Open Source Chemistry Software - Page 6

J-ICE stands for Jmol interface for crystallographic and electronic properties. Is an extension of the powerful, platform independent molecular visualizer Jmol, towards crystallographic and electronic properties. More info will be given soon.

MCDL is a small Java molecular viewer/editor for chemical structures, stored in Modular Chemical Descriptor Language linear notation. Features include accurate structure diagram generation, and Kekule chemical structure creation from aromatic bond list.

Mass-Up is an Open-Source mass spectrometry utility for proteomics designed to support the preprocessing and analysis of MALDI-TOF mass spectrometry data. Mass-Up includes several tools and operations to load, preprocess and analyze MALDI-TOF data.

Nature is an open source library for computing thermochemical and kinetic properties of complex gas mixtures. The library supports the CHEMKIN data format and a native script for defining complex gas mixtures. Nature is written in C# and does not depend on any third party tool or library. Nature interoperates natively with any .NET language including the FTN95: Fortran 95 compiler. The primary goal of the project is to deliver the open source that provides the foundation for potentially complex CFD solutions capable of carrying computing in the distributed environment and particularly the Cloud computing.

Periodic table of the chemical elements for Java (J2ME) enabled devices. http://kenai.com/projects/periodic/pages/Home

NanoHive is a modular simulator used for modelling the physical world at a nanometer scale. The intended purpose of the simulator is to act as a tool for the study and development of nanotech entities. The project will also focus on the simulation of complex biological applications such as Targeted Drug Delivery by simulating nanowires, magnetic nanoparticles and others. Updates will follow from January 2017.

qmol is a simple molecular weight calculator, available for Linux and Windows, derived from Tomislav Gountchev's KMol. You can enter a formula, (e.g. CH3(CH2)2OH) and get its molecular weight (60.0959 g/mol) and its elemental composition (C3H8O: C 59.96; H 13.42; O 26.62 %). See the features list below for more details or consult the wiki page: https://sourceforge.net/p/qmol/wiki/Home/. For Windows binary and source code see the files section: https://sourceforge.net/projects/qmol/files/ Binary packages (rpm/deb) for openSUSE Leap 15.2-42.2, xUbuntu 20.10-19.10, 17.04, Fedora 33, CentOS 8, Scientific Linux 7, and Debian 10.0-8.0 can be found at: http://download.opensuse.org/repositories/home:/lineinthesand/

EasyChem is designed to draw chemical molecules in an intuitive way, with a very high quality (designed for book-publishing). Exporting is done to various formats (PostScript, Fig, LaTeX, etc.) to help you integrate your drawing in any software you use.

ChemHelper is aimed at high school students and anybody that does not have a good understanding of chemistry. The objective is to have a program that can teach the basics of chemistry, by having interactive tutorials.

Solve equations, view charts and graphs, make conversions, balance equations and more. Chemistry Calculator.

This is an open source implementation of molecular formula calculation by high resolution MS and MS/MS data as described in M. Meringer, S. Reinker, J. Zhang, A. Muller: MS/MS Data Improves Automated Determination of Molecular Formulas by Mass Spectrometry. MATCH Commun. Math. Comput. Chem. 65, 259-290, 2011. The software user manual is available here: https://www.researchgate.net/publication/307964728_MOLGEN-MSMS_Software_User_Manual Example MS and MS/MS data files for GenForm can be downloaded here: https://sourceforge.net/p/genform/code/HEAD/tree/trunk/data/ A first program call could look like this: GenForm ms=SinapinicAcidMs.txt msms=SinapinicAcidMsMs.txt exist out

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

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.

KherveFitting is a fully Open Source XPS Fitting software that is simple , snappy, easy to use and available across all platforms (Windows, Mac OS, Linux). The software is written in Python using well known libraries: Numpy, lmfit, matplotlib, panda. KherveFitting can open Excel files (.xlsx) or import/convert VAMAS files (.vms) into Excel format. Four background types available: Linear, Shirley, Smart, Adaptive Smart. Drag the red lines on the plot to set the background range. Fit single peaks or doublets. Doublet splitting values are stored in 'DS.txt'. Intensity ratios for doublets: 0.5 for p-shell, 0.67 for d-shell, 0.75 for f-shell. Each peak uses two rows: values in the first row, constraints in the second. Check out the examples in the DATA folder Source files: https://github.com/gkerherve/KherveFitting

MSQuant is a tool for quantitative proteomics/mass spectrometry and processes spectra and LC runs to find quantitative information about proteins and peptides. Though automated it also allows manual inspection and change.

The macOS version of PHREEQC, a program developed by the U.S. Geological Survey for speciation, batch-reaction, one-dimensional transport, and inverse geochemical calculations

Python module for manipulation of Crystallographic Information Framework (CIF) files

PyNanoLab contains a variety of tools to complete the data analysis, statistics, curve fitting, and basic machine learning application. Visualization in pynanolab is based on matplotlib. The setup tools is desinged to control and set-up all the details of the figure with a GUI.

Raman Data Search and Storage (RDSS) software was developed as an analytical tool for a fast and accurate identification of unknown minerals by comparison of their spectra with the indexed library of data. A search function was implemented to enable users to find a specific peak value. Using the asterisk character (*) as a placeholder for one or more unknown peak value(s), the software will return the best match(es). Besides the search utility by the Raman band positions, which was proven to be priceless in the interpretation of Raman spectra, the RDSS software gives the user the ability to display and inspect the Raman spectra quickly and very efficiently. Users can zoom into the Raman spectrum, shift in any direction the wavenumber and the intensity axes, and if any part of the spectral display is clicked, that region will be highlighted and the specific wavenumber returned. A photo for every sample entry stored in the database is also available.

An editor for small organic molecules, written in C using gtk+. It can read and write SMILES and cml and can save to dia's file format. It is suitable for creating chemical molecule diagrams for lower level chemistry/ochem lab reports.

mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.

sciNote is an open source electronic lab notebook (ELN) that helps you manage your laboratory work and stores all your experimental data in one place. sciNote is specifically designed for life science students, researchers, lab technicians and group leaders.

A web-based LIMS (Laboratory Information Management System) · Built in Plone · Professionally supported · Making waves · bi:ka (Zulu): tell it as it is More information and links to manuals, user forums, support and translations are available at https://www.bikalims.org/support-and-service-provision Bika community: www.bikalims.org Main project sponsor, Bika Lab Systems: www.bikalabs.com Inquiries: lemoene@bikalabs.com

Cocoa/Objective-C chemical analysis and computation program; includes gas laws, solutions/solubility, stoichiometry, periodic tables, et alii.