Open Source Chemistry Software - Page 5

BioNLP-Corpora is a repository of biomedically and linguistically annotated corpora and biomedical data sources. There are many resources available in separate packages in this project.

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

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

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.

OpenGrowth is a research program which grows new ligands in proteins by connecting small organic fragments. The details can be found in the original publication "OpenGrowth: an automated and rational algorithm for finding new protein ligands" (J. Med. 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. Chem. Inf. Mod., http://pubs.acs.org/doi/abs/10.1021/acs.jcim.6b00610). For any questions, please send emails exclusively at opengrowth-discuss@lists.sourceforge.net.

PUPIL (Program for User Package Interface and Linking), is a software environment that allows developers to link quickly and efficiently together multiple pieces of software in a fully automated multi-scale simulation. More specifically, it supports QM/MM MD simulations where the user might choose among any of the different MD engines and QM engines, which are connected to PUPIL as external programs through a tiny specific interface. One of the main advantages here is that the user can use most of the functionalities that may have those external programs interfaced without the necessity to be reimplemented again on independent interfaces. In fact, this simulation interface concentrates all the common code involved in the coupling terms of the QM/MM approach.

Simulation of back reflection Laue diffraction images.

VMS Draw provides general utilities (e.g. normalization, conversion, and other manipulations of several spectra at the same time) and a flexible graphical user interface (GUI) for an easy use by non-specialists which allows a seamless flow of information between experimentally and theoretically oriented researchers. Finally, it permits effective interactions with other electronic structure codes [e.g., nuclear magnetic resonance (NMR), microwave] even if Gaussian 16 offers the widest set of methods for computational spectroscopy.

sdf file viewer

sdsorter provides convenient routines for manipulating the contents of sdf molecular data files based on the embedded sd tags.

IQuant is an automated pipeline for quantitative proteomics based upon isobaric tags. It integrates post-processing tool of protein identification and advanced statistical algorithms to process the MS/MS signals generated from the peptides labeled by isobaric tags for quantification. IQuant can run from a graphical user interface (GUI) as well as a command-line interface and work with both Windows and Linux system. This website contains the IQuant software, an example data labeled by iTRAQ-8plex for testing and a user's manual. If you have any question about IQuant, please contact me: wenbo@genomics.cn. The source code of IQuant can be found here "https://sourceforge.net/p/iquant/code/".

The oxDNA code has been moved to https://github.com/lorenzo-rovigatti/oxDNA, please go there for new releases.

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

Balances any complex chemical equation easily. Version: v 1.0 and v 2.0 both are available.

A very simple program. For balancing chemical equations and for converting units (Temperature, Weight, Pressure, Volume, Radiation, etc). It is coded with Qt Creator For Win 64 bit and Linux 64 bit, using Qt lib. I am working on a Linux version. I have tested it with Kubuntu 18.04 and 20.10 and OpenSUSE Tumbleweed. It is 64 bit. I compiled with Qt Creator. Best of all, I provide the source code and ALSO THE EXECUTABLE FOR LINUX! -Tested with Kubuntu 18.04, 20.10, 22.04 -Tested with OpenSUSE Tumbleweed -Tested with Ubuntu 20.04, 22.04 -Tested with Linux Mint 20.1 (XFCE interface)

DIANNA (Diffraction Analysis of Nanopowders) is a free software developed to simulate atomic models of structures from an ensemble of nanoparticles and to calculate their whole X-ray powder diffraction patterns and the radial distribution function. The main objects of investigation are the particles whose coherent scattering domains do not exceed several nm. DIANNA is based on the ab initio method using the Debye scattering equation. This method makes it possible to obtain information on the atomic structure, shape and size of nanoparticles. It can be applied also to non-periodic materials or coherently ordered structures. How to use: 1. Unzip the archive. 2. Run the "Dianna_Startup.exe" file. 3. Use "Help" through the menu. Required: • Windows 7 or newer • Microsoft .NET Framework 4: www.microsoft.com/en-US/download/details.aspx?id=17851 (Web Installer, 1 Mb) www.microsoft.com/en-us/download/details.aspx?id=17718 (Standalone Installer, 48 Mb) • Microsoft Visual C+

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.

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

A Mac OS X App to time your film development processes, f.ex. rotary process phases (like E6, C41). New processes can be added simply by adding a CSV file.

Quantities provides an interface to the use of numbers which are associated with a dimension and a unit (physical quantities) in computer calculations (quantity calculus) just like C++ built-in types.

Bioinformatics related demos and tutorials using the R programming language for large biological data. Licence: Creative Commons Attribution-NonCommercial 4.0 International License

ccwatcher monitors the progress of computational chemistry calculations during runtime. It has both a GUI and a "Command Line Interface" to which it parses important output and plots SCF energies.

A Java program to paint the experimental and theoretical data obtained of STM and AFM.