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mutagenesis.py

from pymol.wizard import Wizard
from pymol import cmd
from chempy import io

import pymol
import os
import string
import traceback

sele_name = "_mutate_sel"
bump_name = "_bump_check"

obj_name = "mutation"
tmp_name = "_tmp_mut"
tmp_obj1 = "_tmp_obj1"
tmp_obj2 = "_tmp_obj2"
tmp_obj3 = "_tmp_obj3"

default_mode = "current"
default_rep = "lines"

default_dep = 'dep'

class Mutagenesis(Wizard):

    count = 0
    cutoff = 3.5
    
    def __init__(self):

        cmd.unpick()
        
        Wizard.__init__(self)

        self.dep = default_dep

        self.ind_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
                                           "/data/chempy/sidechains/sc_bb_ind.pkl")
        self.load_library()
        self.status = 0 # 0 no selection, 1 mutagenizing
        self.bump_check = 1
        self.error = None
        self.object_name = None
        self.modes = [
            'current'
            ]
        self.mode = default_mode
        self.rep = default_rep
        residues = self.ind_library.keys()
        residues.extend(['GLY','PRO','ALA'])
        residues.sort()
        self.modes.extend(residues)
        self.mode_name={}
        for a in self.modes:
            self.mode_name[a] = "-> "+a
        self.mode_name['current']="No Mutation"

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


        self.reps = [
            'lines',
            'sticks',
            'spheres',
            'dots'
            ]

        self.rep_name = {
            'lines' : "Show Lines",
            'sticks' : "Show Sticks",
            'spheres' : "Show Spheres",
            'dots' : "Show Dots",
            }

        self.dep_name = {
            'dep' : "Backbone-Dependent",
            'ind' : "Backbone-Independent"
            }

        smm = []
        smm.append([ 2, 'Representation', '' ])
        for a in self.reps:
            smm.append([ 1, self.rep_name[a], 'cmd.get_wizard().set_rep("'+a+'")'])
        self.menu['rep']=smm

        self.deps = [ 'dep', 'ind' ]
        smm = []
        smm.append([ 2, 'Rotamers', '' ])
        for a in self.deps:
            smm.append([ 1, self.dep_name[a], 'cmd.get_wizard().set_dep("'+a+'")'])
        self.menu['dep']=smm

        if 'pk1' in cmd.get_names('selections'):
            cmd.select(sele_name,"(byres pk1)")
            cmd.unpick()
            cmd.enable(sele_name)
            self.status = 1
            self.error = None
            self.do_library()
            cmd.refresh_wizard()

    def load_library(self):
        if self.dep == 'dep':
            if not hasattr(self,'dep_library'):
                self.dep_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
                                           "/data/chempy/sidechains/sc_bb_dep.pkl")
            
    def set_mode(self,mode):
        if mode in self.modes:
            self.mode = mode
        if self.status==1:
            self.do_library()
        cmd.refresh_wizard()
        
    def set_rep(self,rep):
        if rep in self.reps:
            self.rep=rep
        cmd.hide("("+obj_name+")")
        cmd.show('lines',obj_name) # always show lines      
        cmd.show(self.rep,obj_name)
        cmd.refresh_wizard()

    def set_dep(self,value):
        if value!=self.dep:
            self.dep = value
            self.load_library()
            if sele_name in cmd.get_names("all"):
                self.do_library()
            cmd.refresh_wizard()
        
    def get_panel(self):
        return [
            [ 1, 'Mutagenesis',''],
            [ 3, self.mode_name[self.mode],'mode'],
            [ 3, self.rep_name[self.rep],'rep'],
            [ 3, self.dep_name[self.dep],'dep'],                              
            [ 2, 'Apply' , 'cmd.get_wizard().apply()'],         
            [ 2, 'Clear' , 'cmd.get_wizard().clear()'],
            [ 2, 'Done','cmd.set_wizard()'],
            ]

    def cleanup(self):
        global default_mode,default_rep,default_dep
        default_mode = self.mode
        default_rep = self.rep
        default_dep = self.dep
        self.clear()
        
    def clear(self):
        self.status=0
        cmd.delete(tmp_obj1)
        cmd.delete(tmp_obj2)
        cmd.delete(tmp_obj3)
        cmd.delete(sele_name)
        cmd.delete(obj_name)
        cmd.delete(bump_name)
        cmd.refresh_wizard()
        
    def apply(self):
        if self.status==1:
            # find the name of the object which contains the selection
            new_name = None
            obj_list = cmd.get_names('objects')
            for a in obj_list:
                if cmd.get_type(a)=="object:molecule":
                    if cmd.count_atoms("(%s and %s)"%(a,sele_name)):
                        new_name = a
                        break
            src_frame = cmd.get_state()
            if new_name==None:
                print " Mutagenesis: object not found."
            else:
                auto_zoom = cmd.get_setting_text('auto_zoom')
                cmd.set('auto_zoom',"0",quiet=1)
                if self.mode!="current":
                    # create copy w/o residue
                    cmd.create(tmp_obj1,"(%s and not %s)"%(new_name,sele_name))
                    # save copy for bonded atom reference
                    cmd.create(tmp_obj3,new_name)
                    # transfer the selection to copy
                    cmd.select(sele_name,"(%s in %s)"%(tmp_obj3,sele_name))
                    # create copy with mutant in correct frame
                    cmd.create(tmp_obj2,obj_name,src_frame,1)
                    cmd.set_title(tmp_obj2,1,'')
                    cmd.delete(new_name)
                    # create the merged molecule
                    cmd.create(new_name,"(%s or %s)"%(tmp_obj1,tmp_obj2),1) # only one state in merged object...
                    # now connect them
                    cmd.bond("(%s in %s and n;N)"%(new_name,tmp_obj2),
                                "(name C and (%s in (neighbor %s)))"%
                                (new_name,sele_name))
                    cmd.bond("(%s in %s and n;C)"%(new_name,tmp_obj2),
                                "(name N and (%s in (neighbor %s)))"%
                                (new_name,sele_name))
                    # now transfer selection back to the modified object
                    cmd.delete(tmp_obj1)
                    cmd.delete(tmp_obj2)
                    cmd.delete(tmp_obj3)
                    self.clear()
                    # and return to frame 1
                    cmd.frame(1)
                    cmd.refresh_wizard()               
                else:
                    # create copy with conformation in correct state
                    cmd.create(tmp_obj2,obj_name,src_frame,1)
                    # save existing conformation on undo stack
#               cmd.edit("((%s in %s) and name ca)"%(new_name,sele_name))
                    cmd.push_undo("("+sele_name+")")
                    # modify the conformation
                    cmd.update(new_name,tmp_obj2)
#               cmd.unpick()
                    cmd.delete(tmp_obj2)
                    self.clear()
                    # and return to frame 1
                    cmd.frame(1)
                    cmd.refresh_wizard()                              
                cmd.set('auto_zoom',auto_zoom,quiet=1)
                    
    def get_prompt(self):
        self.prompt = None
        if self.status==0:
            self.prompt = [ 'Pick a residue...']
        elif self.status==1:
            self.prompt = [ 'Select a conformational state, or pick a new residue...' ]
        return self.prompt

    def do_library(self):
        cmd.feedback("push")
        cmd.feedback("disable","selector","everythin")
        cmd.feedback("disable","editor","actions")

        self.prompt = [ 'Loading rotamers...']
        
        auto_zoom = cmd.get_setting_text('auto_zoom')
        cmd.set('auto_zoom',"0",quiet=1)
        cmd.frame(0)
        cmd.delete(tmp_name)
        if self.mode=="current":
            pymol.stored.resn=""
            cmd.iterate("(%s and n;ca)"%sele_name,"stored.resn=resn")
            res_type = pymol.stored.resn
            cmd.create(tmp_name,sele_name,1,1)         
        else:
            res_type = self.mode
            cmd.fragment(string.lower(self.mode),tmp_name)
            cmd.remove("("+tmp_name+" and hydro)")
            # copy identifying information
            cmd.iterate("(%s and n;ca)"%sele_name,"stored.chain=chain")
            cmd.alter("(%s)"%tmp_name,"chain=stored.chain")
            cmd.iterate("(%s and n;ca)"%sele_name,"stored.resi=resi")
            cmd.alter("(%s)"%tmp_name,"resi=stored.resi")
            cmd.iterate("(%s and n;ca)"%sele_name,"stored.segi=segi")
            cmd.alter("(%s)"%tmp_name,"segi=stored.segi")
            cmd.iterate("(%s and n;ca)"%sele_name,"stored.ss=ss")
            cmd.alter("(%s)"%tmp_name,"ss=stored.ss")
            # move the fragment
            if ((cmd.count_atoms("(%s and n;cb)"%tmp_name)>0) and
                 (cmd.count_atoms("(%s and n;cb)"%sele_name)>0)):
                cmd.pair_fit("(%s and n;ca)"%tmp_name,
                                 "(%s and n;ca)"%sele_name,
                                 "(%s and n;cb)"%tmp_name,
                                 "(%s and n;cb)"%sele_name,
                                 "(%s and n;c)"%tmp_name,
                                 "(%s and n;c)"%sele_name,
                                 "(%s and n;n)"%tmp_name,
                                 "(%s and n;n)"%sele_name)
            else:
                cmd.pair_fit("(%s and n;ca)"%tmp_name,
                                 "(%s and n;ca)"%sele_name,
                                 "(%s and n;c)"%tmp_name,
                                 "(%s and n;c)"%sele_name,
                                 "(%s and n;n)"%tmp_name,
                                 "(%s and n;n)"%sele_name)
            # fix the carbonyl position...
            cmd.iterate_state(1,"(%s and n;o)"%sele_name,"stored.list=[x,y,z]")
            cmd.alter_state(1,"(%s and n;o)"%tmp_name,"(x,y,z)=stored.list")

        cartoon = (cmd.count_atoms("(%s and n;ca and rep cartoon)"%sele_name)>0)
        sticks = (cmd.count_atoms("(%s and n;ca and rep sticks)"%sele_name)>0)
            
        cmd.delete(obj_name)
        key = res_type
        lib = None
        if self.dep == 'dep':
            try:
                result = cmd.phi_psi("%s"%sele_name)
                if len(result)==1:
                    (phi,psi) = result[result.keys()[0]]
                    (phi,psi) = (int(10*round(phi/10)),int(10*(round(psi/10))))
                    key = (res_type,phi,psi)
                    if not self.dep_library.has_key(key):
                        (phi,psi) = (int(20*round(phi/20)),int(20*(round(psi/20))))
                        key = (res_type,phi,psi)                    
                        if not self.dep_library.has_key(key):
                            (phi,psi) = (int(60*round(phi/60)),int(60*(round(psi/60))))
                            key = (res_type,phi,psi)
                    lib = self.dep_library.get(key,None)
            except:
                pass
        if lib == None:
            key = res_type
            lib = self.ind_library.get(key,None)
            if (lib!= None) and self.dep == 'dep':
                print ' Mutagenesis: no phi/psi, using backbone-independent rotamers.'
        if lib != None:
            state = 1
            for a in lib:
                cmd.create(obj_name,tmp_name,1,state)
                if res_type=='PRO':
                    cmd.unbond("(%s & name N)"%obj_name,"(%s & name CD)"%obj_name)
                for b in a.keys():
                    if b!='FREQ':
                        cmd.set_dihedral("(%s & n;%s)"%(obj_name,b[0]),
                                         "(%s & n;%s)"%(obj_name,b[1]),
                                         "(%s & n;%s)"%(obj_name,b[2]),
                                         "(%s & n;%s)"%(obj_name,b[3]),
                                         a[b],state=state)
                    else:
                        cmd.set_title(obj_name,state,"%1.1f%%"%(a[b]*100))
                if res_type=='PRO':
                    cmd.bond("(%s & name N)"%obj_name,"(%s & name CD)"%obj_name)                
                state = state + 1
            cmd.delete(tmp_name)
            print " Mutagenesis: %d rotamers loaded."%len(lib)
            if self.bump_check:
                cmd.delete(bump_name)
                cmd.create(bump_name,
                "(((byobj %s) within 6 of (%s and not name n+c+ca+o+h+ha)) and (not (%s)))|(%s)"%
                           (sele_name,obj_name,sele_name,obj_name),singletons=1)
                cmd.color("gray50",bump_name+" and elem c")
                cmd.set("seq_view",0,bump_name,quiet=1)
                cmd.hide("everything",bump_name)
                cmd.bond("(n;N and (%s in (neighbor %s)))"%(bump_name,sele_name),
                         "(n;C and (%s in %s))"%(bump_name,obj_name))
                cmd.bond("(n;C and (%s in (neighbor %s)))"%(bump_name,sele_name),
                         "(n;N and (%s in %s))"%(bump_name,obj_name))
                cmd.protect("%s and not (%s in (%s and not name n+c+ca+o+h+ha))"%
                            (bump_name,bump_name,obj_name))
                cmd.sculpt_activate(bump_name)
                cmd.show("cgo",bump_name)
                # draw the bumps
                cmd.set("sculpt_vdw_vis_mode",1,bump_name)
                state = 1
                for a in lib:
                    cmd.sculpt_iterate(bump_name,state=state)
                    state = state + 1
        else:
            cmd.create(obj_name,tmp_name,1,1)
            print " Mutagenesis: no rotamers found in library."
        cmd.set("seq_view",0,obj_name,quiet=1)
        pymol.util.cbaw(obj_name)
        cmd.hide("("+obj_name+")")
        cmd.show(self.rep,obj_name)
        cmd.show('lines',obj_name) #neighbor  always show lines
        if cartoon:
            cmd.show("cartoon",obj_name)
        if sticks:
            cmd.show("sticks",obj_name)
        cmd.set('auto_zoom',auto_zoom,quiet=1)
        cmd.delete(tmp_name)
        cmd.frame(0)
        cmd.unpick()
        cmd.feedback("pop")

    def do_select(self,selection):
        if self.status!=0:
            cmd.delete(obj_name)
        cmd.select(sele_name,"(byres first (%s))"%selection)
        cmd.unpick()
        cmd.enable(sele_name)
        self.status = 1
        self.error = None
        self.do_library()
        cmd.delete(selection)
        cmd.refresh_wizard()
        cmd.deselect()
        return 1
    
    def do_pick(self,bondFlag):
        if bondFlag:
            self.error = "Error: please select an atom, not a bond."
            print self.error
        else:
            if self.status!=0:
                cmd.delete(obj_name)
            cmd.select(sele_name,"(byres pk1)")
            cmd.unpick()
            cmd.enable(sele_name)
            self.status = 1
            self.error = None
            self.do_library()
        cmd.refresh_wizard()




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