viewmol(1) a graphical front end for computational chemistry programs

SYNOPSIS

viewmol

DESCRIPTION

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. The program's capabilities include:

  • Building and editing of molecules
  • Visualization of the geometry of a molecule
  • Tracing of a geometry optimization or a MD trajectory
  • Animation of normal vibrations or to show them as arrows
  • Drawing of IR, Raman, and inelastic neutron scattering spectra
  • Drawing of an MO energy level or density of states diagram
  • Drawing of basis functions, molecular orbitals, and electron densities
  • Display of forces acting on each atom in a certain configuration
  • Display of Miller planes in crystals
  • Calculation of thermodynamic properties for molecules andreactions
  • Drawings generated by viewmol can be saved as TIFF, HPGL, or PostScript files
  • Animations of normal modes can be converted to a video file (MPEG), e.~g. for inclusion into World Wide Web documents (requires additional programs available on the Internet)
  • Interface to the freeware ray tracing program RAYSHADE (input file generation and use of RAYSHADE from within viewmol)
  • Input and output in a variety of formats, new formats can be added easily by the user viewmol includes a Python interpreter for automation.

At present viewmol includes input filters for DISCOVER, DMOL, GAMESS, GAUSSIAN 9X, GULP, MOPAC, and TURBOMOLE outputs as well as for PDB files (viewmol is therefore suited as a viewer for structural data on the World Wide Web). Structures can be saved as MSI car-files, MDL files, and TURBOMOLE coordinate files. viewmol's file format has been added to BABEL so that BABEL can serve as an input as well as an output filter for coordinates.

viewmol supports a space ball as input device.

The support programs for converting to and from the various coordinate file types may potentially be useful as stand alone utilities. They are split between /usr/share/viewmol (scripts) and /usr/lib/viewmol (C binaries), but individual documentation for them is not available.

AUTHOR

viewmol was written by Jörg-Rüdiger Hill <[email protected]>.

This manual page was written by Drew Parsons <[email protected]> for the Debian GNU/Linux system (but may be used by others).

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