Open Source Chemistry Software - Page 6

The Chemical Manager application can be of great help to Organic Chemistry Departments. University research groups will benefit from using this application, since it was optimized for their needs. Currently, Technion Chemistry department is benefiting from it.

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

A Suite of Programs implementing a fast approach to the Debye Function Analysis (DFA) of powder diffraction data from nanocrystalline and/or non-ordered materials. See J. Appl. Cryst. 2015, 48, 2026-2032

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.

The JCAMP-DX project is the reference implemention of the IUPAC JCAMP-DX spectroscopy data standard.

This is a standalone program for a) the calculation of diffusion coefficients of sorbates inside nanoporous materials at different loadings by using transition rate constants and for b) solving the master equation for a system consisted of a large number of unit cells per each direction. It is based on the following published paper "Kolokathis, P. D., Braun, O. M.. J. Comput. Chem. 2019, 40, 2053– 2066. DOI: 10.1002/jcc.25857"

SME LibreAquarium is an Aquarium management system with a Simulation Model Engine (SME) that makes a prediction of the possible measurement values for the different pollutants that affect to these aquatics systems (NO3,PO4, Fe). The simulator consults the recorded analysis to calculate a prediction of the NO3, PO4, Fe, that the these aquatic system produce. It also uses a central (fish, plant and invertebrates) database to check if the actual parameters are Ok, depending on the species that live in the Aquarium. With all the records, the Simulation Model predicts the algae risk too (low,medium,high) and the algae type(green,cyanotic.) using the Redfield coefficient. Appart from that, the program tries to bring another modest contribution to Open Source Software and the World of Aquariums. SME LibreAquarium helps to daily maintenace of the aquarium with habitants control(fishes,plants, invertebrates), expenses, statistics, alarms, etc.

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.

MGFp is open parser implementation for the Mascot Generic Format (MGF). It uses bison/flex to define a formal grammar and provides the necessary C++ adapter classes. The software is provided under a BSD license. Development on SF.net has ceased. You can find the project at http://kirchnerlab.github.com/libmgf/

µic is a modelling engine for simulations of microstructural development. It takes localied behaviours as input from the user and integrates the global behaviour, with the calculation of all interactions as required by the application.

Mychem is a chemoinformatics extension for MySQL.

Octet is an object-oriented molecular representation framework written in Java.

Attn: the latest version of PeptideProphet must be obtained as part of the Trans-Proteomic Pipeline package at http://sourceforge.net/projects/sashimi/.

PySpline is a graphical, cross-platform program for processing X-ray absorption spectroscopy (XAS) and Extended X-ray absorption fine structure (EXAFS) data. It allows processing parameters to be adjusted and observe the effect on R-space data.

Scalable Molecular Analysis Solver for High-performance computing systems (SMASH) is massively parallel software for quantum chemistry calculations and released under the Apache 2.0 open source license. It is currently capable of energy, analytical gradient, and geometry optimization calculations of Hartree-Fock theory and Density Functional Theory (DFT), and energy calculations of Second-order Moller-Plesset (MP2) perturbation theory. DFT calculations can be performed on 100,000 CPU cores with high parallel efficiency.

SPARTA is a parallel DSMC code for performing simulations of low-density gases in 2d or 3d. Particles advect through a hierarchical Cartesian grid that overlays the simulation box. The grid is used to group particles by grid cell for purposes of performing collisions and chemistry. Physical objects with triangulated surfaces can be embedded in the grid, creating cut and split grid cells.

The TheoDORE (Theoretical Density, Orbital Relaxation and Exciton analysis) package is a general purpose program suite for the analysis of excited states obtained from quantum chemical excited state calculations. Wavefunction analysis is based on state and transition density matrices, which provides a unified formalism applicable independent of the wavefunction model. 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

UPDATE: LATEST VERSION AT http://git.durrantlab.com//jdurrant/wisp Allostery can occur by way of subtle cooperation among protein residues (e.g., amino acids) even in the absence of large conformational shifts. Dynamical network analysis has been used to model this cooperation, helping to computationally explain how binding to an allosteric site can impact the behavior of a primary site often many angstroms away. Traditionally, computational efforts have focused on the most optimal path of correlated motions leading from the allosteric to the primary active site. We present a program called Weighted Implementation of Suboptimal Paths (WISP) capable of rapidly identifying additional suboptimal pathways that may also play important roles in the transmission of allosteric signals. Aside from providing signal redundancy, suboptimal paths traverse residues that, if disrupted through pharmacological or mutational means, could modulate the allosteric regulation of important drug targets.

Bmrblib is a Python API abstracting the Biological Magnetic Resonance Data Bank (BioMagResBank or BMRB) NMR-STAR format (http://www.bmrb.wisc.edu/). It allows the writing of NMR-STAR files for BMRB data deposition and the reading and easy extraction of data from files residing in the BMRB data bank, all without knowledge of the Self-Defining Text Archive and Retrieval (STAR) format.

MatNMR is a highly flexible toolbox for processing 1D and 2D NMR/EPR spectra in MATLAB and creating high-quality 1D, 2D or 3D plots. Fully GUI and/or script-based.

NESSY is an open source software to analyse NMR relaxation dispersion data of either CPMG or R1p (R1rho) dispersion experiments. The graphical interface enables simple management of large experimental data sets and simple and automated analysis. NESSY automatically calculates effective transverse relaxation rate (R2eff) and performs model selection between different relaxation dispersion models.

The program Orthos is developed to performed simulation (including nonlinear least-squares fitting) of EPR spectra of nitroxide biradicals. The program capabilities include simulation of rigid-limit and slow-motional spectra, of both isotropic and aligned samples. The spectra of multiple paramagnetic species, both bi- and monoradicals can be modeled. NB: Please note that now (as of Nov 2016) the distribution is being updated so that to improve reliability, OS-universality, and the quality of documentation. If you have any troubles installing/compiling/using the software, please contact me. I would be glad to help.

Schur is a standalone program for interactively calculating properties of Lie groups and symmetric functions. Schur has been designed to answer questions of relevance to a wide range of problems of interest to chemists, mathematicians, computer scientists,...

The program does nmr product operator calculations for one, two, three and four spins. Receiver phase cycling is possible in conjunction with pulse phase cycling to simulate coherence pathway selection. An extensive manual and help files are included. Currently running under Linux and Windows.

xylib is a portable library for reading x-y data from powder diffraction, spectroscopy and other experimental methods. Supported formats: VAMAS, pdCIF, Bruker, Philips, Rigaku DAT, Sietronics CPI, DBWS/DMPLOT, Koalariet XDD and others.