Split selection

From PyMOLWiki
Jump to: navigation, search

Given an initial selection, Split_selection will create two new selections. One, called 'lo,' will have all the atoms with IDs lower than your input atom (actually input residue's alpha carbon); and the second selection is 'hi,' which contains the atoms with IDs higher than the initial (residue's alpha carbon) atom.

The Code

import pymol
from pymol import cmd
 
def get_index_list(s):
	"""
	Given an atom selection, return the list of atom IDs in this selection
	"""
	return map(lambda x: x.index, cmd.get_model(s).atom)
 
def get_single_index(s):
	"""
	Get the ID of the first alpha carbon in the selection, S
	"""
	# assume CA
	return get_index_list( "n. CA and (br. %s)" % s)[0]
 
def split_selection(s):
	"""
	PARAMS
	    s
	        An atom selection.
 
	RETURNS
	    None
 
	SIDE EFFECTS
	    Creates two new selections, called lo and hi.  Lo will have all atoms in the same molecule
	    with atom IDs less than the alpha carbon ID in S.  Hi will have all the atoms in the same
	    molecule with IDs greater than the atom ID of the alpha carbon in S.
 
	EXAMPLE
	    run /path/to/this/script/split_selection.py
	    fetch 1cll
	    select i. 79
	    split_selection (sele)
	    # now look at the 'hi' and 'lo' selections.
 
	AUTHOR: Jason Vertrees, 2010.
	"""
	l = get_index_list("bm. " + s)
	m = min(l)
	M = max(l)
	# assume using alpha carbons
	selected_index = get_single_index( "n. CA and (br. sele)" )
 
	low_sel_name = cmd.get_unused_name("lo")
	hi_sel_name  = cmd.get_unused_name("hi")
 
	cmd.select(low_sel_name, "ID %d-%d" % (m,selected_index-1))
	cmd.select(hi_sel_name, "ID %d-%d" % (selected_index+1,M))
 
cmd.extend("split_selection", split_selection)

See Also

Script_Library

Personal tools
Namespaces
Variants
Actions
Navigation
Toolbox