24 projects tagged "Chemistry"
Updated 16 Nov 2004
Viewmol
| Pop | 56.89 |
|---|---|
| Vit | 2.56 |
Viewmol is a program for building and editing molecules as well as for the visualization of outputs from quantum chemical and molecular mechanics programs. Currently supported are Gaussian 9x, Gamess, Discover, DMol/DSolid/DMol3, Gulp, Mopac, Turbomole, and PDB files. Properties visualized include geometry (with various drawing modes), vibration (animated or with arrows), optimization history/MD trajectories, MO energy level diagram, MOs, basis functions, and electron density. Drawings can be saved as TIFF, HPGL, Postscript, and input files for Rayshade. Viewmol has an embedded Python interpreter for automation. The program is language independent and currently "speaks" English, French, German, Russian, or Spanish.
Updated 14 Feb 2012
VMD
| Pop | 132.19 |
|---|---|
| Vit | 17.11 |
VMD (Visual Molecular Dynamics) is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. VMD uses OpenGL and OpenGL Programmable Shading Language for high performance rendering of large structures.
Updated 07 Jan 2010
BKChem
| Pop | 111.00 |
|---|---|
| Vit | 13.58 |
BKChem is a chemical drawing program.
Updated 01 Apr 2003
frowns
| Pop | 22.32 |
|---|---|
| Vit | 1.00 |
frowns is a chemoinformatics toolkit geared toward rapid development of chemistry-related algorithms.
Updated 23 Mar 2004
ODPdom
| Pop | 19.05 |
|---|---|
| Vit | 1.00 |
ODPdom is a simple DOM (Document Object Model) parser. It can process large XML files.
Updated 04 Aug 2004
PhosphoFind
| Pop | 18.55 |
|---|---|
| Vit | 1.00 |
PhosphoFind locates and quantifies phosphorylated peptides and proteins from a set of four MALDI mass spectra run in linear positive, linear negative, reflectron positive, and reflectron negative modes.
Updated 24 Aug 2004
pyPeriod
| Pop | 21.70 |
|---|---|
| Vit | 56.49 |
pyPeriod is a periodic table of elements. A wxPython and a Tkinter GUI are included. It enables calculation of molecular masses and shows data for every element.
Updated 16 Jan 2007
esra
| Pop | 27.42 |
|---|---|
| Vit | 2.46 |
Esra is a scriptable, scalable, and highly hackable molecular mechanics library for Java. Its primary purpose is the statistical analysis of trajectory data generated with packages such as GROMOS, GROMACS, or AMBER, but it can also be used as a standalone package for performing simple molecular dynamics and Monte-Carlo simulations. It can be scripted with Jython, Mathematica, or Matlab.
Updated 07 Dec 2010
BALL
| Pop | 43.68 |
|---|---|
| Vit | 3.94 |
The Biochemical ALgorithms Library (BALL) is a framework for rapid application development in molecular modeling and structural bioinformatics. BALL provides an extensive set of data structures as well as classes for molecular mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, NMR shift prediction, and visualization. Its extensibility results from an object-oriented and generic programming approach.
Updated 11 Jan 2006
PyDespike
| Pop | 11.83 |
|---|---|
| Vit | 1.00 |
PyDespike is a graphical cross-platform program for despiking Raman and other spectroscopic data. It supports multiple data scans per file, graph zooming, and an easy, graphical mechanism for removing anomalous spikes due to background noise in Raman data.
