Keywords: viewmol

# 9 Script tools

VIEWMOL can be extended using Python scripts. A number of such scripts are part of the VIEWMOL distribution and come installed in the ``Run script" menu or as output filter. The following scripts are included:

- Demonstration
  This script runs a short demonstration of VIEWMOL's capabilities. It can be interrupted by pressing Ctrl-C.
- Set atom colors

  Figure 15: The dialog to change atom colors

  This script allows to interactively change the colors for an element. It allows to save the changes to the `viewmolrc` file so that manual editing of this file might no longer be necessary. If started from the ``Set atom colors" submenu entry a dialog as shown in Fig. 15 is presented4. The pulldown menu at the top allows to select which element to operate on. It contains all the elements from the molecule(s) currently loaded in VIEWMOL. The four colored boxes and associated buttons allow the selection of the element color, the emission color, the ambient color, and the specular color. Pressing the button brings up a color selection dialog. Beneath the buttons there are two sliders which allow to change the transparency and the shininess for the selected element. The three buttons at the bottom allow the user to confirm the changes and therefore apply them permanently to the molecule(s), to confirm the changes and also save them in the `$HOME/.viewmolrc` file in the users `HOME` directory, or to cancel the changes and reverting back to the original colors.
- Template
  This is a script template which shows how to make Python scripts register themselves with VIEWMOL. It does nothing useful.
- UFF optimization
  If you have TURBOMOLE this script can be used to perform a geometry optimization using the UFF module shipping with TURBOMOLE. The necessary input files are generated, the UFF optimization is performed, and the resulting structure is read back.
- Gaussian 98 input file

  Figure 16: The dialog to create an input file for GAUSSIAN 98

  This script generates a complete input file for GAUSSIAN 98. It is not accessible from the ``Run script" menu, but is installed as output filter and can therefore be accessed through the ``Molecule/Save molecule ..." menu items. The script presents the dialog shown in Fig. 16 which allows setting of various options for GAUSSIAN 98. This script is courtesy of Stephan Schenk (stephan.schenk@uni-jena.de).

#### Footnotes

... presented4
  This script requires Tkinter and the Python Mega Widgets (Pmw) to be installed. Tkinter is usually available with Python. The Python Mega Widgets can be found at http://pmw.sourceforge.net/.