Using BKChem in batch mode

Foreword

In version 0.9.0 of BKChem I have introduced an undocumented batch mode. Depending on command line switches BKChem converted all given files of one type to another etc. The problem of this approach was that it would be necessary to implement a huge number of command line switches to give the user at least some power to do what he wants.

From version 0.10.0-pre1 I have decided to use a completely different approach, based on my experience with custom plugins. In this version, there is only one command line switch (-b) that tells BKChem to start in batch mode. The following argument is a name of a Python script to run.

How does a batch script work

When you start BKChem in batch mode it at first starts all its vital parts and then gives control to the Python script given on command line. All this happens without actually displaying a BKChem window (even though the window is in fact created, so it does not work without X on Unix). After the script has finished its work and the control returns back to BKChem, the program simply terminates.

The anatomy of a batch script is very similar to that of a custom plugin. The script receives a global variable App, which is the actual BKChem instance. In case some further arguments are given on the command line on startup, they are passed as a list in a global variable Args. The script can use these variables in any way it wants, it can also use any standard Python functions and modules.

Sample batch script

In this file you will find complete code of the example discussed bellow. It is a simple batch script that loads all BKChem files in all directories specified on command line, sets font size of all atoms to 12 and re-saves the files. The most important parts of the batch script are discussed bellow. 

if Args:
  for arg in Args:
    update_svgs_in_path( arg)
else:
  print "You must supply a path as first argument to the batch script"

Args is together with App a global variable containing a list of command line arguments given after the script name.

  if App.load_CDML( f, replace=1):
    print "OK"
    for mol in App.paper.molecules:
      for atom in mol.atoms:
        atom.font_size = 12
    App.save_CDML()
    return 1
  else:
    print "ignoring"
    return 0

App.load_CDML returns true when a file is successfully loaded. The replace argument tells BKChem to load the file replacing the current one (instead of opening a new tab), thus we don't have to deal with closing tabs.

From the few lines presented above (and the whole script) in fact only 4 or 5 are really interesting and do really do something. The rest is just a glue, comments and debugging output. In fact writing a batch script could not be easier :)

Please feel free to send me any comments on my English, clarity of the above text and other problems you may have with this brief tutorial.