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# example showing how one might assembled an ordered list of atoms
# from mouse clicked through use of a PyMOL Wizard.
from pymol.wizard import Wizard
from pymol import cmd, util
import pymol
import traceback
click_sele = "_clicked"
disp_sele = "_displayed"
# Wizard class definition
def quote_blanks(st):
st = str(st)
if not len(st):
return "''"
else:
return st
class Clicker(Wizard):
def __init__(self,_self=cmd):
Wizard.__init__(self,_self)
self.cmd.unpick()
self.click_list = []
cmd.select(click_sele,"none",enable=0)
cmd.select(disp_sele,"none",enable=1)
def get_prompt(self):
self.prompt = [ 'Please click a set of atoms one by one (%d clicked so far)...' % len(self.click_list) ]
return self.prompt
def get_panel(self):
return [
[ 2, 'Print Atom List','cmd.get_wizard().print_list()'],
[ 2, 'Remove Last','cmd.get_wizard().remove_last()'],
[ 2, 'Reset Atom List','cmd.get_wizard().reset_list()'],
[ 2, 'Done','cmd.set_wizard()'],
]
def do_select(self,name):
if name!=disp_sele:
self.cmd.select(disp_sele,name + " or ?" + disp_sele,enable=1)
dict = { 'x' : [] }
self.cmd.iterate(disp_sele+" and not ?"+click_sele,
'x.append( (model,segi,chain,resn,resi,name,alt) )',
space=dict)
if len(dict['x']): # toggled on
entry = tuple(map(quote_blanks,dict['x'][0]))
sele_str = "/%s/%s/%s/%s`%s/%s`%s"%entry
self.cmd.select(click_sele,"?"+click_sele+" or "+sele_str,enable=0)
self.click_list.append(sele_str)
self.cmd.refresh_wizard()
else: # toggled off
new_list = []
for entry in self.click_list:
if self.cmd.count_atoms(entry+" and "+disp_sele):
new_list.append(entry)
self.click_list = new_list
self.cmd.select(click_sele,disp_sele,enable=0)
cmd.refresh_wizard()
self.cmd.delete(name)
self.cmd.select(disp_sele,click_sele,enable=1)
def remove_last(self):
self.click_list = self.click_list[:-1]
self.cmd.select(click_sele,"none")
for entry in self.click_list:
self.cmd.select(click_sele,click_sele+" or "+entry)
self.cmd.select(disp_sele,click_sele,enable=1)
self.cmd.refresh_wizard()
def reset_list(self):
self.click_list = []
cmd.select(click_sele,"none",enable=0)
cmd.select(disp_sele,"none",enable=1)
self.cmd.refresh_wizard()
def print_list(self):
cnt = 1
print("Atoms Clicked (in order):")
for entry in self.click_list:
print("Atom %d: %s"%(cnt,entry))
cnt = cnt + 1
def cleanup(self):
self.cmd.delete(disp_sele)
self.cmd.delete(click_sele)
# load an example structure
cmd.load("$TUT/1hpv.pdb")
# color by chain (aesthetics)
util.cbc()
# put the mouse into single-atom selection mode
cmd.set('mouse_selection_mode',0)
# activate the wizard
cmd.set_wizard(Clicker())
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