Open Source Python Chemistry Software - Page 5

Quantum Monte Carlo algorithms expressed in Python. This code calculates electronic properties of atoms and molecules from first principles.

Refl2EXAFS is an utility for the analysis of extended x-ray absorption fine structure (EXAFS) data collected in total reflection mode (reflEXAFS).

Soluton Percenter is a program for making solutions percent. Maked by python and PyQt4 module. For chemists, mathematicians and barmans. Program can create advanced recipes and print them.

A repository of Python extension scripts for use with the Sparky (http://www.cgl.ucsf.edu/home/sparky) NMR assignment package. No packaged releases yet, but there are scripts in the Sourceforge CVS@ http://sparkyscripts.cvs.sourceforge.net/sparkyscripts

Sudsy is a saponification calculator coded in Python. The CLI works fine, but the PyGTK version still needs some work...The interface is designed and it starts up, but some of the callbacks still need to be implemented. Let me know if you can help.

SunlightDPD provides a home for open source codes related to the dissipative particle dynamics (DPD) simulation method. Currently the file release contains the HNC integral equation code.

SuperG is a code library written in Python intended to quickly enable programmers in a scientific environment to manage data files created by dispersed scientific instrumentation.

The CCP1GUI project aims to develop a free, extensible Graphical User Interface to various computational chemistry codes developed by the worldwide academic community, with an emphasis on ab initio Quantum Chemistry codes.

TheoChemPy is a python library providing common functionalities for Theoretical and Computational chemists.

ThermV thermal analysis software package aims to provide the most sophisticated automatic analysis of thermal analysis data (TG/DTG, DTA and DSC). It offers new algorithm for concurrent peak deconvolution at different heating rates and provides full kinetic analysis of these data, including isoconversional methods for Ea, determination of reaction model and full kinetic triplet, Avrami coefficients, and dimensionality of crystal growth for reactions in the solid state. The project is currently in alpha stage, where individual modules will be provided for data analysis. The modules for peak deconvolution, peak profile analysis and determination of Ea and lnA will be provided first. Full GUI will be provided in beta stage. Due to computational limitations, the code is partly programmed in Python and partly in R. Python code will eventually be fully integrated into GUI. R code might remain standalone, although it will be integrated to a highest possible degree. Distributed under GPL

Vibeplot presents a new and attractive way to visualize vibrational analysis from density functional calculations (DFT). It is especially targeted at the chemists. The interface can either be scripted or used interactively with QVibeplot.

A tool for visualization, classification, and quantification of three-dimensional secondary ion mass spectrometry data.

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 quantum optimal control. 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

WebBabel is a python web application using OpenBabel to convert files from one format to another. It runs under Windows, Mac or Linux on your desktop, workstation or laptop. It uses the Jmol (or Marvin) viewer to show the structures being converted.

Sharing lists of molecular structures with associated chemical properties is a common task in computer-aided drug design and medicinal chemistry. WebChem Viewer is a simple, free, open-source program that generates HTML-formatted output that can be viewed in any modern web browser, on any operating system (including mobile), without requiring the installation of additional software. The output can also be easily incorporated into existing web pages. WebChem Viewer is released under the FreeBSD license. It was created by Jacob Durrant, a post-doc in the lab of Rommie E. Amaro.

XD-shell - is a shell (console) interface to XD program which deals with experimental electron density refinement.

BINANA (BINding ANAlyzer) is a python-implemented algorithm for analyzing ligand binding. The program identifies key binding characteristics like hydrogen bonds, salt bridges, and pi interactions. As input, BINANA accepts receptor and ligand files in the PDBQT format. PDBQT files can be generated from the more common PDB file format using the free converter provided with AutoDockTools. As output, BINANA describes ligand binding. NOTE: The latest version of BINANA is now hosted at http://git.durrantlab.com/jdurrant/binana . Versions on SourceForge are not up to date.

--UPDATE-- New Version is now integrated in the official PyMOL plugin repository! --UPDATE-- The BNI (Beyond Normal Interaction)- Tools is a plug in for the PyMOL molecular visualization system which adds additional functionalities and presets to the PyMOL GUI and also adds useful extended commands.

Python software to control Bronkhorst flow controllers via RS232. Works via USB serial converter too.

Cca-forum unifies the Common Component Architecture tools and tutorial. It includes the CCA specifications, the Ccaffeine framework for HPC, and related tools. These support multilanguage scientific and parallel computing.

IMPORTANT! As of version 1.2, cclib development has moved to github. Please use the flowing pages for up-to-date information about cclib: Repository (source code, tracker) - https://github.com/cclib/cclib Online documentation - http://cclib.github.io/ cclib is an open source library, written in Python, for parsing and interpreting the results of computational chemistry packages. It currently parses output files from ADF, Firefly, GAMESS, GAMESS-UK, Gaussian, Jaguar and ORCA.

Since I use GUI tools which only save the molecules to regular zmatrix format. I created a script that would convert the regular format to the special orca format. It is written in python and can be used like this. usage: convert2orcazmatrix.py [-h] -i INPUTFILE [-o OUTPUTFILE]

A drawing program for chemical structure formulas, in the vein of chemtool, BKChem, EasyChem, or Xdrawchem.

defunct

dmaControl is a DMA (differential mobility analyzer) control software for aerosol measurements.