PyVib2 Hints and Tricks

• Animated GIFs under Windows
• Adding new chemical elements to PyVib2

Animated GIFs under Windows

Please make sure that you have properly installed Netpbm and Gifsicle. There are Windows versions of the programs and the Cygwin ports available. The following executables must be accessible from the command prompt (be on PATH):

• ppmcolormap
• pnmremap
• ppmtogif
• gifsicle

Note

PyVib2 1.0 requires the which command to be accessible as well (installed by default with Cygwin). As of PyVib2 1.1, it is not a requirement anymore.

Warning

If you are going to use Netpbm from GnuWin32, the author of PyVib2 does not recommend to install version 10.27. Version 10.18.4 has been found to work properly.

To check if the executables are on PATH:

• start a command prompt (cmd.exe)
• invoke the aformentioned executables

If at least one of the executable has not been found:

• find where the executables physically on the disc are and note their parent directories
• go to Start ‣ Control Panel ‣ System ‣ System properities and select the Advanced tab
• add the directories (separated by ;) to the PATH variable (create one if necessary)
• apply these changes
• open a new command prompt and repeat the tests. Do not use a command prompt started before the changes have been applied.

Finally, test if gifs can be produced properly:

• save benzene_test.ppm to any directory, the background color of this image is #646464

• start a command prompt and change to that directory

• perform the following two calls:

  c:\> pnmcolormap 256 benzene_test.ppm > palette
  c:\> pnmremap -mapfile palette benzene_test.ppm | ppmtogif --transparent=#646464 > benzene_test.gif

• the produced transparent benzene_test.gif should look like this:

  

Adding new chemical elements to PyVib2

If you are opening a file and the program is complaining “Unknown element XX”, then you have to introduce that element to PyVib2 by adding the relevant line to the pse.dat and isotopes.dat files.

If you are using either of the “frozen” program versions available for Mac OS X/Windows, then the two files are to be found in the pyviblibdata/util subdirectory of where the correspondent distribution archive has been unpacked.

Otherwise, please execute a couple of Python statements that should print the directory where the files are:

>>> import pyviblib, sys, os
>>> sys.stdout.write(os.path.join(pyviblib.get_rootdir(), 'util', '\n'))

Please refer to the manual (version 1.0: section 4.13 on page 67) to learn how to add the necessary data to the files.