Logo Search packages:      
Sourcecode: pymol version File versions  Download package

sculpting.py

from pymol.wizard import Wizard
from pymol import cmd
from pymol import util

import pymol

sele_pre = "sw_"
sele_prefix_len = len(sele_pre)

cent_sele = sele_pre+ "cent"
free_sele = sele_pre+ "free"
fix_sele = sele_pre+ "fix"
excl_sele = sele_pre+ "excl"

default_mode = 'by_resi'
default_radius = 6.0
default_cushion = 6.0

class Sculpting(Wizard):

   cutoff = 3.5
   
   def __init__(self):

      Wizard.__init__(self)
      
      self.status = 0 # 0 no atoms selections, 1 atom selected
      self.error = None
      self.object_name = None
      self.radius = default_radius
      self.cushion = default_cushion
      
      # mode selection subsystem
      
      self.mode = default_mode
      self.modes = [
         'ligand_rx',
#         'ligand_re',         
#         'by_atom',
         'by_resi',
         ]

      self.mode_name = {
         'by_atom':'Atom Shells',
         'by_resi':'Residue Shells',
         'ligand_rx' :'Residue v. Fixed',
         'ligand_re' :'Residue v. Free',                  
         'ligand_cx' :'Chain v. Fixed',
         'ligand_ce' :'Chain v. Free',                  
         }

      smm = []
      smm.append([ 2, 'Selection Mode', '' ])
      for a in self.modes:
         smm.append([ 1, self.mode_name[a], 'cmd.get_wizard().set_mode("'+a+'")'])
      self.menu['mode']=smm

      self.menu['radius'] = [[ 2, 'Mobile Atom Sphere', '' ],
                             [1, '4.0 A Radius','cmd.get_wizard().set_radius(4)'],
                             [1, '5.0 A Radius','cmd.get_wizard().set_radius(5)'],
                             [1, '6.0 A Radius','cmd.get_wizard().set_radius(6)'],
                             [1, '8.0 A Radius','cmd.get_wizard().set_radius(8)'],
                             [1, '10.0 A Radius','cmd.get_wizard().set_radius(10)'],
                             [1, '15.0 A Radius','cmd.get_wizard().set_radius(15)'],
                             [1, '20.0 A Radius','cmd.get_wizard().set_radius(20)'],
                             ]
                              
      self.menu['cushion'] = [[ 2, 'Fixed Atom Cushion', '' ],
         [1, '2.0 A Cushion','cmd.get_wizard().set_cushion(2)'],
         [1, '3.0 A Cushion','cmd.get_wizard().set_cushion(3)'],
         [1, '4.0 A Cushion','cmd.get_wizard().set_cushion(4)'],
         [1, '6.0 A Cushion','cmd.get_wizard().set_cushion(6)'],
         [1, '8.0 A Cushion','cmd.get_wizard().set_cushion(8)'],
         [1, '10.0 A Cushion','cmd.get_wizard().set_cushion(10)'],
         [1, '12.0 A Cushion','cmd.get_wizard().set_cushion(12)'],                              

         ]

# generic set routines

   def set_mode(self,mode):
      if mode in self.modes:
         self.mode = mode
      cmd.refresh_wizard()

   def set_radius(self,radius):
      self.radius=radius
      self.update_selections()
      cmd.refresh_wizard()
      
   def set_cushion(self,cushion):
      self.cushion=cushion
      self.update_selections()
      cmd.refresh_wizard()
      
   def update_selections(self):
      if self.status==1:
         if self.mode=='by_resi':
            cmd.select(free_sele,"((byobj %s) and byres ((%s) x; %8.3f))"%
                       (cent_sele,cent_sele,self.radius))
            cmd.select(fix_sele,"((byobj %s) and (not %s) and byres ((%s) x; %8.3f))"%
                       (cent_sele,free_sele,cent_sele,self.radius+self.cushion))
            cmd.select(excl_sele,"((byobj %s) and (not (%s|%s)))"%
                       (cent_sele,free_sele,fix_sele))
         elif self.mode=='ligand_rx':
            cmd.select(free_sele,"((byobj %s) and byres (%s))"%
                       (cent_sele,cent_sele))
            cmd.select(fix_sele,"((byobj %s) and (not %s) and byres ((%s) x; %8.3f))"%
                       (cent_sele,free_sele,free_sele,self.cushion))
            cmd.select(excl_sele,"((byobj %s) and (not (%s|%s)))"%
                       (cent_sele,free_sele,fix_sele))
         cmd.protect("(byobj %s)"%cent_sele)
         cmd.deprotect(free_sele)
         cmd.flag('exclude',"(byobj %s)"%cent_sele,"clear")
         cmd.flag('exclude',excl_sele,"set")
         cmd.color('grey',excl_sele)
         cmd.zoom(free_sele,3.0)
         util.cbac(fix_sele)
         util.cbag(free_sele)
         cmd.disable('indicate')
         cmd.disable(cent_sele)            
         cmd.disable(free_sele)
         cmd.disable(fix_sele)
         cmd.disable(excl_sele)
         cmd.unpick()
         
         self.status = 1
         
   def set_object_mode(self,mode):
      if mode in self.object_modes:
         self.object_mode = mode
      self.status = 0
      cmd.refresh_wizard()
      
   def get_panel(self):
      return [
         [ 1, 'Sculpting',''],
         [ 3, self.mode_name[self.mode],'mode'],
         [ 3, "Radius: %3.1f A"%self.radius,'radius'],
         [ 3, "Cushion: %3.1f A"%self.cushion,'cushion'],
         [ 2, 'Relocate','cmd.get_wizard().free_all()'],
         [ 2, 'Done','cmd.set_wizard()'],
         ]

   def free_all(self):
      if self.status==1:
         cmd.deprotect("(byobj %s)"%cent_sele)
         cmd.protect(fix_sele)
         cmd.flag('exclude',"(byobj %s)"%cent_sele,"clear")
         util.cbag("(byobj %s)"%cent_sele)
      self.clear()
      cmd.refresh_wizard()
      
   def clear(self):
      cmd.delete(sele_pre+"*")
      self.status = 0
      cmd.refresh_wizard()
      
   def cleanup(self):
      global default_mode, default_radius, default_cushion
      default_mode = self.mode
      default_radius = self.radius
      default_cushion = self.cushion
      self.clear()
      
   def get_prompt(self):
      self.prompt = None
      if self.status==0:
         self.prompt = [ 'Please pick the center atom...']
      if self.error!=None:
         self.prompt.append(self.error)
      return self.prompt
   
   def do_pick(self,bondFlag):
      global dist_count
      if not self.status:
         if cmd.select(cent_sele,"pk1"):
            self.status = 1
            self.update_selections()
         cmd.refresh_wizard()
         return 1
      else:
         return 0
      

Generated by  Doxygen 1.6.0   Back to index