— procedure: *to-jligand-secret-file-name*

JLigand sends Coot a file that contains filenames for the link and new dictionary/restraints.

— procedure: *jligand-home-env*

Define an environment variable for the place where jligand.jar resides in a canonical distribution

— procedure: *imol-jligand-link*

jligand internal parameter

— procedure: get-file-mtime file-name

this could be in utils

— procedure: start-jligand-listener

every fraction of a second look to see if *from-jligand-secret-link-file-name* has been updated. If so, then run the handle-read-from-jligand-file function.

— procedure: launch-jligand-function

This happens when user clicks on the "Launch JLigand" button. It starts a jligand and puts it in the background.

— procedure: click-select-residues-for-jligand

This happens when user clicks on the "Select Residues for JLigand" (or some such) button. It expects the user to click on atoms of the two residues involved in the link.