Open Source MATLAB Chemistry Software
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MATLAB Chemistry Software
View 109 business solutionsBrowse free open source MATLAB Chemistry Software and projects below. Use the toggles on the left to filter open source MATLAB Chemistry Software by OS, license, language, programming language, and project status.
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chethermo
Software for Introductory Chemical Engineering Thermodynamics
Introductory Chemical Engineering Thermodynamics helps readers master the fundamentals of applied thermodynamics as practice today. The text is distinctive in making the molecular perspectives accessible at the introductory level and connecting properties with practical applications. This site distributes the software for the textbook. If you are a 'user', then you want to download the archive from 'Download' icon or the 'Files' link. If you want the latest version of a particular file, then use the 'Code' link and look in the 'trunk' folder for the main development and 'branches' for any side projects. Please note that the 'Files' releases are periodic, and that the 'Code' files may contain development files or code that is different from the 'Files' content. -
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JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.
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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 experiments involving ultrashort light pulses in photo-induced physics or chemistry, including quantum optimal control. Allowing for visualization of dynamics 'on the fly', WavePacket is easy to use . 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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Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes. It can be used from MATLAB, Python, C++, or Fortran.
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Ocean Optics Sample Pack
Sample code for Ocean Optics OmniDriver spectrometer device driver
Sample code demonstrating how to use OmniDriver to drive Ocean Optics full range of spectrometers from C, C++, C#, Java, LabVIEW, Delphi, MATLAB and more. -
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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 of deuterium incorporation from a spectrum with isotopic fine structure resolved. Given a peptide sequence or elemental formula, the distribution of deuterium-associated mass-to-charge ratios is calculated based on a particular charge state corresponding to the molecular species resolved in an input mass spectrum. Peaks in the input mass spectrum fitting within bins corresponding to these values are used to determine the distribution of deuterium incorporated. -
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easy-dhpsf
GUI for fitting 3D single-molecule images using the double-helix PSF
This package of MATLAB routines with accompanying GUI allows scientific users to measure the 3D location of single molecules when using the double-helix point spread function (DH-PSF) widefield microscope. Version 2 also includes code that facilitates combining localization data from two spectral channels using a locally-weighted quadratic 3D registration function Features - Double-Gaussian estimator is calibrated via an axial scan of bright immobile fluorescent emitters (e.g. beads) - DH localization is performed through template matching and subsequent double Gaussian fitting - Tiff stacks of SM images are analyzed using template matching followed by double-Gaussian fitting to extract estimates of the molecule positions - Two spectral channels are registered by generating a locally-weighted quadratic mapping function from control point pairs -
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MetaOpen
Metabolomics Bioinformatics Tools
Our bioanalytical research exploits practical and efficient high-throughput technologies for the analyses of complex mixtures derived from living systems. This will facilitate the development of preventive, predictive and personalized medicine for specific diseases and will promote health and wellness. We use a number of high-throughput analytical platforms including multidimensional liquid chromatography-mass spectrometry (MDLC-MS) for proteomics, and for metabolomics; liquid chromatography-mass spectrometry (LC-MS), and comprehensive two-dimensional gas chromatography-mass spectrometry (GCxGC/TOF-MS). Each type of analysis affords limited analyte coverage of molecules present in a patient sample and therefore provides only a partial molecular profile for an individual patient. These diverse analytical data must be integrated with advanced bioinformatics methods for accurate evaluation of health and detection of disease susceptibility. -
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ASALI
ASALI is an open-source code for chemical engineers
Do you work with chemical reactors? Are you curious about them? ASALI is the open-source code that you are looking for. Chemical reactor models, transport/thermodynamic properties of gases, equilibrium calculations. ASALI couples all these features with an user friendly graphical interface. Modeling chemical reactors has never been so easy. -
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Blueprint XAS is a Matlab-based suite designed for the processing and analysis of near-edge x-ray absorption spectroscopy (XAS) data. The suite is designed primarily to assist users in exploring reasonable fit solutions while minimizing user bias.
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MS2Browser
LC-MS/MS data browser designed for siderophore analysis
MS2Browser is a tool for interactive pre-processing, analysis and visualization of LC-MS/MS data. Input is an mzXML file with centroided LC-MS/MS data. The program is written in MatLab and it was designed for the analysis of siderophores (iron transporting small molecules) in bacterial media. Some of the functionality and use of MS2Browser is described as part as an open-access book chapter: http://www.intechopen.com/books/applications-from-engineering-with-matlab-concepts/small-molecule-lc-ms-ms-fragmentation-data-analysis-and-application-to-siderophore-identification A siderophore structural database assembled for this project can be found alongside the MS2Browser software (.cfw format to be used with ChemBioFinder(TM) ). NOTE: The program is written for personal use to assist siderophore analysis using high-resolution LC-MS/MS data. Please contact me if you have any questions about its use, bugs, etc. -
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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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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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This package includes a collection of MATLAB files which are designed to: 1. Given a calibration scan of the image of a point emitter with an engineered point spread function (PSF), 2. 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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nwhess2freq
Calculates frequencies/modes from an nwchem generated hessian
This is a simple Octave script which calculates the frequencies/normal modes from an nwchem generated hessian matrix. The advantage of having a separate script for this is that you can use the same hessian to calculate frequencies for different isotopic substitutions i.e. you only have to run one nwchem calculation. The script is finished in its current form in the sense that it is feature complete. Feel free to amend, translate, copy, steal etc. See the README in the code repository for instructions. Installation: Simply download the file and start Octave in the download directory. -
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Software developed for the analysis of Neutron Reflectivity data.
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CS Miner
A tool for Navigating in Chemical Space
CS-Miner stands for Chemical Space Miner and is a software tool for navigating in chemical space of compound databases. It helps for deriving appropriate classification models and performing virtual screening. Download it via: http://csminer.com/csm/?p=7 A quick tutorial is available through: http://csminer.com/csm/?p=8 -
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ChelomEx
Isotope assisted discovery of metal chelating agents from LC-MS data
ChelomEx identifies chromatographic features of metal complexes and associated free ligands or other related adducts in high-resolution LC-MS data. A built-in graphical user interface and compound library aid in the efficient evaluation of the results. If you use ChelomEx for your research, please cite our Analytical Chemistry paper that describes the software (http://dx.doi.org/10.1021/ac503000e). To comment, send bug reports or suggestions for additional features to be implemented in future versions please send me a message. The current version ChelomEx 1.2 from 06 January 2016 includes the following changes to the original version (ChelomEx 1.0): - function to filter discovered isotope patterns after the first analysis step (isotope pattern search), accessible in the Isotope Pattern toolbar (v1.2) - updates for compatibility with MatLab versions after 2014b (v1.2) - siderophore database update (v1.1) - can now also analyze negative mode data (v1.1) - bug fixes (v1.1) -
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DRCS (Dimensionless Reaction Coordinate Software) calculates a dimensionless reaction coordinate for chemical reactions that can be used to classify transition states (and other geometries along a reaction path) as either early or late.
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EDA is Graphical User Interface and Matlab compiled application for filtration of LC-MS or GC-MS, based on probalistic methods. Including peaks and compounds segmentation with various visualizations. This software can be used for metabolomics, proteomics
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Extended Bioaccumulation Framework (ExBAF) is a tool for assessing bioaccumulation in foodwebs. Supports several bioaccumulation models and provides tools for analysis and visualization.
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HOT is a package of Matlab and Octave compatible functions that manage thermodynamic data for a wide range of species. Functions calculate almost all the most common thermodynamic quantities of mixtures. Python users may also want to look at PYroMat at https://chmarti1.github.io/PYroMat/index.html
