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

charge.py

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

default_mode = 'labchg'

class Charge(Wizard):

   def __init__(self):

      Wizard.__init__(self)
      
      self.modes = [
         'labchg',
         'addchg',
         'cpychg',
         'zrochg',
         'mzochg',
         'cbachg',
         'movchg',
         'rbachg',
         'sumchg',
         ]

      self.mode = default_mode
      self.status = 0
      
      self.mode_name = {
         'labchg':'Show',
         'cpychg':'Copy',
         'addchg':'Add',
         'zrochg':'Zero',
         'mzochg':'Move & Zero (atom)',
         'cbachg':'Move & Zero (resi)',
         'movchg':'Move & Remove (atom)',
         'rbachg':'Move & Remove (resi)',
         'sumchg':'Get Total Charge'
         }
      
      # initialize mode menu
      
      smm = []
      smm.append([ 2, 'Atom Charge Mode', '' ])
      for a in self.modes:
         smm.append([ 1, self.mode_name[a], 'cmd.get_wizard().set_mode("'+a+'")'])

      self.menu['mode']=smm
      
      self.memory = 0
         

   def get_panel(self):
      return [
         [ 1, 'Charge Wizard',''],
         [ 3, self.mode_name[self.mode],'mode'],
         [ 2, 'Clear','cmd.get_wizard().clear()'],
         [ 2, 'Done','cmd.set_wizard()'],
         ]

   def cleanup(self):
      global default_mode
      default_mode = self.mode
      self.clear()
      
   def clear(self):
      self.set_status(0)
      if 'wcharge' in cmd.get_names('selections'):
         if self.mode!='sumchg':
            cmd.edit("wcharge")
            cmd.label("pkmol",'') # fastest clear command
         else:
            cmd.label("wcharge",'') # fastest clear command            
         cmd.delete("wcharge")
         cmd.unpick()
      cmd.unpick()
      cmd.refresh_wizard()
      
   def get_prompt(self):
      self.prompt = None
      if self.mode == 'cpychg':
         if self.status==0:
            self.prompt = [ 'Pick source atom...' ]
         elif self.status==1:
            self.prompt = [ 'Pick destination atom on which to assign charge %6.4f'%self.partial_charge ]
      if self.mode == 'addchg':
         if self.status==0:
            self.prompt = [ 'Pick source atom...' ]
         elif self.status==1:
            self.prompt = [ 'Pick destination atom on which to add charge %6.4f'%self.partial_charge ]
      if self.mode == 'mzochg':
         if self.status==0:
            self.prompt = [ 'Pick source atom to copy and zero...' ]
         elif self.status==1:
            self.prompt = [ 'Pick destination atom on which to add charge %6.4f'%self.partial_charge ]
      if self.mode == 'movchg':
         if self.status==0:
            self.prompt = [ 'Pick source atom to copy and destroy...' ]
         elif self.status==1:
            self.prompt = [ 'Pick destination atom on which to add charge %6.4f'%self.partial_charge ]
      if self.mode == 'sumchg':
         if self.status==0:
            self.prompt = [ 'Pick an atom on the chain...' ]
         if self.status==1:
            self.prompt = [ 'Total charge on the chain is %6.4f'%self.partial_charge,
                            'Pick an atom on the chain...' ]
      if self.mode == 'cbachg':
         if self.status==0:
            self.prompt = [ 'Pick source residue to copy and zero...' ]
         elif self.status==1:
            self.prompt = [ 'Pick destination residue on which to add charges.']
      if self.mode == 'rbachg':
         if self.status==0:
            self.prompt = [ 'Pick source residue to copy and remove...' ]
         elif self.status==1:
            self.prompt = [ 'Pick destination residue on which to add charges.']
      if self.mode == 'zrochg':
            self.prompt = [ 'Pick atom on which to zero charge...' ]


      if self.mode == 'labchg':
            self.prompt = [ 'Pick atom on which to show charge...' ]

      if "wcharge" in cmd.get_names('selections'):
         pymol.stored.charge = 0
         if cmd.iterate("(byres wcharge)",
                        "stored.charge = stored.charge + partial_charge"):
            self.prompt.insert(0,"Total charge on the residue is %6.4f"%pymol.stored.charge)
            
      return self.prompt
   
   def set_mode(self,mode):
      if mode in self.modes:
         self.mode = mode
      self.status = 0
      cmd.refresh_wizard()
      
   def set_status(self,status):
      self.status = status
      cmd.refresh_wizard()

   def do_pick(self,bondFlag):
      if bondFlag:
         print " Error: please select a single atom"
         
      if self.mode == 'cpychg':
         # picking up
         if self.status==0:
            if cmd.iterate("(pk1)","stored.charge = partial_charge"):
               self.partial_charge = pymol.stored.charge
               self.status = 1
               cmd.label("(pk1)","'%6.4f'%partial_charge")
               cmd.select("wcharge","(pk1)")
               cmd.unpick()
               cmd.enable("wcharge")
               
         # dropping off
         elif self.status==1:
            pymol.stored.charge=self.partial_charge
            if cmd.alter("(pk1)","partial_charge = stored.charge"):
               self.status = 0
               cmd.label("(pk1)","'%6.4f'%partial_charge")
               cmd.select("wcharge","(pk1)")
               cmd.unpick()
               cmd.enable("wcharge")

      if self.mode == 'cbachg' or self.mode == 'rbachg':
         # picking up
         if self.status==0:
            pymol.stored.chg_dict = {}
            if cmd.iterate("(byres pk1)","stored.chg_dict[name] = partial_charge"):
               self.charge_dict = pymol.stored.chg_dict
               self.status = 1
               cmd.label("(byres pk1)","'%6.4f'%partial_charge")
               cmd.select("wcharge","(byres pk1)")
               cmd.unpick()
               cmd.enable("wcharge")
               
         # dropping off
         elif self.status==1:
            pymol.stored.valid_atoms = []
            if cmd.iterate("(byres pk1)","stored.valid_atoms.append(name)"):
               kees = self.charge_dict.keys()
               valid_dict = {}
               for a in pymol.stored.valid_atoms:
                  if a in kees:
                     valid_dict[a] = 1
               pymol.stored.chg_dict = self.charge_dict
               # copy/add charges
               for a in valid_dict.keys():
                  cmd.alter("((byres pk1) and name %s)"%a,
                            "partial_charge = partial_charge + stored.chg_dict[name]")
                  if self.mode == 'rbachg':
                     cmd.remove("((wcharge) and name %s)"%a)
                  else:
                     cmd.alter("((wcharge) and name %s)"%a,
                               "partial_charge = 0")
               self.status = 0
               # update labels
               cmd.label("(wcharge or (byres pk1))","'%6.4f'%partial_charge")
               # show which atoms had charges moved
               cmd.select("wcharge","(none)")
               for a in valid_dict.keys():
                  cmd.select("wcharge","(wcharge or ((byres pk1) and name %s))"%a)
               cmd.unpick()
               cmd.enable("wcharge")

      if self.mode == 'addchg':
         # picking up
         if self.status==0:
            if cmd.iterate("(pk1)","stored.charge = partial_charge"):
               self.partial_charge = pymol.stored.charge
               self.status = 1
               cmd.label("(pk1)","'%6.4f'%partial_charge")
               cmd.select("wcharge","(pk1)")
               cmd.unpick()
               cmd.enable("wcharge")
               
         # dropping off
         elif self.status==1:
            pymol.stored.charge=self.partial_charge
            if cmd.alter("(pk1)","partial_charge = partial_charge + stored.charge"):
               self.status = 0
               cmd.label("(pk1)","'%6.4f'%partial_charge")
               cmd.select("wcharge","(pk1)")
               cmd.unpick()
               cmd.enable("wcharge")
               
      if self.mode == 'mzochg':
         # picking up
         if self.status==0:
            if cmd.iterate("(pk1)","stored.charge = partial_charge"):
               self.partial_charge = pymol.stored.charge
               self.status = 1
               cmd.label("(pk1)","'%6.4f'%partial_charge")
               cmd.select("wcharge","(pk1)")
               cmd.unpick()
               cmd.enable("wcharge")
               
         # dropping off
         elif self.status==1:
            pymol.stored.charge=self.partial_charge
            if cmd.alter("(pk1)","partial_charge = partial_charge + stored.charge"):
               self.status = 0
               cmd.label("(pk1)","'%6.4f'%partial_charge")
               cmd.alter("(wcharge)","partial_charge=0")
               cmd.label("(wcharge)","'%6.4f'%partial_charge")               
               cmd.select("wcharge","(pk1)")
               cmd.unpick()
               cmd.enable("wcharge")

      if self.mode == 'movchg':
         # picking up
         if self.status==0:
            if cmd.iterate("(pk1)","stored.charge = partial_charge"):
               self.partial_charge = pymol.stored.charge
               self.status = 1
               cmd.label("(pk1)","'%6.4f'%partial_charge")
               cmd.select("wcharge","(pk1)")
               cmd.unpick()
               cmd.enable("wcharge")
               
         # dropping off
         elif self.status==1:
            pymol.stored.charge=self.partial_charge
            if cmd.alter("(pk1)","partial_charge = partial_charge + stored.charge"):
               self.status = 0
               cmd.label("(pk1)","'%6.4f'%partial_charge")
               cmd.remove("wcharge")
               cmd.select("wcharge","(pk1)")
               cmd.unpick()
               cmd.enable("wcharge")

      if self.mode == 'zrochg':
         if cmd.alter("(pk1)","partial_charge = 0.0"):
            cmd.label("(pk1)","'%6.4f'%partial_charge")
            cmd.select("wcharge","(pk1)")
            cmd.unpick()
            cmd.enable("wcharge")
               
      if self.mode == 'labchg':
         cmd.label("(pk1)","'%6.4f'%partial_charge")
         cmd.select("wcharge","(pk1)")
         cmd.unpick()
         cmd.enable("wcharge")
               
      if self.mode == 'sumchg':
         pymol.stored.charge = 0.0
         if cmd.iterate("(pkmol)","stored.charge = stored.charge + partial_charge"):
            self.partial_charge = pymol.stored.charge
            self.status = 1
            cmd.select("wcharge","(pkmol)")
            cmd.unpick()
            cmd.enable("wcharge")
         
      cmd.refresh_wizard()

Generated by  Doxygen 1.6.0   Back to index