Web Services - Sample 06: Using the JavaScript API

The PyMOL JavaScript API re-exposes PyMOL's Python programming interface directly to the JavaScript layer in an object-oriented way.

var pymol = new PyMOL(); // create PyMOL object instance for server of this page

var cmd = pymol.cmd; // assign a global symbol for the PyMOL cmd API

cmd.load('$PYMOL_PATH/test/dat/pept.pdb)

cmd.zoom('pept///1/',0,0,0,1)

cmd.zoom('all',0,0,0,2)

This eliminates the need for encoding your PyMOL commands as URL query strings and makes it possible to write JavaScript programs in your web page which control PyMOL in much the same way Python programs do.

cmd.reinitialize()
cmd.load("$PYMOL_PATH/test/dat/1tii.pdb")
cmd.show_as("cartoon")
list = cmd.get_chains("polymer")
for chain in list:
    cmd.color("auto","chain "+chain)

cmd.reinitialize();
cmd.load("$PYMOL_PATH/test/dat/1tii.pdb");
cmd.show_as("cartoon");
list = cmd.get_chains("polymer");
for(var i=0;i<list.length;i++) {
    cmd.color("auto","chain "+list[i]);
}