Print Steam Tables; Plot diagrams and cycles from equations of state
...Compiling and execution utilizes the GNU Scientific Library derivative functions and the Boost.signals2 and Boost.bind libraries. Unix-based operating systems also require the Boost program options library. The repository is structured as described in https://nvie.com/posts/a-successful-git-branching-model/ . -
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TheoDORE
Theoretical Density, Orbital Relaxation and Exciton analysis
...TheoDORE is interfaced to a number of quantum chemical programs (Q-Chem, Columbus, Turbomole, ...) and can be used for a wide range of excited state methods (MR-CI, ADC, CC, TDDFT). It is written in a modular fashion to allow for an easy extension of these capabilities. Code development moved to github: https://github.com/felixplasser/theodore-qc -
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QMForge reads output from various quantum mechanical calculations and provides tools for analyzing these results. Specifically, population (Mulliken and C-squared), fragment, and charge decomposition analyses are available. See https://qmforge.net for more info.
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OpenGrowth
OpenGrowth is a program which constructs de novo ligands for proteins.
...Chem., http://dx.doi.org/10.1021/acs.jmedchem.5b00886). To use OpenGrowth, you will need OpenGrowth_1.0.zip and Resources_1.0.2.zip that can be found by clicking on the Files menu in the horizontal bar at the top (https://sourceforge.net/projects/opengrowth/files). OpenGrowthGUI, FOG2.0, and the 3Mer-Screen stand-alone can be found in OpenGrowth_1.0.zip. To prepare new fragments you need BuildingFragments_1.0.1.zip and the scripts for MD simulations are in MD-Scripts_1.0.1.zip. SMoG2016.tar.gz allows to compute a score with the newly developed function (J. ... -
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chemfiles
Modern library for chemistry file reading and writing
...Chemfiles provides an interface to access this information which is - unified: the same code will work with all the supported formats; - simple: the interface is easy to use and extensively documented. This is only a mirror of the main repository, development of chemfiles happens on Github, at https://github.com/chemfiles/chemfiles/ -
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FullFun
A software package for fullerenes and their functionalized derivatives
...The CSIOpt program predicts the most stable isomers of charged fullerenes and endohedral metallofullerenes. The XSIOpt program predicts the most stable addition patterns for a given endohedral fullerene C2nX2m. For downloading FullFun, please go to our new web page: https://campusys.qui.uam.es/?page_id=1491 -
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Open-source Python software library and GUI desktop environment for direct bioinformatic analysis of mass-spectrometry data through powerful scripting tools and interfaces to many machine data formats, database search engines, and peptide data formats. For a copy of the source code, check out our Github repositories: mzDesktop: https://github.com/MaxAlex/mzDesktop multiplierz: https://github.com/MaxAlex/multiplierz
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!!! PTEROS DEVELOPMENT MOVED TO GITHUB !!! New project page: https://github.com/yesint/pteros New documentation page: https://yesint.github.io/pteros/ Pteros is the C++ library for custom molecular modeling and simulations codes designed for researchers, not for C++ gurus. Provides facilities for PDB, XTC and TRR files IO, powerful selections, geometry transformations, RMSD fitting and alignment, etc.
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...Perform a phase retrieval algorithm based on maximum likelihood estimation (MLE) of a phase aberration term which is added to the theoretical pupil function of the imaging system. 3. Use the phase-retrieved pupil function to perform single-emitter localization. Accompanying publication available here: https://doi.org/10.1364/OE.25.007945
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WavePacket
Dynamics of quantum systems, controlled by external fields
...With its visualization of quantum dynamics generated 'on the fly', WavePacket is suitable for teaching quantum mechanics as well as for research projects, see also the numerous demonstration examples . The Matlab/Octave version is mature and has been used in production for decades. The C++/Python version has been superseded by https://github.com/ulflor/wavepacket. Using tensor train techniques, the additional WaveTrain package aims at beating the curse of dimensionalit -
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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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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. -
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[OBSOLETE, check Github repository: https://github.com/LBT-CNRS/MDDriver) MDDriver is a library allowing a user to easily couple molecular visualisation tools with simulation code through a network. It allows to carry out interactive molecular dynamics, visualize simulation results and drive a simulation in interactive time.
