Extend

From PyMOLWiki
Jump to: navigation, search

Extend is an API-only function which binds a new external function as a command into the PyMOL scripting language. In other words, when you write a function and want PyMOL to recognize the new command, you extend the command into PyMOL. Once extended, the function name is recognized like other function names (example below). Typically, extend is the last line of a PyMOL script.

Contents

PYMOL API

cmd.extend(string name,function function)

PYTHON EXAMPLE

def foo(moo=2): print moo
cmd.extend('foo',foo)

The following would now work within PyMOL:

PyMOL>foo
2
PyMOL>foo 3
3
PyMOL>foo moo=5
5
PyMOL>foo ?
 
Usage: foo [ moo ]

NOTES

For security reasons, new PyMOL commands created using "extend" are not saved or restored in sessions.

You may want to set auto_arg to enable auto-completion for your command's arguments.

SEE ALSO



"extend" used in selections

"extend" can also be used in selection statements to grow a selection based on covalent bonds. This behavior is illustrated on residue 64 of PDB file 1KAO where we initially select one atom and then "extend" that selection by one and three covalent bonds.

Extend0.png Extend1.png Extend3.png
select (resi 64 and n. cz) select (resi 64 and n. cz) extend 1 select (resi 64 and n. cz) extend 3

Personal tools
Namespaces
Variants
Actions
Navigation
Toolbox