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| arka | 0.11 | GPL | GUI for Genpak (gp) set of bioinformatics utilities. | Arka is a program that (1) serves as a graphical interface for any command line driven programs, with the focus on the programs from the GP package (see http://www.bioinformatics.org/genpak/) (2) has some nice funtions on it's one. Main scope of the program is the manipulation and visualisation of DNA / RNA / protein sequences. The GP package contains many command-line utilities which fullfill a whole bunch of tasks (from DNA sequence searches to restriction analysis and determining the melting temperature of oligonucleotides). While those programs are convenient to use in batch processing and CGI scripts (which was the purpose of those programs), they lack a nice GUI. Arka remembers the options for the GP programs and knows what both the programs and the options do. Besides, it has some gadgets on its own. It requires GTK+, but doesn't need GNOME. Also, it is small and quick. |
| bkchem | 0.5.2 | GPL | Python 2D chemical structure drawing tool | BKchem is a free (as in free software :o) chemical drawing program. It was concieved and written by Beda Kosata. Supported file formats are SVG and CML. The output looks best with the Adobe SVG viewer, but sodipodi and batik do a reasonable job as well. |
| chemtool | 1.6 | GPL | Chemtool is a program for 2D drawing organic molecules | Chemtool is a program for drawing organic molecules easily and store them as a X bitmap, Xfig or EPS file. It runs under the X Window System using the GTK widget set. |
| easychem | 0.3 | GPL | 2D molecular drawing program | EasyChem is a program designed to draw chemical molecules. The problem in all existing programs is: they intend to be easy to use at first try, kind of a quick-and-dirty approach. EasyChem would be a bit difficult to learn, but when you master it, you can be very fast, and with a huge precision. In fact, it's just like a specialized vectorial drawing tool. |
| gabedit | 1.1.4 | BSD | GUI for comupational chemistry | Gabedit is a graphical interface to Molpro2000 and Gaussian98 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. |
| garlic | 1.4 | GPL | Free molecular viewer and editor | Garlic is a full-featured molecular viewer and editor. It is intended mainly for biological macromolecules (proteins and DNA) in PDB format. It can also render high-quality images for presentations or publishing. |
| gchempaint | 0.4.0 | GPL | GNOME 2D chemical structure drawing tool | GChemPaint is a 2D chemical structures editor for the Gnome-2 desktop. GChemPaint is a multi-document application and will be a bonobo server so that some chemistry could be embedded in Gnome applications such as Gnumeric and Abiword. |
| gcrystal | 0.5.4 | GPL | GNOME crystal structure visualization | GCrystal is a light, GNOME2-incorporated model visualizer for crystal structures. |
| gcu | 0.1.7 | LGPL | Backend for Gnome chemistry applications | The Gnome Chemistry Utils provide C++ classes and GTK2 widgets related to chemistry. They are currently used in Gnome Crystal (gcrystal) and Gnome Chemistry Paint (gchempaint). |
| gdis | 0.81 | GPL | A molecular and crystal model viewer | gdis is a graphical program for displaying and manipulating molecular and crystal systems. |
| genchemlab | 0.6 | GPL | General Chemistry Lab Simulator - "GenChemLab" | GenChemLab is an OpenGL-based application intended to simulate several common general chemistry exercises. It is meant to be used to help students prepare for actual lab experience. It could also be used in cases where laboratory facilites are not accessible, for instance in K-12 schools or home schooling. At present, supported experiments include titration, calorimetry, freezing point depression, vapor pressure, and spectrophotometry. |
| ghemical | 1.01 | GPL | Molecular mechanics and quantum mechanics frontend for GNOME. | Ghemical is a computational chemistry software package released under the GNU GPL. Ghemical is written in C++. It has a graphical user interface (in fact, a couple of them), and it supports both quantum-mechanics (semi-empirical and ab initio) models and molecular mechanics models (there is an experimental Tripos 5.2-like force field for organic molecules). Also a tool for reduced protein models is included. Geometry optimization, molecular dynamics and a large set of visualization tools are currently available. |
| gnome-chemistry-utils | 0.2.3 | LGPL | Backend for Gnome chemistry applications | The Gnome Chemistry Utils provide C++ classes and GTK2 widgets related to chemistry. They are currently used in Gnome Crystal (gcrystal) and Gnome Chemistry Paint (gchempaint). |
| gp | 0.26 | GPL | A set of basic utilities for manipulating DNA / RNA / protein sequences. | This is a set of small programs for biologists working with sequence data. The programs are written as a sort of `biological' extension to the standard Unix tools (sed, awk, grep and the whole myriad of little, useful tools). They accept standard input and can spawn the data to standard output, so you can place them in a pipe as any other Unix command or use them in a cgi script. All programs are written in ANSI C, and are supposed to 1) aid manipulate large data sets in intensive batch processing, and 2) faciliate production of cgi-based local web servers providing some basic functions. |
| gromacs | 3.1.4 | GPL | Molecular dynamics package (non-mpi version) | GROMACS is a versatile and extremely well optimized package to perform molecular dynamics computer simulations and subsequent trajectory analysis. It is developed for biomolecules like proteins, but the extremely high performance means it is used also in several other field like polymer chemistry and solid state physics. This version has the dynamic libs and executables; to hack new utility programs you also need the headers and static libs in gromacs-dev. Linux kernel 2.4 or later is STRONGLY recommended on Pentium III and later processors since GROMACS then can use assembly loops with SSE instructions. You can also perform parallel simulations if you install gromacs-lammpi. |
| kmovisto | 0.7.0 | GPL | Molecule viewer and 3-D exporter | KMovisto is a free molecule viewer. This program imports GAUSSIAN or XYZ files and exports POVRay, VRML or XYZ files. |
| molrender | 2.1.5 | GPL | Graphical molecular rendering program. | This package graphically renders 3D molecules based on the output of computational chemistry packages like mpqc. |
| mpqc | 2.1.5 | GPL | Ab-inito chemistry program. | MPQC is the Massively Parallel Quantum Chemistry Program. It computes properties of atoms and molecules from first principles using the time independent Schrödinger equation. It runs on a wide range of architectures ranging from individual workstations to symmetric multiprocessors to massively parallel computers. Its design is object oriented, using the C++ programming language. If you want to use this program on a distributed (parallel) network, you'll also have to install the libmpich package. |
| openbabel | 1.100.1 | GPL | Chemistry software file format converter | Open Babel is a project designed to pick up where Babel left off, as a cross-platform program and library designed to interconvert between many file formats used in molecular modeling and computational chemistry. |
| polyxcalc | 0.7.0 | GPL | Calculation GUI from polyxmass | polyxcalc is a GUI (graphical user interface) program that enables the user to perform any chemical mass calculations onto any molecular mass. polyxcalc is Polymer Definition-aware and can store user-defined chemical recipes, thus being both extensible and programmable. |
| polyxdef | 0.7.0 | GPL | Polymer design GUI from polyxmass | polyxdef is a GUI (graphical user interface) program that enable the user to define a brand new polymer chemistry from scratch by defining the chemical properties of a given polymer. |
| polyxedit | 0.7.0 | GPL | Sequence editor GUI from polyxmass | polyxedit is a GUI (graphical user interface) program that enables the user to edit polymer sequences and simulate chemical reactions on a given polymer sequence so as to later simulate mass spectrometric data obtained on the resulting polymer sequence. This module will understand any polymer definition type that is generated using the polyxdef (see here) module of the polyxmass mass spectrometry software suite. |
| polyxmass | 0.7.0 | GPL | Software suite for mass spectrometry of polymers | The polyxmass mass spectrometric software is a computer framework for mass spectrometry specifically for polymers. This project is modular and involves a number of packages. This wrapper installs the entire binary suite and the user manual. |
| polyxmassdata | 0.7.0 | GPL | Data files for polyxmass suite | polyxmassdata is a non-programmatic package that contains a number of data files needed to operate the polyxmass mass spectrometry software suite. In particular, it contains the atoms' definition file which is absolutely required for proper operation of the polyxmass mass spectrometry software suite. It also contains a number of polymer definition files that are useful to the user so as to understand the process that leads to a proper polymer definition which may be later used in the polymer calculator module (see polyxcalc) or in the polymer editing module. The polymer definition process can be achieved using a specific module, called polyxdef. |
| pymol | 0.93 | Python | PyMOL Molecular Graphics System | PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. It is fully extensible and available free to everyone via the "Python" license. Although a newcomer to the field, PyMOL can already be used to generate stunning images and animations with unprecedented ease. It can also perform many other valuable tasks (such as editing PDB files) to assist you in your research. |
| viewmol | 2.4 | GPL | Molecule viewer and editor | Viewmol is a graphical front end for computational chemistry programs. It is able to graphically aid in the generation of molecular structures for computations and to visualize their results. At present Viewmol includes input filters for Discover, DMol, Gamess, Gaussian 9x, Gulp, Mopac, and Turbomole outputs as well as for PDB files. |
| XCombust | 1.0 | GPL | An elemental analysis calculator | XCombust gives you the %mass of each element for a given chemical formula. It can also help identify multiples of solvent or contaminant molecules from an incorrect elemental analysis. |
| xdrawchem | 1.7.6 | BSD | 2D chemical structures drawing tool | XDrawChem is a two-dimensional molecule drawing program for Unix operating systems. It is similar in functionality to other molecule drawing programs such as ChemDraw (TM, CambridgeSoft). It can read and write MDL Molfiles and CML files to allow sharing between XDrawChem and other chemistry applications. |
| Xentark | 2.1.0 | GPL | CRK computational engine | The Chemical Resource Kit is several interdependent application packages, which collectively combine to form an integrated tool to assist with certain chemical information problems. Xentark is the computational arm of the Chemical Resource Kit. It has no graphical interface, and is usually spawned by using Xykron to setup the parameters then launch the calculation. Nonetheless, it is a standalone application, and may be run from the command line. |
| xmakemol | 5.11 | GPL | Simple XYZ molecule editor and GL viewer | XMakemol can be used to view and manipulate atomic and molecular data given in xyz format. XMakemol can produce output in PostScript (black and white or colour)and in xpm format (which can be translated to gif format using xpmtoppm and ppmtogif). XMakemol can also produce a series of xpm files which can be translated into an animated gif file using the bundled utility xmake_anim.pl (formerly gmake_anim.pl). |
| Xortoth | 2.1.0 | GPL | CRK dataserver and web interface | The Chemical Resource Kit is several interdependent application packages, which collectively combine to form an integrated tool to assist with certain chemical information problems. Xortoth sets up a SQL database and a web interface at: http://localhost/CRK |
| Xuru | 2.1.0 | GPL | CRK scheduling and clustering daemon | The Chemical Resource Kit is several interdependent application packages, which collectively combine to form an integrated tool to assist with certain chemical information problems. Xuru is a daemon which controls scheduling and clusters for CRK calculations. |
| Xykron | 2.1.0 | GPL | CRK graphical frontend | The Chemical Resource Kit is several interdependent application packages, which collectively combine to form an integrated tool to assist with certain chemical information problems. Xykron is the graphical front-end to the whole Chemical Resource Kit. It is monolithic in nature, and provides the primary gateway to the whole package. Seemless interfaces are provided to two types of so-called Realms: direct access to local files, and online access to repositories, managed through the Xortoth 3-tier mechanism. NOTE: To install examples and templates, execute: $ install-CRK-demos |
There is sufficient light for those who desire to see,
and there is sufficient darkness for those of contrary disposition.
— Blaise Pascal, Pensees 149
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