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Sourcecode: pymol version File versions

filter.py

# filter wizard
# no-frills tool for quickly filtering docked compounds, etc.

import os,sys
from pymol.wizard import Wizard
from pymol import cmd
import pymol
import string
import traceback
# global dictionary for saving result on a per-object basis

static_dict = {}

# last/current object being filtered

default_object = None

# browing mode

default_browse = 1

accept_str = "Accept"
defer_str = "Defer"
reject_str = "Reject"

# class definition (class name must match wizard name with cap)

class Filter(Wizard):

   def __init__(self):

      # initialize parent class
      
      Wizard.__init__(self)
      
      # restore previous state from global storage

      self.dict = static_dict
      self.object = default_object
      self.browse = default_browse
      self.avail_objects = []
      self.state_dict = {}
      
      # if we don't have a current object, choose the first multi-state object
      
      if self.object == None:
         for a in cmd.get_names('objects'):
            if cmd.get_type(a)=='object:molecule':
               if cmd.count_states(a)>1:
                  self.object = a
                  break

      # menu for
      
      self.menu['browse'] = [
         [2, 'Browse Mode',''],
         [1, 'Browse All','cmd.get_wizard().set_browse(1)'],
         [1, 'Browse Accepted','cmd.get_wizard().set_browse(2)'],
         [1, 'Browse Rejected','cmd.get_wizard().set_browse(3)'],
         [1, 'Browse Deferred','cmd.get_wizard().set_browse(4)'],
         [1, 'Browse Remaining','cmd.get_wizard().set_browse(5)'],         
         ]

      self.count_object()
      self.load_state_dict()
      self.update_object_menu()
      cmd.set_key('F1',lambda s=self:s.accept())
      cmd.set_key('F2',lambda s=self:s.reject())
      cmd.set_key('F3',lambda s=self:s.defer())
      cmd.set_key('right',lambda s=self:s.forward())
      cmd.set_key('left',lambda s=self:s.backward())
      
   def update_object_menu(self):

      # find objects with > 1 state
      
      self.avail_objects = []
      
      for a in cmd.get_names('objects'):
         if cmd.get_type(a)=='object:molecule':
            if cmd.count_states(a)>1:
               self.avail_objects.append(a)

      # now create the object menu
      
      self.menu['object'] = [[2,'Select Object','']] 
      for a in self.avail_objects:
         self.menu['object'].append([ 1,a,'cmd.get_wizard().set_object("%s")'%(a) ])
      self.menu['object'].append([ 1,'None','cmd.get_wizard().set_object(None)'])
      
   def set_browse(self,browse):
      # allow user to focus on only a subset of the compounds
      self.browse = browse
      if self.browse == 1:
         print " Filter: Browsing all compounds."
         cmd.mset() # all states visible
      elif self.object==None:
         print " Filter-Error: please choose an object first"
      else: 
         self.check_object_dict()
         if self.browse == 2:
            print " Filter: Browsing accepted compounds."
            target = accept_str
         elif self.browse == 3:
            print " Filter: Browsing rejected compounds."            
            target = reject_str
         elif self.browse == 4:
            print " Filter: Browsing deferred compounds."                        
            target = defer_str
         lst = []
         sd = self.state_dict
         sdo = self.dict[self.object]
         if self.browse<5:
            for a in sdo.keys():
               if sdo[a]==target:
                  lst.append(sd[a])
         else:
            print " Filter: Browsing remaining compounds"
            for a in sd.keys():
               if not sdo.has_key(a):
                  lst.append(sd[a])
         lst.sort()
         if len(lst)==0:
            print " Filter-Error: No matching compounds."
         cmd.mset(string.join(map(str,lst),' '))
         cmd.rewind()
      cmd.refresh_wizard()

   def check_object_dict(self):
      # make sure we have a valid entry for this object in our dictionary
      
      if not self.dict.has_key(self.object):
         self.dict[self.object]={} # create dictionary to store results

   def adjust(self,decision,inc):
      # utility routine to increment/decrement counters 
      if decision == accept_str:
         self.acce = self.acce + inc
      elif decision == reject_str:
         self.reje = self.reje + inc
      elif decision == defer_str:
         self.defe = self.defe + inc

   def load_state_dict(self):
      # establish relationship between names and states
      # ASSUMPTION: identifiers will be unique
      self.state_dict = {}
      sd = self.state_dict
      so = self.object
      if so!=None:
         cnt = cmd.count_states(so)
         for a in range(1,cnt+1):
            sd[cmd.get_title(so,a)] = a

   def count_object(self):
      # record how many molecular are in an object, etc.
      self.check_object_dict()
      if self.object!=None:
         self.acce = 0
         self.reje = 0
         self.defe = 0
         self.togo = 0
         self.tota = cmd.count_states(self.object)
         sdo=self.dict[self.object]
         self.togo = self.tota-len(sdo)
         for a in sdo.keys():
            dec = sdo[a]
            self.adjust(dec,1)
      
   def set_object(self,obj_name):
      self.object = obj_name
      self.count_object()
      self.load_state_dict()
      cmd.refresh_wizard()
      
   def get_panel(self):

      # returns Wizard panel for PyMOL to display
      
      # 1 = title/text
      # 2 = button
      # 3 = pop-up menu
      
      self.update_object_menu()
      if self.object != None:
         save_str = 'Save %s.txt'%self.object
      else:
         save_str = ""
      return [
         [ 1, 'Filtering Wizard',''],
         [ 3, self.menu['browse'][self.browse][1], 'browse' ],
         [ 3, str(self.object), 'object' ],
         [ 2, 'Accept (F1)','cmd.get_wizard().accept()'],
         [ 2, 'Reject (F2)','cmd.get_wizard().reject()'],
         [ 2, 'Defer (F3)','cmd.get_wizard().defer()'],
         [ 2, 'Forward (->)','cmd.get_wizard().forward()'],                  
         [ 2, 'Back (<-)','cmd.get_wizard().backward()'],
         [ 2, save_str,'cmd.get_wizard().save()'],
         [ 2, 'Refresh','cmd.refresh_wizard()'],                  
         [ 2, 'Done','cmd.set_wizard()'],
         ]

   def get_prompt(self):

      # returns text prompt
      
      self.prompt = None
      if self.object == None:
         self.prompt = [ 'Please select a multi-state object...' ]
      else:
         cnt = cmd.count_states(self.object)
         self.prompt = [ '%s: %d total, %d accepted, %d rejected, %d deferred, %d remaining'%(
            self.object,self.tota,self.acce,self.reje,self.defe,self.togo) ]
         state = cmd.get_state()
         ident = cmd.get_title(self.object,state)
         sdo=self.dict[self.object]
         if sdo.has_key(ident):
            self.prompt.append('%s: %s'%(ident,sdo[ident]))
         else:
            self.prompt.append('%s?'%(ident))
      return self.prompt

   def count(self,entry,str):
      # keep track of how many compounds are in which category
      
      self.check_object_dict()
      sdo = self.dict[self.object]
      if sdo.has_key(entry):
         self.adjust(sdo[entry],-1)
      else:
         self.togo = self.togo - 1
      sdo[entry] = str
      self.adjust(sdo[entry],1)      
         
   def accept(self):
      # accept compound and advance
      if self.object==None:
         print " Filter-Error: Please choose an object first"
      else:
         state = cmd.get_state()
         ident = cmd.get_title(self.object,state)
         print " Filter: Accepting '%s'"%ident
         self.count(ident,accept_str)
      cmd.forward()         
      cmd.refresh_wizard()
      
   def reject(self):
      # reject compound and advance
      if self.object==None:
         print " Filter-Error: Please choose an object first"
      else:
         state = cmd.get_state()
         ident = cmd.get_title(self.object,state)
         print " Filter: Rejecting '%s'"%ident
         self.check_object_dict()
         self.count(ident,reject_str)
      cmd.forward()         
      cmd.refresh_wizard()
      
   def defer(self):
      # defer compound and advance
      if self.object==None:
         print " Filter-Error: Please choose an object first"
      else:
         state = cmd.get_state()
         ident = cmd.get_title(self.object,state)
         print " Filter: Deferring '%s'"%ident
         self.check_object_dict()
         self.count(ident,defer_str)
      cmd.forward()
      cmd.refresh_wizard()

   def forward(self):
      # go forward and update information
      cmd.forward()
      cmd.refresh_wizard()
      
   def backward(self):
      # go backward and update information      
      cmd.backward()
      cmd.refresh_wizard()
      
   def save(self):
      # write compounds to a file
      if self.object==None:
         print " Filter-Error: please choose an object first"
      else:
         self.check_object_dict()         
         fname = self.object+".txt"
         try:
            f=open(fname,'w')
            f.close()
         except:
            print " Filter-Warning: '"+fname+"' in current directory is not writable."
            print " Filter-Warning: attempting to write in home directory."
            if sys.platform[0:3]!="win":
               fname = "$HOME/"+fname
               fname = os.path.expandvars(fname)               
            else:
               fname = "$HOMEPATH\\"+fname
               fname = os.path.expandvars(fname)
               fname = "$HOMEDRIVE"+fname
               fname = os.path.expandvars(fname)
         try:
            f=open(fname,'w')
            sd = self.state_dict
            sdo = self.dict[self.object]
            f.write('Object\t"%s"\n'%(self.object))
            f.write('Total\t%d\nAccepted\t%d\nRejected\t%d\nDeferred\t%d\nRemaining\t%d\n\n'%(
               self.tota,
               self.acce,
               self.reje,
               self.defe,
               self.togo))
            # sort output in order of states            
            lst = []
            for a in sd.keys():
               lst.append((sd[a],a))
            lst.sort()
            # write list with decisions
            for a in lst:
               if sdo.has_key(a[1]):
                  f.write('%d\t"%s"\t"%s"\n'%(a[0],a[1],sdo[a[1]]))
               else:
                  f.write('%d\t"%s"\t"?"\n'%(a[0],a[1]))
            f.close()
            print " Filter: Wrote '%s'."%fname
         except:
            traceback.print_exc()
            print " Filter-Error: Unable to write '%s'."%fname
            
   def cleanup(self):
      # save current state in global vars...
      global default_object,default_browse,static_dict
      default_object = self.object
      default_browse = self.browse
      static_dict = self.dict
      # restore key actions
      cmd.set_key('F1',None)
      cmd.set_key('F2',None)
      cmd.set_key('F3',None)
      cmd.set_key('right',cmd.forward)
      cmd.set_key('left',cmd.backward)


         

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