[[Science::chemistry]]

GAMGI: GAMGI (General Atomistic Modelling Graphic Interface) is a program to build, view, and analyze atomic strucures such as molecules, crystals, glasses, liquids, etc. It aims to be useful for: the scientific community working in Atomistic Modelling that needs a graphic interface to build input data and to view and analyse output data, calculated with Ab-Initio and Molecular Mechanics programs; the scientific community at large studying chemistry, physics, materials science, geology, etc., that needs a graphic interface to view and analyse atomic structural information and to prepare images for presentations in classes and seminars; teaching chemistry and physics in secondary schools and universities; science promotion in schools, exhibitions and science museums.

GDIS: "GDIS' is a GTK/OpenGL based program for displaying isolated molecules, periodic systems, and crystalline habits. It also acts as a GUI to packages such as GAMESS, GULP, and POVRay to provide energy minimizations and publication quality rendering.

GElemental: gElemental is a periodic table viewer that provides detailed information on the chemical elements. It is a port of GPeriodic to C++ and gtkmm, and it offers an improved UI, an updated and corrected data set, a better data format, a list view, and easier coloration.

GPeriodic: GPeriodic is a periodic table application for GNU/Linux. It allows you to browse through a periodic table of the elements, and view detailed information on each of the elements. 118 elements are currently listed.

GROMACS: GROMACS simulates molecular dynamics. It is primarily designed for biochemical molecules like proteins and lipids that have many complicated bonded interactions, but since it is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) it is also used for research on non-biological systems, e.g. polymers. GROMACS is user-friendly, with topologies, parameter files, and error messages written in clear text format. There is a lot of consistency checking, but no scripting language: all programs use a simple interface with command line options for input and output files.

Gabedit: 'Gabedit' is a graphical interface to the Molpro and Gaussian computational chemistry packages, running locally or on a remote server. It includes a 3D molecule editor and viewer. Most major molecular file formats are supported, and graphics can be exported in many formats.

Gdpc: 'gdpc' is a tool for visualising the output files of a molecular dynamic simulation. It can be customized to read almost any input file format, animate it, and output images of each frame.

GenChemLab: 'GenChemLab' is an OpenGL-based application intended to simulate several common general chemistry laboratory exercises. It is meant to be used to help students prepare for actual lab experience. Supported experiments include titration, calorimetry, freezing point depression, vapor pressure, electrochemistry, and spectrophotometry.

Ghemical: Ghemical is a molecular modelling software package with a GUI (one for the GLUT library, and another for GNOME), and some nice 3D-visualization tools. It supports methods based on both molecular mechanics and quantum mechanics (using MOPAC7, and MPQC for QM). The geometry optimization (for MM and QM) and molecular dynamics (for MM) algorithms are included.

ImageJ: ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.4 or later virtual machine.

Interval RPN Calculator: This terminal app runs on PCs or laptops running Windows, OSX or GNU/Linux. It attempts to mimic the functionality of an HP ReversePolishNotation [RPN] calculator with the added enhancement of interval output. So along with your answer, you get a good idea of its trustworthiness.

Jmol: Jmol is a molecule viewer and editor. It is a collaboratively developed visualization and measurement tool for chemical scientists. It can read a variety of file types and print and export images. It can animate the results of simulations.

KNIME: KNIME [naim] is a user-friendly graphical workbench for the entire analysis process: data access, data transformation, initial investigation, powerful predictive analytics, visualisation and reporting. The open integration platform provides over 1000 modules (nodes), including those of the KNIME community and its extensive partner network.

Kci: The kc program is a "kinetic compiler". This means it is able to transform chemical equations into simulation programs.

Lamprop: 'lamprop' calculates some properties of fiber-reinforced composite laminates. It calculates engineering properties like Ex, Ey, Gxy, thermal properties CTE_x and CTE_y, physical properties like density and laminate thickness, and stiffness and compliance matrices.

Lhendraw: Chemical drawing program for the cdx/cdxml formats. This one tries to be as close and completely as possible to the proprietary reference implementation without forfeiting the KISS principle. It offers a database-less search function and a headless mode for automated editing

Librsb: librsb is a library for sparse matrix computations featuring the Recursive Sparse Blocks (RSB) matrix format. This format allows cache efficient and multi-threaded (that is, shared memory parallel) operations on large sparse matrices. The most common operations necessary to iterative solvers are available, e.g.: matrix-vector multiplication, triangular solution, rows/columns scaling, diagonal extraction / setting, blocks extraction, norm computation, formats conversion. The RSB format is especially well suited for symmetric and transposed multiplication variants. On these variants, librsb has been found to be faster than Intel MKL's implementation for CSR. Most numerical kernels code is auto generated, and the supported numerical types can be chosen by the user at build time. librsb implements the Sparse BLAS standard, as specified in the BLAS Forum documents.

MayaChemTools

MayaChemTools is a growing collection of Perl scripts, modules, and classes to support day-to-day computational discovery needs. The current release of MayaChemtools provides command line scripts for the following tasks:

Manipulation of SD, CSV/TSV, Sequence/Alignments, and PDB files
Analysis of data in SD, CSV/TSV, and Sequence/Alignments files
Information about data in SD, CSV/TSV, Sequence/Alignments, PDB, and fingerprints files
Exporting data from Oracle and MySQL tables into text files
Properties of periodic table elements, amino acids, and nucleic acids
Generation of fingerprints corresponding to atom neighborhoods, atom types, E-state indicies, extended connectivity, MACCS keys, path lengths, topological atom pairs, topological atom triplets, topological atom torsions, topological pharmacophore atom pairs, and topological pharmacophore atom triplets
Generation of fingerprints with atom types corresponding to atomic invariants, DREIDING, E-state, functional class, MMFF94, SLogP, SYBYL, TPSA and UFF
Calculation of similarity matrices using a variety of similarity and distance coefficients
Calculation of physicochemical properties including rotatable bonds, van der Waals molecular volume, hydrogen bond donors and acceptors, logP (SLogP), molar refractivity (SMR), topological polar surface area (TPSA), and so on

Melting: Melting computes, for a nucleic acid duplex, the enthalpy and entropy of the helix-coil transition, and then its melting temperatures. Three types of hybridisation are possible: DNA/DNA, DNA/RNA, and RNA/RNA. The program uses the method of nearest-neighbors. The set of thermodynamic parameters can easily be changed, for instance following an experimental breakthrough.

Minfx: The minfx project is a Python package for numerical optimisation, being a large collection of standard minimisation algorithms. This includes the line search methods: steepest descent, back-and-forth coordinate descent, quasi-Newton BFGS, Newton, Newton-CG; the trust-region methods: Cauchy point, dogleg, CG-Steihaug, exact trust region; the conjugate gradient methods: Fletcher-Reeves, Polak-Ribiere, Polak-Ribiere +, Hestenes-Stiefel; the miscellaneous methods: Grid search, Simplex, Levenberg-Marquardt; and the augmented function constraint algorithms: logarithmic barrier and method of multipliers (or augmented Lagrangian method).

OpenBabel: Openbabel is a program and library designed to interconvert between many file formats used in molecular modeling and computational chemistry. The command-line utility that comes with OpenBabel is meant to be a replacement for the original 'babel' program, to translate between various chemical file formats. The library includes the file-translation code as well as utilities to help develop other free software chemistry software.

OpenChrom: OpenChrom is data analysis a tool for gas chromatography and mass spectrometry. Its functionality and algorithms can be extended using a flexible plugin approach. File formats from various vendors are supported.

Pathomx: Pathomx is a workflow-based tool for the analysis and visualisation of experimental data. Initially created as a tool for metabolomic data analysis is has been extended and can now be used for any scientific and non-scientific data analysis. The software functions as a hybrid of workflow and script-based approaches to analysis. Using workflows it is possible to construct rapid, reproducible analysis constructs for experimental data. By combining this with custom inline scripting it is possible to perform any analysis imaginable. Workflows can be dynamically re-arranged to test different approaches and saved to track the development of your approach. Saved workflows can also be shared with other users or groups, allowing instant reproduction of results and methods. Tools can export images as publication-ready high resolution images in common formats.

Polyxmass: Polyxmass is a mass spectrometry software. It allows the definition of polymer chemistries and the simulation/analysis of mass spectrometric data obtained on (bio)polymers.

PyMOL: PyMOL is a molecular visualization system created by Warren Lyford DeLano and commercialized initially by DeLano Scientific LLC, which was a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities. It is currently commercialized by Schrödinger, Inc. PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, such as proteins. PyMOL is one of a few free visualization tools available for use in structural biology. The Py portion of the software's name refers to the fact that it extends, and is extensible by the Python programming language. PyMOL uses OpenGL Extension Wrangler Library (GLEW) and Freeglut, and can solve Poisson–Boltzmann equations using the Adaptive Poisson Boltzmann Solver.

Pycomedi: This package provides an object-oriented interface to the Comedi drivers. The standard Python interface bundled with Comedilib is a simple SWIG clone of the C interface. In pycomedi, we convert the functions into class methods (see pycomedi.classes), so you don't have to worry about dragging around opaque types like comedi_t * device pointers. We also bundle related constants together in _Enums and _Flags (see pycomedi.constants), to make handling common operations like flag manipulations simpler. Finally, there are a number of utility classes (see pycomedi.utility) to make common tasks like creating instructions or reading hardware-timed analog input easier.

Relax: relax is a program designed for the study of molecular dynamics of organic molecules, proteins, RNA, DNA, sugars, and other biomolecules through the analysis of experimental NMR data. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model or ensemble analysis and frame order dynamics theories using anisotropic NMR parameters such as RDCs and PCSs, the investigation of stereochemistry in dynamic ensembles, and the analysis of relaxation dispersion.

Rstudio: An integrated development environment (IDE) for R. R is a programming language and software environment. RStudioIt includes a console, syntax-highlighting editor that supports direct code execution, tools for plotting, history, debugging and workspace management.

Thermopy: Some utilities for Thermodynamics and Thermochemistry.

XDrawChem: XDrawChem is a 2D molecule drawing program. Features include fixed length and fixed angle drawing, a ring tool to automatically draw rings, and automatic alignment of structures (for reactions). The programs supports MDL Molfile and CML (Chemical Markup Language) file formats.

Xem: Chemistry program that calculates Ph balance. You specify acids and bases from a given list, and in what concentration and volume, and the program figures the Ph.

Xmakemol: XMakemol is a mouse-based program, written using the LessTif widget set, for viewing and manipulating atomic and other chemical systems. It reads XYZ input and renders atoms, bonds and hydrogen bonds.
Features include:
- Animating multiple frame files - Interactive measurement of bond lengths, bond angles and torsion angles - Control over atom/bond sizes - Exporting to Xpm, Encapsulated PostScript and XYZ formats - Toggling the visibility of groups of atoms - Editing the positions of subsets of atoms

Z--PeerLibrary: PeerLibrary is an free software project developing a collaborative online community where scholars and researchers can discover, read, and discuss scholarly literature all within one site. This project focuses on expediting access to publications, enabling public recordings of analysis and insights on said publications, and encouraging collaboration and openness in the development of science.

Free Software Foundation!

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