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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)

00029 class Filter(Wizard):

    def __init__(self,_self=cmd):

        # initialize parent class
        
        Wizard.__init__(self,_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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