Chemical Mime.

Supporting scripts and code.

This is still work in progress (January 2003).

The purpose of this work is to provide a means for dealing with files of chemical subtypes interactively with autoview within the pager and separately from the attachment menu. The idea is to take full advantage of these two distinct ways of "viewing" the attachment, which appear to be unique to mutt.

The autoview scripts should do two things:-

• Give some information about the content of the file.
• Give some indication how the file can properly be "viewed" from the attachment menu.

Mutt in conjunction with the mailcap file allows two different options in the attachment menu. The use of "test=RunningX" in the mailcap entry allows a choice of action depending whether XWindows is running or not. For many chemical types this choice is insufficient so we use a wrapper script to display a menu of more than two choices.

1. pdb files as attachments.
2. Gaussian input files as attachments.
3. Gaussian output files as attachments.
4. Mopac input files as attachments.
5. Mopac output files as attachments.

I now support pdb files in the autoview output by a script called pdb_handler. This script is just a bunch of echo commands that write out a message explaining about different types of pdb files. Note that:-

• pdb files can be straight ASCII, but I have found some with no line breaks and thus a single long line that gets encoded as "quoted-printable".
• Chime can handle pdb files that have been compressed with gzip, but there is no gz extension. I have still to check this. Such files are encoded as "base64".

In the attachment menu, I currently point the mailcap entry to a bash script called view_pdb which has the menu items in the table below. Note that the first entry is the same as the pager action, as it will be for all attachment menu scripts making these useful where only one mailcap entry can be used. They are also useful for mailers where you only get one hit at the attachment. One such mailer is pine and here are some comparisions between mutt and pine for viewing chemical attachments.

Gaussian input files normally have the extension "com", but it has become accepted that the correct extension in the mime.types file is "gau". There is some confusion whether the type/subtype is chemical/x-gaussian or chemical/x-gaussian-input. We will use the latter. These files can be "viewed" by xmol or Rasmol. In the pager, I use a simple script called gau_handler that gives some information and then prints the top 10 lines of the input file.

In the attachment menu we use a bash script called view_g94input to allow the choices in the table below.

The script called sub_gau copies the file to a designated work directory and submits the job for running in a NQS queue. The work directory and various queue parameters are set in the sub_gau script which is written in perl.

Gaussian output files ("log files") can be quite long. They can be read by xmol to give an animation of the steps towards finding an optimised structure and perhaps other "viewers". In the pager, I use a perl script called gaussian_output that prints the title (of the first step, if a multi-step job), the number of lines, and the archive section (for all steps if a multi-step job).

In the attachment menu the mailcap entry is a bash script called view_g94output which offers a menu of the choices in the table below.

The third option is a little more complex than the others. The Fortran program (I have this very strange notion that code for parsing Gaussian output should be written in Fortran!) creates a temporary xyz file:-

ln -s $1 link
/usr/local/bin/g94opt2xyz > /tmp/tt$$.xyz

which is then feed to xmol with:-

xmol -readFormat xyz /tmp/tt$$.xyz

"link" and the temporary file are then deleted. For some reason I could not get normal piping to work here.

The forth option is even more complex. This uses Jan Labanowski's improvement to the xvibs program, which takes a G94 output file from a frequency run as input and produces several xyz files (one for each vibration). The script generates a menu of these xyz files so you can select a particular vibration for viewing as a xmol animation.

Mopac input files normally have the extension "dat", but it has become accepted that the correct extension in the mime.types file is "mop". There is some confusion whether the type/subtype is chemical/x-mopac or chemical/x-mopac-input. We will use the latter. These files can be "viewed" by xmol or Rasmol. In the pager, I use a simple script called mop_handler that gives some information and then prints the top 12 lines of the input file.

In the attachment menu we use a bash script called view_mopinput to allow the choices in the table below.

Note: It appears that xmol does not actually accept cartesian coordinates, but the mopic flag will do exactly what the mopii flag does - accept mopac style internal coordinates.

The netscape option is untested, but may work on SGI if Chime is installed.

The scripts that mutt uses in the attachment menu can also be used in the pine mailer.