The toolbar is a user interface component that appears in the main Chimera window, typically on the left-hand side. The purpose of the toolbar is to hold buttons that invoke commonly used functionality (e.g., displaying protein backbone) and sets of buttons that comprise the entire interface to an extension (e.g., playing molecular dynamics movies).
There are four items associated with the button: an icon,, a Python function, a short description, and an URL to a full description. The icon is displayed in the button, and determines the size of the button. The Python function is called when the button is pressed. The description appears as balloon help text. The full description is displayed when context help is invoked.
The code below illustrates how to a button on the toolbar. The code must be executed from a file (i.e., it cannot be typed in via the Python command line in the main Chimera window). The icon associated with the button is an image file named ToolbarButton.tiff in the same directory as the Python source code. The short description is ``Show Main Chain''. The Python function displays protein backbone and hides all other atoms and bonds, and the code in the body of the function is explained in greater detail in Molecular Editing Using Python.
Import system modules used in this example.
The regular expression module,
Import Chimera modules used in this example.
The
Function
Create a button in the toolbar.
The first argument to The code in this example consists of two portions: defining the actual functionality
in function mainchain and presenting an user interface to the functionality.
While the example is presented as a single Python source file, there are good
reasons for dividing the code into multiple source files and using a Python
package instead. The advantages of the latter approach is illustrated in Packaging
an Extension. The example code must be saved in a disk file named re, is used for matching atom names.
The operating system module, os, is used for constructing the icon
file name (see below).
import re
import os
chimera module is needed to access the molecular data.
import chimera
mainchain sets the display status of atoms
and requires no arguments. The body of the function is
identical to the example described in
Molecular Editing Using Python.
def mainchain():
MAINCHAIN = re.compile("^(N|CA|C)$", re.I)
for m in chimera.openModels.list(modelTypes=[chimera.Molecule]):
for a in m.atoms:
a.display = MAINCHAIN.match(a.name) != None
chimera.tkgui.app.toolbar.add is the icon,
which is either the path to an image file, or the name of a standard
Chimera icon (which is the base name of an image file found in the
"share/chimera/images" directory in the Chimera installation directory).
In this case, since ToolbarButton.tiff is not an absolute path, the
icon will be looked for under that name in both the current directory
and in the Chimera images directory.
The second argument is the Python function to be called when the button
is pressed (a.k.a., the "callback function").
The third argument is a short description of what the button does
(used typically as balloon help).
The fourth argument is the URL to a full description.
For this example the icon name is ToolbarButton.tiff;
the Python function is mainchain;
the short description is "Show Main Chain";
and there is no URL for context help.
chimera.tkgui.app.toolbar.add('ToolbarButton.tiff', mainchain, 'Show Main Chain', None)
Code Notes
Running the Example
ToolbarButton.py
(note that the .py extension is required). The
icon tiff file must
be save to a file named 'ToolbarButton.tiff' in the same directory.
Chimera may be then invoked
with the code file name on the command line, e.g.,
chimera ToolbarButton.py