import os, re, sys, glob, shutil import Tkinter, Pmw, tkFileDialog import subprocess import webbrowser import chimera from chimera import runCommand from chimera.baseDialog import ModelessDialog import PyRy3D_Extension from Page1_functions import P1F from Page3_functions import P3F from Paths import Paths from Dialogs import Display from WidgetState import WS work_already=Pmw.EntryField() import tkMessageBox import ttk from threading import Thread P1F=P1F(); P3F=P3F(); Paths=Paths(); Display=Display(); WS=WS() class PyRyDialog(ModelessDialog): name = "PyRy3D Extension" buttons = ("Close") help = ("http://genesilico.pl/pyry3d/index.php?option=com_content&view=article&id=56&Itemid=201", PyRy3D_Extension) title = "PyRy3D Extension" def fillInUI(self, parent): #----- U S E R S I N T E R F A C E self.parento = parent self.StatusPathFrame = Tkinter.Frame(parent) self.StatusPathFrame.pack() #----- FRAME FOR DETERMINING PYRY3D PATH self.pyry3dpath_dialog() #----- SEPARATING THE WINDOW IN TWO? self.StatusFrame = Tkinter.LabelFrame(self.StatusPathFrame,text="PYRY3D EXTENSION STATUS:",fg="blue",pady=3,padx=3) #self.StatusFrame.grid(row=0,column=0,sticky="nsew", padx=10, pady=5) self.StatusLabel = Tkinter.Label(self.StatusFrame, text="Please specify your PyRy3D path.", fg="blue") self.StatusLabel.pack() #----- CREATING AND PACKING THE NOTEBOOK self.notebook=Pmw.NoteBook(parent) self.notebook.pack(fill = 'both', expand = 1, padx = 10, pady = 10) #########----- ADDING NOTEBOOK'S FIRST PAGE - OPEN MODELS self.page1=self.notebook.add("Models") page1=self.page1 self.notebook.tab("Models").focus_set() #----- ADDING FIRST PAGE'S CONTENT #----- FIRST FRAME (MODELS ADDING BUTTONS + MAPS / COMPONENTS LISTS): df0=Tkinter.Frame(page1,bd=1,relief="ridge",pady=3,padx=3) df0.pack(fill="x") self.complist=[] self.dens_button=Tkinter.Button(df0,text="Add density map...",command=self.choosemap) self.dens_button.pack(side='left',fill="x") self.comp_button=Tkinter.Button(df0,text="Add structure...",command=self.choosecomp) self.comp_button.pack(side='left',fill="x") df=Tkinter.Frame(page1,bd=1,relief="ridge",pady=3,padx=3) df.pack(fill="x") fixedFont = Pmw.logicalfont('Fixed') self.mapli = Pmw.ScrolledText(df, labelpos = 'n', label_text='', columnheader = 1, rowheader = 0, rowcolumnheader = 0, usehullsize = 1, hull_width = 420, hull_height = 120, text_wrap='none', Header_foreground = 'blue', text_padx = 4, text_pady = 4, Header_padx = 4, ) self.mapli.grid(row=0,columnspan=2) up1=["Map ready to open: (not required)"] headerLine = '' for column in range(len(up1)): headerLine = headerLine + ('%-7s ' % (up1[column],)) headerLine = headerLine[:-3] self.mapli.component('columnheader').insert('0.0', headerLine) self.mapli.configure( text_state = 'disabled', Header_state = 'disabled') self.struli = Pmw.ScrolledText(df, columnheader = 1, rowheader = 0, rowcolumnheader = 0, usehullsize = 1, hull_width = 420, hull_height = 220, text_wrap='none', Header_foreground = 'blue', text_padx = 4, text_pady = 4, Header_padx = 4, ) self.struli.grid(row=1,columnspan=2,sticky="nsew") up2=["Structures ready to open: (at least two required)"] headerLine = '' for column in range(len(up2)): headerLine = headerLine + ('%-7s ' % (up2[column],)) headerLine = headerLine[:-3] self.struli.component('columnheader').insert('0.0', headerLine) self.struli.configure( text_state = 'disabled', Header_state = 'disabled') #----- SECOND FRAME - OPEN FILES / CLEAR STRUCTURES BUTTONS of=Tkinter.Frame(page1,bd=1,relief="ridge",pady=3,padx=3) of.pack(fill="x") self.open_button=Tkinter.Button(of,text="Load data",command=self.openandsaveall) self.clear_button=Tkinter.Button(of,text="Clear data",command=self.clear) self.new_session_button=Tkinter.Button(of,text="New session",command=self.new_session) self.open_button.grid(row=0,column=0,sticky="ew") self.clear_button.grid(row=0,column=1,sticky="ew") self.new_session_button.grid(row=0,column=2,sticky="ew") self.new_session_button.configure(state="disabled") #########----- ADDING NOTEBOOK'S SECOND PAGE - SIMULATION / SCORE self.page2=self.notebook.add("Sim/Score") #----- ADDING SECOND PAGE'S CONTENT #----- PREPARATION FRAME1: CONFIGURATION PARAMETERS self.conf_params_frame=Tkinter.Frame(self.page2,bd=1,relief="ridge",pady=3,padx=3) self.conf_params_frame.pack(fill="x") sscf=self.conf_params_frame self.cfg_v=Tkinter.IntVar(sscf) self.cfg_v.set(1) self.ss_cfg_win_checkbutton=Tkinter.Radiobutton(sscf,text="Get parameters from parameters window",variable=self.cfg_v,value=1,command=lambda: self.cfg_choice(self.cfg_v)) self.ss_cfg_win_checkbutton.grid(row=1,column=0,columnspan=2,sticky="w") self.ss_params_button=Tkinter.Button(sscf,text="Parameters window...",command=P3F.show_params_window) self.ss_params_button.grid(row=2,column=0,sticky="w") self.ss_cfg_fil_checkbutton=Tkinter.Radiobutton(sscf,text="Get parameters from configuration file",variable=self.cfg_v,value=2,command=lambda: self.cfg_choice(self.cfg_v)) self.ss_cfg_fil_checkbutton.grid(row=3,column=0,columnspan=2,sticky="w") self.ss_cfg_fil_entry=Pmw.EntryField(sscf,labelpos="w",label_text="Configuration file:",entry_bg="white",entry_width=15) self.ss_cfg_fil_entry.grid(row=4,column=0,sticky="e") self.ss_cfg_fil_button=Tkinter.Button(sscf,text="Browse",command=self.ss_choose_cfg) self.ss_cfg_fil_button.grid(row=4,column=1,sticky="e") self.cfg_choice(self.cfg_v) #----- PREPARATION FRAME2: RESTRAINTS self.restraints_frame=Tkinter.Frame(self.page2,bd=1,relief="ridge",pady=3,padx=3) self.restraints_frame.pack(fill="x") rsf=self.restraints_frame res_v=Tkinter.IntVar(rsf) res_v.set(1) self.res_empty_radiobutton=Tkinter.Radiobutton(rsf,text="Do not use experimental restraints",variable=res_v,value=1,command=lambda: self.res_choice(res_v)) self.res_empty_radiobutton.grid(row=1,column=0,columnspan=2,sticky="w") self.res_fil_radiobutton=Tkinter.Radiobutton(rsf,text="Use restraints file from hard drive",variable=res_v,value=2,command=lambda: self.res_choice(res_v)) self.res_fil_radiobutton.grid(row=2,column=0,columnspan=2,sticky="w") self.res_fil_entry=Pmw.EntryField(rsf,labelpos="w",label_text="Restraints file:",entry_bg="white",entry_width=15) self.res_fil_entry.grid(row=3,column=0,sticky="e") self.res_fil_button=Tkinter.Button(rsf,text="Browse",command=self.ss_choose_resfile) self.res_fil_button.grid(row=3,column=1,sticky="e") self.res_choice(res_v) #----- PREPARATION FRAME2: SEQUENCES self.sequence_frame=Tkinter.Frame(self.page2,bd=1,relief="ridge",pady=3,padx=3) self.sequence_frame.pack(fill="x") sframe=self.sequence_frame self.simseq_v=Tkinter.IntVar(sframe) self.simseq_v.set(1) self.seq_gen_radiobutton=Tkinter.Radiobutton(sframe,text="Generate sequences automatically",variable=self.simseq_v,value=1,command=lambda: self.seq_choice(self.simseq_v)) self.seq_gen_radiobutton.grid(row=1,column=0,columnspan=2,sticky="w") self.seq_fil_radiobutton=Tkinter.Radiobutton(sframe,text="Use sequence file from hard drive",variable=self.simseq_v,value=2,command=lambda: self.seq_choice(self.simseq_v)) self.seq_fil_radiobutton.grid(row=2,column=0,columnspan=2,sticky="w") self.seq_fil_entry=Pmw.EntryField(sframe,labelpos="w",label_text="Fasta file:",entry_bg="white",entry_width=15) self.seq_fil_entry.grid(row=3,column=0,sticky="e") self.seq_fil_button=Tkinter.Button(sframe,text="Browse",command=self.ss_choose_seqfile) self.seq_fil_button.grid(row=3,column=1,sticky="e") self.seq_text_radiobutton=Tkinter.Radiobutton(sframe,text="Input sequences manually",variable=self.simseq_v,value=3,command=lambda: self.seq_choice(self.simseq_v)) self.seq_text_radiobutton.grid(row=4,column=0,columnspan=2,sticky="w") self.seq_text_button=Tkinter.Button(sframe,text="Input window...",command=self.display_text_sequence_window) self.seq_text_button.grid(row=5,column=0,sticky="w") #### self.seq_text_win=Tkinter.Tk() self.seq_text_win.title("Sequences") self.seq_text_wf=Tkinter.LabelFrame(self.seq_text_win,text="Sequences") self.seq_text_wf.pack(fill="x") seq_text__label=Tkinter.Label(self.seq_text_wf,text="Use the field below to enter your sequences in FASTA format. \nEnter sequences for all structures.",fg="blue").pack(fill="x") self.seq_text_li = Pmw.ScrolledText(self.seq_text_wf, columnheader = 0, rowheader = 0, rowcolumnheader = 0, usehullsize = 1, hull_width = 400, hull_height = 300, text_wrap='none', text_padx = 4, text_pady = 4, ) self.seq_text_li.pack(fill="x") self.seq_text_f2=Tkinter.Frame(self.seq_text_win,bd=1,relief="ridge",pady=3,padx=3) self.seq_text_f2.pack(fill="x") closeseq_text__button=Tkinter.Button(self.seq_text_f2,text="Apply and close",width=10,command=self.seq_text_win.withdraw) closeseq_text__button.pack(side='right') seq_text_help_button=Tkinter.Button(self.seq_text_f2,text="Help",width=10,command=lambda: webbrowser.open("http://genesilico.pl/pyry3d/concepts#sequences")) seq_text_help_button.pack(side='left') self.seq_text_win.withdraw() ### self.seq_choice(self.simseq_v) #----- OUTPUT DIR FRAME self.outdir_frame=Tkinter.Frame(self.page2,bd=1,relief="ridge",pady=4,padx=4) self.outdir_frame.pack(fill="x") odfr=self.outdir_frame self.outdir_entry=Pmw.EntryField(odfr,labelpos="w",label_text="Output directory:",entry_bg="white",entry_width=15) self.outdir_entry.grid(row=0,column=0,sticky="e") self.outdir_button=Tkinter.Button(odfr,text="Browse",command=self.ss_choose_outdir) self.outdir_button.grid(row=0,column=1,sticky="e") #----- ACTIONS FRAMES self.autoscore_frame=Tkinter.Frame(self.page2,bd=1,relief="ridge",pady=4,padx=4) self.autoscore_frame.pack(fill="x") self.autoscore_button=Tkinter.Button(self.autoscore_frame,text="Calculate PyRy3D score for displayed complex",width=37,command=self.score_complex) self.autoscore_button.pack(fill="x") self.autoscore_button.configure(state="disabled") self.simulation_frame=Tkinter.Frame(self.page2,bd=1,relief="ridge",pady=4,padx=4) self.simulation_frame.pack(fill="x") self.simulation_button=Tkinter.Button(self.simulation_frame,text="Perform PyRy3D simulation",width=37,command=self.simulate_complex_fin) self.simulation_button.pack(fill="x") self.simulation_button.configure(state="disabled") self.threshold_frame=Tkinter.Frame(self.page2,bd=1,relief="ridge",pady=4,padx=4) self.threshold_frame.pack(fill="x") self.threshold_button=Tkinter.Button(self.threshold_frame,text="Calculate density threshold",width=37,command=self.calc_threshold) self.threshold_button.pack(fill="x") #########----- ADDING NOTEBOOK'S THIRD PAGE - INPUT GENERATOR self.page3=self.notebook.add("Input Gen") #----- ADDING THIRD PAGE'S CONTENT self.ingen1_frame=Tkinter.Frame(self.page3,bd=1,relief="ridge",pady=3,padx=3) self.ingen1_frame.pack(fill="x") ig1f=self.ingen1_frame ig1_label=Tkinter.Label(ig1f,text="Choose input files to generate:") ig1_label.grid(row=0,column=0,columnspan=2,sticky="w") ig_str_v=Tkinter.IntVar() ig_map_v=Tkinter.IntVar() ig_seq_v=Tkinter.IntVar() self.ig_str_checkbutton=Tkinter.Checkbutton(ig1f,text="Structures",variable=ig_str_v,command=lambda: self.ig_check_elements(ig_str_v,ig_map_v,ig_seq_v)) self.ig_str_checkbutton.grid(row=1,column=0,sticky="w") self.ig_map_checkbutton=Tkinter.Checkbutton(ig1f,text="Density map",variable=ig_map_v,command=lambda: self.ig_check_elements(ig_str_v,ig_map_v,ig_seq_v)) self.ig_map_checkbutton.grid(row=2,column=0,sticky="w") self.ig_seq_checkbutton=Tkinter.Checkbutton(ig1f,text="Sequences",variable=ig_seq_v,command=lambda: self.ig_check_elements(ig_str_v,ig_map_v,ig_seq_v)) self.ig_seq_checkbutton.grid(row=3,column=0,sticky="w") ig_res_v=Tkinter.IntVar() ig_res_v.set(0) ig_con_v=Tkinter.IntVar() ig_con_v.set(0) def ig_choose_resfile(): Paths.ig_respath=P3F.ig_choose_resfile(self.page3,self.ig_res_entry) self.ig_res_checkbutton=Tkinter.Checkbutton(ig1f,text="Restraints",variable=ig_res_v,command=lambda: self.ig_check_res(ig_res_v)) self.ig_res_checkbutton.grid(row=4,column=0,sticky="w") self.ig_res_entry=Pmw.EntryField(ig1f,labelpos="w",label_text="Restraints file:",entry_width=17,entry_bg="white") self.ig_res_entry.grid(row=5,column=0,sticky="w") self.ig_res_button=Tkinter.Button(ig1f,text="Browse",command=ig_choose_resfile) self.ig_res_button.grid(row=5,column=1,sticky="w") self.ig_con_checkbutton=Tkinter.Checkbutton(ig1f,text="Configuration file",variable=ig_con_v,command=lambda: self.ig_check_con(ig_con_v)) self.ig_con_checkbutton.grid(row=6,column=0,sticky="w") self.ig_con_button=Tkinter.Button(ig1f,text="Parameters window...",command=P3F.show_params_window) self.ig_con_button.grid(row=7,column=0,sticky="w") self.ingen2_frame=Tkinter.Frame(self.page3,bd=1,relief="ridge",pady=3,padx=3) self.ingen2_frame.pack(fill="x") ig2f=self.ingen2_frame def ig_choose_output_folder(): Paths.ig_outpath=P3F.ig_choose_output_folder(self.page3,self.ig_out_entry) self.ig_out_entry=Pmw.EntryField(ig2f,labelpos="w",label_text="Generate files in:",entry_width=17,entry_bg="white") self.ig_out_entry.grid(row=0,column=0,sticky="w") self.ig_out_button=Tkinter.Button(ig2f,text="Browse",command=ig_choose_output_folder) self.ig_out_button.grid(row=0,column=1,sticky="w") self.ingen3_frame=Tkinter.Frame(self.page3,bd=1,relief="ridge",pady=3,padx=3) self.ingen3_frame.pack(fill="x") def ig_generate_input_files(): try: P1F.writeAllPDBs(Paths.temppath,Paths.mappath) P3F.generate_input_files(Paths.ig_outpath,Paths.temppath,Paths.ig_respath,Paths.mappath, ig_con_v.get(),ig_str_v.get(),ig_res_v.get(),ig_seq_v.get(),ig_map_v.get(),nowindow=0) except Exception as e: tkMessageBox.showwarning("Error", e) self.ingen_button=Tkinter.Button(self.ingen3_frame,text="Generate defined input files",command=ig_generate_input_files) self.ingen_button.grid() self.ig_check_res(ig_res_v) self.ig_check_con(ig_con_v) #########----- ADDING NOTEBOOK'S FOURTH PAGE - ANIMATION GENERATOR self.page4=self.notebook.add("Animations") page4=self.page4 def set_anim_movie_out(): path=tkFileDialog.askdirectory(parent=parent,initialdir="/",title="Choose directory") self.anim_dir_entry.setvalue(path) def set_anim_img_out(): path=tkFileDialog.askdirectory(parent=parent,initialdir="/",title="Choose directory") self.anim_img_out.setvalue(path) def generate_movie(): from Movies import Anim try: A=Anim() A.dirpath=self.anim_dir_entry.getvalue() A.paths=A.get_paths() A.wait=5 A.step=self.rec_entry.getvalue() A.img_outdir=self.anim_img_out.getvalue() A.output=self.anim_out_entry.getvalue() A.format=self.anim_format.getvalue() A.size_x=self.anim_dimensions_x_entry.getvalue() A.size_y=self.anim_dimensions_y_entry.getvalue() if A.dirpath == "" or A.paths == "" or A.wait == "" or A.step == "" or A.output == "" or A.format == "": tkMessageBox.showinfo("PyRy3D info", "Please fill all the fields except size and image directory before continuing.") elif len(chimera.openModels.list()) == 0: tkMessageBox.showinfo("PyRy3D info", "Please open and position your shape descriptor first.") elif len(chimera.openModels.list()) > 1: tkMessageBox.showinfo("PyRy3D info", "Only your shape descriptor should be opened in Chimera before starting.") else: A.generate_alt() except Exception as e: tkMessageBox.showwarning("Error", e) def anim_get_inpdir(): path=tkFileDialog.askdirectory(initialdir="/",title="Choose input folder") self.anim_dir_entry.setvalue(path) self.anim_dir_entry.configure(entry_state="disabled") potential_frames = os.listdir(path) self.potential_frames_number = len(potential_frames) def anim_get_imgdir(): path=tkFileDialog.askdirectory(initialdir="/",title="Choose input folder") self.anim_img_out.setvalue(path) self.anim_img_out.configure(entry_state="disabled") def anim_calc_frames(): frac = self.potential_frames_number / int(self.rec_entry.getvalue()) self.rec_lab3.configure(text=str(frac)) def anim_get_outfile(): allowed_format = "."+self.anim_format.getvalue() path=tkFileDialog.asksaveasfilename(initialdir="/",title="Choose output file",filetypes=[("movie files",allowed_format)]) self.anim_out_entry.setvalue(path) self.anim_out_entry.configure(entry_state="disabled") #----- ADDING FOURTH PAGE'S CONTENT self.anim_f0=Tkinter.Frame(page4,bd=1,relief="ridge",pady=3,padx=3) self.anim_f0.pack(fill="x") self.anim_text=Tkinter.Label(self.anim_f0,text="Before starting the animation generation,\nopen and position your shape descriptor in the\nChimera graphics window.",fg="blue") self.anim_text.pack() self.anim_f1=Tkinter.Frame(page4,bd=1,relief="ridge",pady=3,padx=3) self.anim_f1.pack(fill="x") self.anim_dir_entry=Pmw.EntryField(self.anim_f1,labelpos="w",label_text="PyRy3D output files:",entry_width=10,entry_bg="white") self.anim_dir_entry.pack(side="left") self.anim_dir_button=Tkinter.Button(self.anim_f1,text="Browse",command=anim_get_inpdir) self.anim_dir_button.pack(side="left") self.anim_f2=Tkinter.Frame(page4,bd=1,relief="ridge",pady=3,padx=3) self.anim_f2.pack(fill="x") self.rec_entry=Pmw.EntryField(self.anim_f2,labelpos="w",label_text="Record 1 in",entry_width=5,entry_bg="white",validate={"validator":"real"}, command=anim_calc_frames) self.rec_entry.pack(side="left") self.rec_lab=Tkinter.Label(self.anim_f2,text=" files") self.rec_lab.pack(side="left") self.anim_f3=Tkinter.Frame(page4,bd=1,relief="ridge",pady=3,padx=3) self.anim_f3.pack(fill="x") self.rec_lab2=Tkinter.Label(self.anim_f3,text="Number of frames:").pack(side="left") self.rec_lab3=Tkinter.Label(self.anim_f3,text="0") self.rec_lab3.pack(side="left") self.rec_calc_button = Tkinter.Button(self.anim_f3,text="Calculate",command=anim_calc_frames) self.rec_calc_button.pack(side="left") self.anim_f4=Tkinter.Frame(page4,bd=1,relief="ridge",pady=3,padx=3) self.anim_f4.pack(fill="x") self.anim_out_entry=Pmw.EntryField(self.anim_f4,labelpos="w",label_text="Save movie file as:",entry_width=20,entry_bg="white") self.anim_out_entry.grid(row=0,column=0,sticky="w") self.anim_out_button=Tkinter.Button(self.anim_f4,text="Browse",command=anim_get_outfile) self.anim_out_button.grid(row=0,column=1,sticky="w") self.anim_format=Pmw.OptionMenu(self.anim_f4,labelpos="w",label_text="Movie format:",initialitem="mov", items=["h264","vp8","theora","mov","avi","mp4","mp2","mpeg"]) self.anim_format.grid(row=1,column=0,sticky="w") self.anim_f6=Tkinter.Frame(page4,bd=1,relief="ridge",pady=3,padx=3) #self.anim_f6.pack(fill="x") self.anim_img_out=Pmw.EntryField(self.anim_f6,labelpos="w",label_text="Save images in:",entry_width=15,entry_bg="white") #self.anim_img_out.pack(side="left") self.anim_img_but=Tkinter.Button(self.anim_f6,text="Browse",command=anim_get_imgdir) #self.anim_img_but.pack(side="left") self.anim_f5=Tkinter.Frame(page4,bd=1,relief="ridge",pady=3,padx=3) self.anim_f5.pack(fill="x") self.anim_dimensions_x_entry=Pmw.EntryField(self.anim_f5,labelpos="w",label_text="Movie size: width:",entry_width=5,entry_bg="white",validate={"validator":"real"}) self.anim_dimensions_x_entry.pack(side="left") self.anim_dimensions_y_entry=Pmw.EntryField(self.anim_f5,labelpos="w",label_text="height:",entry_width=5,entry_bg="white",validate={"validator":"real"}) self.anim_dimensions_y_entry.pack(side="left") self.anim_f8=Tkinter.Frame(page4,bd=1,relief="ridge",pady=3,padx=3) self.anim_f8.pack(fill="x") self.anim_start=Tkinter.Button(self.anim_f8,text="Generate movie",command=generate_movie) self.anim_start.pack(side="right") #self.anim_help=Tkinter.Button(self.anim_f8,text="Help",width=10,command=lambda: webbrowser.open("http://genesilico.pl/pyry3d/index.php?option=com_content&view=article&id=52&Itemid=199#3.2")) #self.anim_help.pack(side="right") #----- ADDING FOURTH PAGE'S CONTENT #########----- ADDING NOTEBOOK'S FIFTH PAGE - RANKING self.page5=self.notebook.add("Ranking") page5=self.page5 #----- ADDING FIFTH PAGE'S CONTENT # THE WAY STRUCTURES ARE LOADED self.p51_frame=Tkinter.Frame(self.page5,bd=1,relief="ridge",pady=3,padx=3) p51=self.p51_frame p51.pack(fill="x") self.rank_fc_v=Tkinter.IntVar() self.rank_fc_v.set(0) self.p5_fromchimera_check=Tkinter.Radiobutton(p51,text="Load complexes and map from Chimera window",variable=self.rank_fc_v,value=0, command=self.ranking_inp_choose) self.p5_fromchimera_check.grid(row=0,sticky="w") self.p5_fromfiles_check=Tkinter.Radiobutton(p51,text="Load complexes and map from files",variable=self.rank_fc_v,value=1, command=self.ranking_inp_choose) self.p5_fromfiles_check.grid(row=1,sticky="w") # INPUT STRUCTURES self.p54_frame=Tkinter.Frame(self.page5,bd=1,relief="ridge",pady=3,padx=3) p54=self.p54_frame p54.pack(fill="x") self.p5_input_entry=Pmw.EntryField(p54,labelpos="w",label_text="Structures directory:",entry_width=15,entry_bg="white",entry_state="disabled",label_state="disabled") self.p5_input_entry.grid(row=0,column=0,sticky="e") self.p5_input_button=Tkinter.Button(p54,text="Browse",command=self.ranking_input_set) self.p5_input_button.grid(row=0,column=1,sticky="w") # PARAMETERS self.p55_frame=Tkinter.Frame(self.page5,bd=1,relief="ridge",pady=3,padx=3) self.p55_frame.pack(fill="x") p55 = self.p55_frame self.p5_cfg_v=Tkinter.IntVar(sscf) self.p5_cfg_v.set(1) self.p5_cfg_win_checkbutton=Tkinter.Radiobutton(p55,text="Get parameters from parameters window",variable=self.p5_cfg_v,value=1,command=lambda: self.p5_cfg_choice(self.p5_cfg_v)) self.p5_cfg_win_checkbutton.grid(row=2,column=0,columnspan=2,sticky="w") self.p5_params_button=Tkinter.Button(p55,text="Parameters window...",command=P3F.show_params_window) self.p5_params_button.grid(row=3,column=0,sticky="w") self.p5_cfg_fil_checkbutton=Tkinter.Radiobutton(p55,text="Get parameters from configuration file",variable=self.p5_cfg_v,value=2,command=lambda: self.p5_cfg_choice(self.p5_cfg_v)) self.p5_cfg_fil_checkbutton.grid(row=4,column=0,columnspan=2,sticky="w") self.p5_cfg_entry=Pmw.EntryField(p55,labelpos="w",label_text="Configuration file:",entry_width=15,entry_bg="white") self.p5_cfg_entry.grid(row=5,column=0,sticky="e") self.p5_cfg_button=Tkinter.Button(p55,text="Browse",command=self.ranking_cfg_set) self.p5_cfg_button.grid(row=5,column=1,sticky="w") # RESTRAINTS self.p56_frame=Tkinter.Frame(self.page5,bd=1,relief="ridge",pady=3,padx=3) self.p56_frame.pack(fill="x") p56=self.p56_frame self.p5_res_v=Tkinter.IntVar(p56) self.p5_res_v.set(1) self.p5_empty_radiobutton=Tkinter.Radiobutton(p56,text="Do not use experimental restraints",variable=self.p5_res_v,value=1,command=lambda: self.p5_res_choice(self.p5_res_v)) self.p5_empty_radiobutton.grid(row=1,column=0,columnspan=2,sticky="w") self.p5_fil_radiobutton=Tkinter.Radiobutton(p56,text="Use restraints file from hard drive",variable=self.p5_res_v,value=2,command=lambda: self.p5_res_choice(self.p5_res_v)) self.p5_fil_radiobutton.grid(row=2,column=0,columnspan=2,sticky="w") self.p5_res_entry=Pmw.EntryField(p56,labelpos="w",label_text="Restraints file:",entry_width=15,entry_bg="white") self.p5_res_entry.grid(row=3,column=0,sticky="e") self.p5_res_button=Tkinter.Button(p56,text="Browse",command=self.ranking_res_set) self.p5_res_button.grid(row=3,column=1,sticky="w") self.p5_res_choice(self.p5_res_v) # SEQUENCES self.p57_frame=Tkinter.Frame(self.page5,bd=1,relief="ridge",pady=3,padx=3) self.p57_frame.pack(fill="x") p57=self.p57_frame self.p5_simseq_v=Tkinter.IntVar(p57) self.p5_simseq_v.set(1) self.p5_seq_gen_radiobutton=Tkinter.Radiobutton(p57,text="Generate sequences automatically",variable=self.p5_simseq_v,value=1,command=lambda: self.p5_seq_choice(self.p5_simseq_v)) self.p5_seq_gen_radiobutton.grid(row=1,column=0,columnspan=2,sticky="w") self.p5_seq_fil_radiobutton=Tkinter.Radiobutton(p57,text="Use sequence file from hard drive",variable=self.p5_simseq_v,value=2,command=lambda: self.p5_seq_choice(self.p5_simseq_v)) self.p5_seq_fil_radiobutton.grid(row=2,column=0,columnspan=2,sticky="w") self.p5_seq_entry=Pmw.EntryField(p57,labelpos="w",label_text="Fasta file:",entry_width=15,entry_bg="white") self.p5_seq_entry.grid(row=3,column=0,sticky="e") self.p5_seq_button=Tkinter.Button(p57,text="Browse",command=self.ranking_seq_set) self.p5_seq_button.grid(row=3,column=1,sticky="w") self.p5_seq_text_radiobutton=Tkinter.Radiobutton(p57,text="Input sequences manually",variable=self.p5_simseq_v,value=3,command=lambda: self.p5_seq_choice(self.p5_simseq_v)) self.p5_seq_text_radiobutton.grid(row=4,column=0,columnspan=2,sticky="w") self.p5_seq_text_button=Tkinter.Button(p57,text="Input window...",command=self.display_text_sequence_window) self.p5_seq_text_button.grid(row=5,column=0,sticky="w") self.p5_seq_choice(self.p5_simseq_v) # MAP AND SORTING self.p58_frame=Tkinter.Frame(self.page5,bd=1,relief="ridge",pady=3,padx=3) self.p58_frame.pack(fill="x") p58=self.p58_frame self.p5_map_entry=Pmw.EntryField(p58,labelpos="w",label_text="Map file:",entry_width=15,entry_bg="white",entry_state="disabled",label_state="disabled") self.p5_map_entry.grid(row=7,column=0,sticky="e") self.p5_map_button=Tkinter.Button(p58,text="Browse",command=self.ranking_map_set) self.p5_map_button.grid(row=7,column=1,sticky="w") self.p5_sort_menu=Pmw.OptionMenu(p58,labelpos="w",label_text="Sort results by:",initialitem="Overall score", items=["Overall score","Collisions","Restraints","Outside box","Map empty space","Density"]) self.p5_sort_menu.grid(row=8,column=0,sticky="e") self.p52_frame=Tkinter.Frame(self.page5,bd=1,relief="ridge",pady=3,padx=3) self.p52_frame.pack(fill="x") self.p5_runranking_button=Tkinter.Button(self.p52_frame,text="Create ranking",command=self.make_ranking) self.p5_runranking_button.pack(side="right") self.p5_cfg_choice(self.p5_cfg_v) #########----- ADDING NOTEBOOK'S SIXTH PAGE - CLUSTERING self.page6=self.notebook.add("Clustering") page6=self.page6 #----- ADDING SIXTH PAGE'S CONTENT self.p61_frame=Tkinter.Frame(self.page6,bd=1,relief="ridge",pady=3,padx=3) p61=self.p61_frame p61.pack(fill="x") self.p6_input_entry=Pmw.EntryField(p61,labelpos="w",label_text="Input directory:",entry_width=15,entry_bg="white") self.p6_input_entry.grid(row=0,column=0,sticky="e") self.p6_input_button=Tkinter.Button(p61,text="Browse", command=self.clust_input_set) self.p6_input_button.grid(row=0,column=1,sticky="w") self.p6_map_entry=Pmw.EntryField(p61,labelpos="w",label_text="Map file:",entry_width=15,entry_bg="white") self.p6_map_entry.grid(row=1,column=0,sticky="e") self.p6_map_button=Tkinter.Button(p61,text="Browse", command=self.clust_map_set) self.p6_map_button.grid(row=1,column=1,sticky="w") ### self.p62_frame=Tkinter.Frame(self.page6,bd=1,relief="ridge",pady=3,padx=3) p62=self.p62_frame p62.pack(fill="x") self.p6_scoretype_menu=Pmw.OptionMenu(p62,labelpos="w",label_text="Score type:",initialitem="pyry3d",items=["ccc","pyry3d"]) self.p6_scoretype_menu.grid(row=0,column=0,sticky="e") self.p6_measuretype_menu=Pmw.OptionMenu(p62,labelpos="w",label_text="Measure type:",initialitem="RMSD",items=["RMSD","TM_Score","GDT_TS"]) self.p6_measuretype_menu.grid(row=1,column=0,sticky="e") self.p6_representation_menu=Pmw.OptionMenu(p62,labelpos="w",label_text="Representation:",initialitem="fa",items=["fa","ca","sphere"]) self.p6_representation_menu.grid(row=2,column=0,sticky="e") ### self.p63_frame=Tkinter.Frame(self.page6,bd=1,relief="ridge",pady=3,padx=3) p63=self.p63_frame p63.pack(fill="x") self.p6_thresh_entry=Pmw.EntryField(p63,labelpos="w",label_text="Density threshold:",entry_width=15,entry_bg="white",validate={"validator":"real"}) self.p6_thresh_entry.grid(row=0,column=0,sticky="e") self.p6_clusthresh_entry=Pmw.EntryField(p63,labelpos="w",label_text="Clustering threshold:",entry_width=15,entry_bg="white",validate={"validator":"real"}) self.p6_clusthresh_entry.grid(row=1,column=0,sticky="e") self.p6_numstruct_entry=Pmw.EntryField(p63,labelpos="w",label_text="Number of structures:",entry_width=15,entry_bg="white",validate={"validator":"real"}) self.p6_numstruct_entry.grid(row=2,column=0,sticky="e") ### self.p635_frame=Tkinter.Frame(self.page6,bd=1,relief="ridge",pady=3,padx=3) p635=self.p635_frame p635.pack(fill="x") self.oligos = Tkinter.IntVar() self.oligos.set(0) self.p6_clustoligos_checkbutton=Tkinter.Checkbutton(p635,text="Structures are oligomers",variable=self.oligos) self.p6_clustoligos_checkbutton.grid(row=0,column=0,sticky="w") self.clustsort = Tkinter.IntVar() self.clustsort.set(0) self.p6_clustsort_checkbutton=Tkinter.Checkbutton(p635,text="Sort results into different folders",variable=self.clustsort,command=self.check_clustsort) self.p6_clustsort_checkbutton.grid(row=1,column=0,sticky="w") self.p6_clustsort_entry=Pmw.EntryField(p635,labelpos="w",label_text="Sort clusters containing at least ",entry_width=5,entry_bg="white",validate={"validator":"real"}) self.p6_clustsort_entry.grid(row=2,column=0,sticky="w") self.p6_clustsort_label=Tkinter.Label(p635,text=" structures") self.p6_clustsort_label.grid(row=2,column=1,sticky="w") self.check_clustsort() ### self.p64_frame=Tkinter.Frame(self.page6,bd=1,relief="ridge",pady=3,padx=3) p64=self.p64_frame p64.pack(fill="x") self.p6_output_entry=Pmw.EntryField(p64,labelpos="w",label_text="Output folder:",entry_width=15,entry_bg="white") self.p6_output_entry.grid(row=0,column=0,sticky="e") self.p6_out_button=Tkinter.Button(p64,text="Browse", command=self.clust_out_set) self.p6_out_button.grid(row=0,column=1,sticky="w") ### self.p65_frame=Tkinter.Frame(self.page6,bd=1,relief="ridge",pady=3,padx=3) p65=self.p65_frame p65.pack(fill="x") self.p6_start_button = Tkinter.Button(p65, text="Start clustering", command = self.start_clustering) self.p6_start_button.pack(side="right") # self.notebook.tab(1).configure(state="disabled") self.notebook.tab(2).configure(state="disabled") self.notebook.tab(3).configure(state="disabled") self.notebook.tab(0).configure(state="disabled") self.notebook.tab(4).configure(state="disabled") self.notebook.tab(5).configure(state="disabled") self.notebook.setnaturalsize() self.p3dp_smartclose() #----- F U N C T I O N S def rank_cfg_set(self): pass def start_clustering(self): try: self.update_status("blue","PLEASE WAIT. CLUSTERING IN PROGRESS...") infolder = self.p6_input_entry.getvalue()#; print infolder score_type = self.p6_scoretype_menu.getvalue()#; print score_type density_map = self.p6_map_entry.getvalue()#; print density_map density_map_threshold = self.p6_thresh_entry.getvalue()#; print density_map_threshold measure = self.p6_measuretype_menu.getvalue()#; print measure threshold = self.p6_clusthresh_entry.getvalue()#; print threshold struct_nr = self.p6_numstruct_entry.getvalue()#; print struct_nr #oligomers representation = self.p6_representation_menu.getvalue()#; print representation output = self.p6_output_entry.getvalue()#; print output if self.oligos.get() == 1: oligomers = "oligo" else: oligomers = None if self.clustsort.get() == 1: sort_num = int(self.p6_clustsort_entry.getvalue()) else: sort_num = None from cluster_complexes import start_clustering start_clustering(infolder,score_type,density_map,density_map_threshold,measure,threshold,struct_nr,representation,output,oligomers,sort_num) self.update_status("lime green","Ready") tkMessageBox.showinfo("Success", "Clustering results files can be found in " + output) except Exception as e: tkMessageBox.showwarning("Error", e) self.update_status("lime green","Ready") def ranking_inp_choose(self): if self.rank_fc_v.get() == 0: self.p5_map_entry.configure(entry_state="disabled",label_state="disabled") self.p5_input_entry.configure(entry_state="disabled",label_state="disabled") self.p5_map_button.configure(state="disabled") self.p5_input_button.configure(state="disabled") self.p5_seq_gen_radiobutton.configure(state="normal") if self.rank_fc_v.get() == 1: self.p5_map_entry.configure(entry_state="normal",label_state="normal") self.p5_input_entry.configure(entry_state="normal",label_state="normal") self.p5_map_button.configure(state="normal") self.p5_input_button.configure(state="normal") self.p5_seq_gen_radiobutton.configure(state="disabled") self.p5_simseq_v.set(2) self.p5_seq_choice(self.simseq_v) self.p5_seq_entry.configure(label_state="normal",entry_state="normal") self.p5_seq_button.configure(state="normal") def cx_make_ranking(self): from Cx_Ranking import odpal odpal() def update_status(self,c,t): self.StatusLabel.configure(text=t,fg=c) def clust_input_set(self): path=tkFileDialog.askdirectory(parent=self.page5,initialdir="/",title="Choose input folder") self.p6_input_entry.setvalue(path) def clust_map_set(self): path=tkFileDialog.askopenfilename(parent=self.page5,initialdir="/",title="Choose density map file") self.p6_map_entry.setvalue(path) def clust_out_set(self): path=tkFileDialog.askdirectory(parent=self.page5,initialdir="/",title="Choose output folder") self.p6_output_entry.setvalue(path) def ranking_input_set(self): path=tkFileDialog.askdirectory(parent=self.page5,initialdir="/",title="Choose input folder") self.p5_input_entry.setvalue(path) def ranking_seq_set(self): path=tkFileDialog.askopenfilename(parent=self.page5,initialdir="/",title="Choose sequences file") self.p5_seq_entry.setvalue(path) def ranking_cfg_set(self): path=tkFileDialog.askopenfilename(parent=self.page5,initialdir="/",title="Choose config file") self.p5_cfg_entry.setvalue(path) def ranking_res_set(self): path=tkFileDialog.askopenfilename(parent=self.page5,initialdir="/",title="Choose restraints file") self.p5_res_entry.setvalue(path) def ranking_map_set(self): path=tkFileDialog.askopenfilename(parent=self.page5,initialdir="/",title="Choose density map file") self.p5_map_entry.setvalue(path) def check_clustsort(self): if self.clustsort.get() == 0: self.p6_clustsort_entry.configure(label_state="disabled") self.p6_clustsort_entry.configure(entry_state="disabled") self.p6_clustsort_label.configure(state="disabled") else: self.p6_clustsort_entry.configure(label_state="normal") self.p6_clustsort_entry.configure(entry_state="normal") self.p6_clustsort_label.configure(state="normal") def pyry3dpath_dialog(self): #self.p3dpd=Tkinter.Tk() #self.p3dpd.title("PyRy3D Path") #self.p3dpd.protocol("WM_DELETE_WINDOW",self.handler_path) self.p3dpd = Tkinter.LabelFrame(self.StatusPathFrame,text="PYRY3D PATH:",fg="blue",pady=3,padx=3) self.p3dpd.pack(fill='both', expand = 1, padx=10, pady=5) p3dpdf1=Tkinter.Frame(self.p3dpd,bd=1,relief="ridge",pady=3,padx=3) p3dpdf1.pack(fill="x") p3dp_label=Tkinter.Label(p3dpdf1,text="Please point the directory that contains PyRy3D software:") p3dp_label.grid(row=0,columnspan=3,sticky="w") self.p3dp_entry=Pmw.EntryField(p3dpdf1,labelpos="w",label_text="PyRy3D path: ",entry_bg="white",entry_width=15) self.p3dp_entry.grid(row=1,column=0,sticky="w") p3dp_button=Tkinter.Button(p3dpdf1,text="Browse",command=lambda: self.pyry3dpath_define()) p3dp_button.grid(row=1,column=1,padx=3,sticky="w") p3dpdf2=Tkinter.Frame(self.p3dpd,bd=1,relief="ridge",pady=3,padx=3) p3dpdf2.pack(fill="x") self.rem_var=Tkinter.IntVar() #self.rem_var.set(0) def tescik(x): print x.get() p3dp_checkbutton=Tkinter.Checkbutton(p3dpdf2,text="Remember the path",onvalue=1,offvalue=0,variable=self.rem_var, command=lambda: tescik(self.rem_var)) #p3dp_checkbutton.variable = self.rem_var #p3dp_checkbutton.pack(side="left") p3dpdf3=Tkinter.Frame(self.p3dpd,bd=1,relief="ridge",pady=3,padx=3) p3dpdf3.pack(fill="x") closep3dpd_button=Tkinter.Button(p3dpdf1,text="OK",command=self.p3dp_smartclose) closep3dpd_button.grid(row=1,column=2,padx=3,sticky="w") try: saved_path_file=open(Paths.pluginpath+"/pyry3d_path.txt","r") saved_path=saved_path_file.readline() saved_path=saved_path.replace("\n","") saved_path_file.close() self.p3dp_entry.setvalue(saved_path) except IOError: pass def p3dp_smartclose(self): #Paths.pyrypath=self.p3dp_entry.getvalue() Paths.pyrypath = Paths.pluginpath + "/PyRy3D" if Paths.pyrypath=="": tkMessageBox.showinfo("PyRy3D directory?", "You have to determine the PyRy3D directory.") else: try: sys.path.append(Paths.pyrypath) from Modules.Config import Config from Modules.Error.Errors import InputError, ConfigError #tkMessageBox.showinfo("Success", "The PyRy3D directory seems to be correct. Press OK to continue.") #if self.rem_var.get() == 1: #saved_path_file=open(Paths.pluginpath+"/pyry3d_path.txt","w") #print >> saved_path_file, self.p3dp_entry.getvalue() self.p3dpd.destroy() self.notebook.tab(0).configure(state="normal") self.notebook.tab(3).configure(state="normal") self.notebook.tab(4).configure(state="normal") self.notebook.tab(5).configure(state="normal") self.StatusFrame.pack(fill='both', expand = 1, padx=10, pady=5) self.update_status("lime green","READY.") except ImportError: tkMessageBox.showwarning("Error", "This directory does not contain PyRy3D software.") def pyry3dpath_define(self): ppath = tkFileDialog.askdirectory() if ppath=="": tkMessageBox.showinfo("PyRy3D directory?", "You have to determine the PyRy3D directory.") else: self.p3dp_entry.setvalue(ppath) #----- FUNCTIONS TRIGGERED BY WIDGETS ON THE --- FIRST PAGE --- def handler(self): pass #tkMessageBox.showwarning("PyRy3D directory?", "You have to determine the PyRy3D directory first.") def handler_main_window(self): pass def handler_parameters(self): pass def handler_path(self): self.p3dpd.withdraw() def choosecomp(self): if self.complist==[]: self.complist=P1F.choosestruct() else: newcomponents=P1F.choosestruct() for i in newcomponents: self.complist.append(i) o=len(self.complist) u=1 labeltext="" for i in self.complist: sname=i.split("/")[-1] if u==1: labeltext=labeltext+"#"+str(u)+" "+sname else: labeltext=labeltext+"\n#"+str(u)+" "+sname u=u+1 self.struli.settext(labeltext) def choosemap(self): Paths.mappath=P1F.choosemap(self.mapli) if Paths.mappath == (): Paths.mappath = "" def clear(self): P1F.clearlist(self.struli) P1F.clearlist(self.mapli) self.complist=[] Paths.mappath="" def new_session(self): rly=tkMessageBox.askyesno("Warning","This will close all opened models. Continue?") if rly == True: self.clear() self.clear_button.configure(state="normal") self.open_button.configure(state="normal") self.dens_button.configure(state="normal") self.comp_button.configure(state="normal") self.new_session_button.configure("disabled") chimera.runCommand("close all") def openandsaveall(self): if len(self.complist) <= 1: tkMessageBox.showinfo("PyRy3D info","You must add at least two structures.") else: rly1=True if Paths.mappath == "" or Paths.mappath == (): rly1=tkMessageBox.askyesno("Warning","No shape descriptor provided. Continue?") if rly1 == True: rly2=tkMessageBox.askyesno("Warning","This will close all opened models before loading new data. Continue?") if rly2 == True: runCommand("close all") P1F.opencommand(Paths.mappath,self.complist) P1F.writeAllPDBs(Paths.temppath,Paths.mappath) runCommand("windowsize 9999 9999") self.open_button.configure(state="disabled") self.dens_button.configure(state="disabled") self.comp_button.configure(state="disabled") self.clear_button.configure(state="disabled") self.new_session_button.configure(state="normal") self.notebook.tab(1).configure(state="normal") self.notebook.tab(2).configure(state="normal") self.notebook.tab(3).configure(state="normal") self.notebook.tab(3).configure(state="normal") #P1F.write_via_ig(Paths.temppath) ODKOMENTOWAC, KIEDY INPUT GENERATOR BEDZIE POPRAWNIE ZMIENIAL NAZWY LANCUCHOW #----- FUNCTIONS TRIGGERED BY WIDGETS ON THE --- SECOND PAGE --- def ss_choose_cfg(self): Paths.configpath=P3F.ig_choose_resfile(self.page3,self.ss_cfg_fil_entry) def ss_choose_resfile(self): Paths.ig_respath=P3F.ig_choose_resfile(self.page3,self.res_fil_entry) def ss_choose_seqfile(self): Paths.user_seqpath=P3F.ig_choose_resfile(self.page2,self.seq_fil_entry) def ss_choose_outdir(self): Paths.ss_outpath=P3F.ig_choose_output_folder(self.page3,self.outdir_entry) if Paths.ss_outpath != "": rly=tkMessageBox.askyesno("Warning","All files in "+Paths.ss_outpath+" will be deleted. Continue?") if rly == True: self.autoscore_button.configure(state="normal") self.simulation_button.configure(state="normal") else: self.outdir_entry.configure(entry_state="normal") self.autoscore_button.configure(state="disabled") self.simulation_button.configure(state="disabled") Paths.ss_outpath="" else: self.outdir_entry.configure(entry_state="normal") Paths.ss_outpath="" self.autoscore_button.configure(state="disabled") self.simulation_button.configure(state="disabled") def cfg_choice(self,variable): if variable.get() == 1: self.ss_cfg_fil_button.configure(state="disabled") self.ss_cfg_fil_entry.configure(label_state="disabled",entry_state="disabled") self.ss_params_button.configure(state="normal") if variable.get() == 2: self.ss_cfg_fil_button.configure(state="normal") self.ss_cfg_fil_entry.configure(label_state="normal",entry_state="normal") self.ss_params_button.configure(state="disabled") def p5_cfg_choice(self,variable): if variable.get() == 1: self.p5_cfg_button.configure(state="disabled") self.p5_cfg_entry.configure(label_state="disabled",entry_state="disabled") self.p5_params_button.configure(state="normal") if variable.get() == 2: self.p5_cfg_button.configure(state="normal") self.p5_cfg_entry.configure(label_state="normal",entry_state="normal") self.p5_params_button.configure(state="disabled") def seq_choice(self,variable): if variable.get() == 1: self.seq_fil_entry.configure(label_state="disabled",entry_state="disabled") self.seq_fil_button.configure(state="disabled") self.seq_text_button.configure(state="disabled") if variable.get() == 2: self.seq_fil_entry.configure(label_state="normal",entry_state="normal") self.seq_fil_button.configure(state="normal") self.seq_text_button.configure(state="disabled") if variable.get() == 3: self.seq_fil_entry.configure(label_state="disabled",entry_state="disabled") self.seq_fil_button.configure(state="disabled") self.seq_text_button.configure(state="normal") def p5_seq_choice(self,variable): if variable.get() == 1: self.p5_seq_entry.configure(label_state="disabled",entry_state="disabled") self.p5_seq_button.configure(state="disabled") self.p5_seq_text_button.configure(state="disabled") if variable.get() == 2: self.p5_seq_entry.configure(label_state="normal",entry_state="normal") self.p5_seq_button.configure(state="normal") self.p5_seq_text_button.configure(state="disabled") if variable.get() == 3: self.p5_seq_entry.configure(label_state="disabled",entry_state="disabled") self.p5_seq_button.configure(state="disabled") self.p5_seq_text_button.configure(state="normal") def res_choice(self,variable): if variable.get() == 1: self.res_fil_entry.configure(label_state="disabled",entry_state="disabled") self.res_fil_button.configure(state="disabled") Paths.ig_respath=None if variable.get() == 2: self.res_fil_entry.configure(label_state="normal",entry_state="normal") self.res_fil_button.configure(state="normal") def p5_res_choice(self,variable): if variable.get() == 1: self.p5_res_entry.configure(label_state="disabled",entry_state="disabled") self.p5_res_button.configure(state="disabled") if variable.get() == 2: self.p5_res_entry.configure(label_state="normal",entry_state="normal") self.p5_res_button.configure(state="normal") def set_user_seq(self): Paths.user_seqpath=P3F.ig_choose_resfile(self.dis_ask_seq,self.useq_entry) def calc_threshold(self,no_out=0,elapsed="0.0"): from Modules.Error.Errors import InputError, ConfigError try: self.update_status("blue","PLEASE WAIT. CALCULATING THRESHOLD...") self.notebook.tab(0).configure(state="disabled") self.notebook.tab(1).configure(state="disabled") self.notebook.tab(2).configure(state="disabled") self.notebook.tab(3).configure(state="disabled") self.notebook.tab(4).configure(state="disabled") self.notebook.tab(5).configure(state="disabled") self.autoscore_button.configure(state="disabled") self.simulation_button.configure(state="disabled") self.threshold_button.configure(state="disabled") if os.path.exists(Paths.simscoreinputpath): shutil.rmtree(Paths.simscoreinputpath) WS.draw_box_grid=1 if not os.path.exists(Paths.simscoreinputpath): os.makedirs(Paths.simscoreinputpath) from Calculate import calculate_threshold from Draw_Plot import Log_Diagram ld=Log_Diagram() P1F.writeAllPDBs(Paths.temppath,Paths.mappath) sequence_file=Paths.simscoreinputpath+"/sequences.fasta" le_config_file=Paths.simscoreinputpath+"/config.txt" if Paths.mappath!="": if Paths.mappath[-3:] == "pdb" or Paths.mappath[-3:] == "PDB": saxs_file_path=Paths.simscoreinputpath+"/"+Paths.mappath.split("/")[-1] map_file_path=None else: map_file_path=Paths.simscoreinputpath+"/"+Paths.mappath.split("/")[-1] saxs_file_path=None else: map_file_path="" saxs_file_path=None P3F.generate_input_files(Paths.simscoreinputpath,Paths.temppath,Paths.ig_respath,Paths.mappath,1,1,0,1,1,nowindow=1) restraints_path=None history_path="history.txt" fullatom="full.pdb" if no_out == 0: opath = Paths.ss_outpath if no_out == 1: if not os.path.exists(Paths.temp_out_path): os.makedirs(Paths.temp_out_path) opath = Paths.temp_out_path opath = Paths.pluginpath+"/threshold_temp" calculated_threshold = calculate_threshold(WS.draw_box_grid,"evaluate",Paths.simscoreinputpath+"/input.tar", map_file_path,restraints_path, sequence_file,le_config_file, opath,history_path=history_path,fullatom=fullatom,sax_path=saxs_file_path,last_elapsed=elapsed) tkMessageBox.showinfo("Threshold calculated", "Density threshold's value for complex's volume is: "+str(calculated_threshold)) shutil.rmtree(Paths.pluginpath+"/threshold_temp") self.threshold_button.configure(state="normal") self.update_status("lime green","READY.") self.notebook.tab(0).configure(state="normal") self.notebook.tab(1).configure(state="normal") self.notebook.tab(2).configure(state="normal") self.notebook.tab(3).configure(state="normal") self.notebook.tab(4).configure(state="normal") self.notebook.tab(5).configure(state="normal") self.autoscore_button.configure(state="normal") self.simulation_button.configure(state="normal") self.threshold_button.configure(state="normal") except Exception as e: tkMessageBox.showwarning("Error", e) self.update_status("lime green","READY.") self.notebook.tab(0).configure(state="normal") self.notebook.tab(1).configure(state="normal") self.notebook.tab(2).configure(state="normal") self.notebook.tab(3).configure(state="normal") self.notebook.tab(4).configure(state="normal") self.notebook.tab(5).configure(state="normal") self.autoscore_button.configure(state="normal") self.simulation_button.configure(state="normal") self.threshold_button.configure(state="normal") def score_complex(self,no_out=0,elapsed="0.0", smode=None): from Modules.Error.Errors import InputError, ConfigError if Paths.ss_outpath == "": tkMessageBox.showwarning("Error", "Please specify the output directory.") else: if os.path.exists(Paths.simscoreinputpath): shutil.rmtree(Paths.simscoreinputpath) WS.draw_box_grid=1 self.update_status("blue","PLEASE WAIT. EVALUATION IN PROGRESS...") self.notebook.tab(0).configure(state="disabled") self.notebook.tab(1).configure(state="disabled") self.notebook.tab(2).configure(state="disabled") self.notebook.tab(3).configure(state="disabled") self.notebook.tab(4).configure(state="disabled") self.notebook.tab(5).configure(state="disabled") self.autoscore_button.configure(state="disabled") self.simulation_button.configure(state="disabled") self.threshold_button.configure(state="disabled") if not os.path.exists(Paths.simscoreinputpath): os.makedirs(Paths.simscoreinputpath) from Calculate import run from Draw_Plot import Log_Diagram try: ld=Log_Diagram() P1F.writeAllPDBs(Paths.temppath,Paths.mappath) if self.simseq_v.get() == 1 or smode == "reopened": print "REOPENED" sequence_file=Paths.simscoreinputpath+"/sequences.fasta" elif self.simseq_v.get() == 2: sequence_file=Paths.user_seqpath elif self.simseq_v.get() == 3: raw_sequence = self.seq_text_li.getvalue() sequence_file=Paths.ss_outpath+"/sequences_inp.fasta" sf = open(sequence_file,"w")#rrr sf.write(raw_sequence) sf.close() if self.cfg_v.get()==2: le_config_file=self.ss_cfg_fil_entry.getvalue() else: le_config_file=Paths.simscoreinputpath+"/config.txt" if Paths.mappath!="": if Paths.mappath[-3:] == "pdb" or Paths.mappath[-3:] == "PDB": saxs_file_path=Paths.simscoreinputpath+"/"+Paths.mappath.split("/")[-1] map_file_path=None else: map_file_path=Paths.simscoreinputpath+"/"+Paths.mappath.split("/")[-1] saxs_file_path=None else: map_file_path="" saxs_file_path=None if Paths.ig_respath!=None: P3F.generate_input_files(Paths.simscoreinputpath,Paths.temppath,Paths.ig_respath,Paths.mappath,1,1,1,1,1,nowindow=1) restraints_path=Paths.simscoreinputpath+"/restraints.txt" else: P3F.generate_input_files(Paths.simscoreinputpath,Paths.temppath,Paths.ig_respath,Paths.mappath,1,1,0,1,1,nowindow=1) restraints_path=None history_path="history.txt" fullatom="full.pdb" if no_out == 0: opath = Paths.ss_outpath if no_out == 1: if not os.path.exists(Paths.temp_out_path): os.makedirs(Paths.temp_out_path) opath = Paths.temp_out_path if map_file_path == "" and restraints_path == None: tkMessageBox.showinfo("PyRy3D info", "You need either a shape descriptor or some distance restraints.") else: resultdir, logfile = run(WS.draw_box_grid,"evaluate",Paths.simscoreinputpath+"/input.tar", map_file_path,restraints_path, sequence_file,le_config_file, opath,history_path=history_path,fullatom=fullatom,sax_path=saxs_file_path,last_elapsed=elapsed) if os.path.exists(Paths.temp_out_path): shutil.rmtree(Paths.temp_out_path) self.update_status("lime green","READY.") self.notebook.tab(0).configure(state="normal") self.notebook.tab(1).configure(state="normal") self.notebook.tab(2).configure(state="normal") self.notebook.tab(3).configure(state="normal") self.notebook.tab(4).configure(state="normal") self.notebook.tab(5).configure(state="normal") self.autoscore_button.configure(state="normal") self.simulation_button.configure(state="normal") self.threshold_button.configure(state="normal") except InputError as e: tkMessageBox.showwarning("Input error", e) self.update_status("lime green","READY.") self.notebook.tab(0).configure(state="normal") self.notebook.tab(1).configure(state="normal") self.notebook.tab(2).configure(state="normal") self.notebook.tab(3).configure(state="normal") self.notebook.tab(4).configure(state="normal") self.notebook.tab(5).configure(state="normal") self.autoscore_button.configure(state="normal") self.simulation_button.configure(state="normal") self.threshold_button.configure(state="normal") except ConfigError as e: tkMessageBox.showwarning("Config error", e) self.update_status("lime green","READY.") self.notebook.tab(0).configure(state="normal") self.notebook.tab(1).configure(state="normal") self.notebook.tab(2).configure(state="normal") self.notebook.tab(3).configure(state="normal") self.notebook.tab(4).configure(state="normal") self.notebook.tab(5).configure(state="normal") self.autoscore_button.configure(state="normal") self.simulation_button.configure(state="normal") self.threshold_button.configure(state="normal") except Exception as e: tkMessageBox.showwarning("Error", e) self.update_status("lime green","READY.") self.notebook.tab(0).configure(state="normal") self.notebook.tab(1).configure(state="normal") self.notebook.tab(2).configure(state="normal") self.notebook.tab(3).configure(state="normal") self.notebook.tab(4).configure(state="normal") self.notebook.tab(5).configure(state="normal") self.autoscore_button.configure(state="normal") self.simulation_button.configure(state="normal") self.threshold_button.configure(state="normal") def simulate_complex_fin(self): from Modules.Error.Errors import InputError, ConfigError if Paths.ss_outpath == "": tkMessageBox.showwarning("Error", "Please specify the output directory.") else: if os.path.exists(Paths.simscoreinputpath): shutil.rmtree(Paths.simscoreinputpath) self.update_status("blue","PLEASE WAIT. SIMULATION IN PROGRESS...") self.notebook.tab(0).configure(state="disabled") self.notebook.tab(1).configure(state="disabled") self.notebook.tab(2).configure(state="disabled") self.notebook.tab(3).configure(state="disabled") self.notebook.tab(4).configure(state="disabled") self.notebook.tab(5).configure(state="disabled") self.autoscore_button.configure(state="disabled") self.simulation_button.configure(state="disabled") self.threshold_button.configure(state="disabled") from Calculate import run from Draw_Plot import Log_Diagram from Modules.Error.Errors import InputError, ConfigError ld=Log_Diagram() P1F.writeAllPDBs(Paths.temppath,Paths.mappath) try: if not os.path.exists(Paths.simscoreinputpath): os.makedirs(Paths.simscoreinputpath) fullatomm="full.pdb" history_path="history.txt" trafl="traject.trafl" if self.simseq_v.get() == 1: sequence_file=Paths.simscoreinputpath+"/sequences.fasta" if self.simseq_v.get() == 2: sequence_file=Paths.user_seqpath if self.simseq_v.get() == 3: raw_sequence = self.seq_text_li.getvalue() sequence_file=Paths.ss_outpath+"/sequences_inp.fasta" sf = open(sequence_file,"w")#rrr sf.write(raw_sequence) sf.close() if self.cfg_v.get()==2: le_config_file=self.ss_cfg_fil_entry.getvalue() else: le_config_file=Paths.simscoreinputpath+"/config.txt" WS.draw_box_grid=1 if Paths.mappath!="": if Paths.mappath[-3:] == "pdb" or Paths.mappath[-3:] == "PDB": saxs_file_path=Paths.simscoreinputpath+"/"+Paths.mappath.split("/")[-1] map_file_path=None else: map_file_path=Paths.simscoreinputpath+"/"+Paths.mappath.split("/")[-1] saxs_file_path=None else: map_file_path="" saxs_file_path=None map_filename=Paths.mappath.split("/")[-1] if Paths.ig_respath!=None: P3F.generate_input_files(Paths.simscoreinputpath,Paths.temppath,Paths.ig_respath,Paths.mappath,1,1,1,1,1,nowindow=1) restraints_path=Paths.simscoreinputpath+"/restraints.txt" else: P3F.generate_input_files(Paths.simscoreinputpath,Paths.temppath,Paths.ig_respath,Paths.mappath,1,1,0,1,1,nowindow=1) restraints_path=None history_path="history.txt" fullatom="full.pdb" if Paths.mappath == "" and Paths.ig_respath == "": tkMessageBox.showinfo("PyRy3D info", "You need either a shape descriptor or some distance restraints.") else: resultdir, logfile, elapsed = run(WS.draw_box_grid,"simulate",Paths.simscoreinputpath+"/input.tar", map_file_path,restraints_path, sequence_file,le_config_file, Paths.ss_outpath,history_path=history_path,fullatom=fullatom,sax_path=saxs_file_path) if fullatomm != None: self.reopen_after_sim(elapsed=elapsed) pass if os.path.exists(Paths.temp_out_path): shutil.rmtree(Paths.temp_out_path) self.update_status("lime green","READY.") self.notebook.tab(0).configure(state="normal") self.notebook.tab(1).configure(state="normal") self.notebook.tab(2).configure(state="normal") self.notebook.tab(3).configure(state="normal") self.notebook.tab(4).configure(state="normal") self.notebook.tab(5).configure(state="normal") self.autoscore_button.configure(state="normal") self.simulation_button.configure(state="normal") self.threshold_button.configure(state="normal") ld.draw_diagram(logfile) except InputError as e: tkMessageBox.showwarning("Input error", e) self.update_status("lime green","READY.") self.notebook.tab(0).configure(state="normal") self.notebook.tab(1).configure(state="normal") self.notebook.tab(2).configure(state="normal") self.notebook.tab(3).configure(state="normal") self.notebook.tab(4).configure(state="normal") self.notebook.tab(5).configure(state="normal") self.autoscore_button.configure(state="normal") self.simulation_button.configure(state="normal") self.threshold_button.configure(state="normal") except ConfigError as e: tkMessageBox.showwarning("Config error", e) self.update_status("lime green","READY.") self.notebook.tab(0).configure(state="normal") self.notebook.tab(1).configure(state="normal") self.notebook.tab(2).configure(state="normal") self.notebook.tab(3).configure(state="normal") self.notebook.tab(4).configure(state="normal") self.notebook.tab(5).configure(state="normal") self.autoscore_button.configure(state="normal") self.simulation_button.configure(state="normal") self.threshold_button.configure(state="normal") except Exception as e: tkMessageBox.showwarning("Error", e) self.update_status("lime green","READY.") self.notebook.tab(0).configure(state="normal") self.notebook.tab(1).configure(state="normal") self.notebook.tab(2).configure(state="normal") self.notebook.tab(3).configure(state="normal") self.notebook.tab(4).configure(state="normal") self.notebook.tab(5).configure(state="normal") self.autoscore_button.configure(state="normal") self.simulation_button.configure(state="normal") self.threshold_button.configure(state="normal") def reopen_after_sim(self,elapsed): runCommand("close all") if Paths.mappath != "": runCommand("open "+Paths.mappath) direct_dirname = Paths.ss_outpath.split("/")[-1] outfiles = os.listdir(Paths.ss_outpath) minsc = -999999999999.99 minfname = "" for o in outfiles: print o if len(o.split("_")) > 1: sc = float(o.split("_")[1]) if sc != 0.0: if sc > minsc: print sc minsc = sc minfname = o runCommand("open "+Paths.ss_outpath+"/"+minfname)#direct_dirname+"_0.0_1_full.pdb.pdb") if Paths.mappath != "": str_n = "1" else: str_n = "0" runCommand("split #"+str_n) #runCommand("rainbow model #"+str_n) P1F.writeAllPDBs(Paths.temppath,Paths.mappath) runCommand("close #"+str_n) new_structs = os.listdir(Paths.temppath) for i in new_structs: runCommand("open "+Paths.temppath+"/"+i) self.score_complex(no_out=1,elapsed=elapsed, smode="reopened") def prepare_ranking_from_window(self): outp = Paths.pluginpath+"/ranking_temp_input" outpf = Paths.pluginpath+"/ready" if not os.path.exists(outp): os.makedirs(outp) else: shutil.rmtree(outp) os.makedirs(outp) if not os.path.exists(outpf): os.makedirs(outpf) os.makedirs(outpf+"/packs") else: shutil.rmtree(outpf) os.makedirs(outpf) os.makedirs(outpf+"/packs") self.update_status("blue","PLEASE WAIT. RANKING COMPLEXES...") count = len(chimera.openModels.list()) - 1 chimera.runCommand("split") count2 = len(chimera.openModels.list()) - 1 cps = count2 / count o = chimera.openModels.list()[1:] for i in xrange(0, len(o), cps): m = o[i:i+cps] for j in m: id_=j.oslIdent()[1:] command="write "+id_+ " "+outp+"/"+id_+".pdb" runCommand(command) name = j.name.split(".")[0] P3F.generate_input_files(outpf,outp,"",Paths.mappath,1,1,0,1,1,nowindow=1,rankmode=1,rankname=name) files = glob.glob(outp+"/*") for f in files: os.remove(f) files = glob.glob(outpf+"/*.pdb") for f in files: os.remove(f) def make_ranking(self): try: if self.p5_cfg_v.get() == 1: cfg_choice = 1 if self.p5_simseq_v.get() == 1: seq_choice = 1 if self.p5_res_v.get() == 1: res_choice = 1 self.p5_runranking_button.configure(state="disabled") self.update_status("blue","PLEASE WAIT. GENERATING RANKING...") from Cx_Ranking import run_king outpf = Paths.pluginpath+"/ready" outp = Paths.pluginpath+"/ranking_temp_input" if self.rank_fc_v.get() == 0: self.prepare_ranking_from_window() outpfp = outpf+"/packs" if self.p5_cfg_v.get() == 1: P3F.generate_input_files(outpf,outp,"",Paths.mappath,1,0,0,0,0,nowindow=1) rank_cfg = outpf+"/config.txt" else: rank_cfg = self.p5_cfg_entry.get() if self.p5_simseq_v.get() == 1: rank_seq = outpf+"/sequences.fasta" elif self.p5_simseq_v.get() == 2: rank_seq = self.p5_seq_entry.get() elif self.p5_simseq_v.get() == 3: raw_sequence = self.seq_text_li.getvalue() rank_seq=outpf+"/sequences_inp.fasta" sf = open(rank_seq,"w")#rrr sf.write(raw_sequence) sf.close() if self.p5_res_v.get() == 1: rank_res = "" else: rank_res = self.p5_res_entry.get() if self.rank_fc_v.get() == 0: rank_input = outpfp rank_map = Paths.mappath #rank_seq = outpf+"/sequences.fasta" else: rank_input = self.p5_input_entry.get() rank_map = self.p5_map_entry.get() rank_seq = self.p5_seq_entry.get() if_rank_res=True if rank_input == "" or rank_seq == "" or rank_cfg == "": tkMessageBox.showwarning("Error", "Please provide paths for your structures, sequences and a configuration file.") else: if rank_res == "": rank_res = None if_rank_res = tkMessageBox.askyesno("Warning", "You didn't provide restraints file. Continue without spatial restraints?") if if_rank_res == True: run_king(self.p5_sort_menu.getvalue(),rank_input,rank_seq,rank_res,rank_map,rank_cfg,Paths.pluginpath+"/ranking") files = glob.glob(outpf+"/*") for f in files: if os.path.isdir(f): shutil.rmtree(f) else: os.remove(f) self.p5_runranking_button.configure(state="normal") self.update_status("lime green","READY.") self.p5_runranking_button.configure(state="normal") except Exception as e: tkMessageBox.showwarning("Error", e) def ig_check_elements(self,str_v,map_v,seq_v): if str_v.get()==1: WS.ig_structures=1 if str_v.get()==0: WS.ig_structures=0 if map_v.get()==1: WS.ig_map=1 if map_v.get()==0: WS.ig_map=0 if seq_v.get()==1: WS.ig_structures=1 str_v.set(1) WS.ig_sequences=1 if seq_v.get()==0: WS.ig_sequences=0 def ig_check_res(self,variable): if variable.get()==1: self.ig_res_entry.configure(label_state="normal",entry_state="normal") self.ig_res_button.configure(state="normal") WS.ig_restraints=1 if variable.get()==0: self.ig_res_entry.configure(label_state="disabled",entry_state="disabled") self.ig_res_button.configure(state="disabled") WS.ig_restraints=0 def ig_check_con(self,variable): if variable.get()==1: self.ig_con_button.configure(state="normal") WS.ig_config=1 if variable.get()==0: self.ig_con_button.configure(state="disabled") WS.ig_config=0 def display_psrwin(self): self.psrwin.deiconify() def display_text_sequence_window(self): self.seq_text_win.deiconify() def set_default_scaling_parameters(self): self.psr01_entry.setvalue("0") self.psr02_entry.setvalue("25") self.psr03_entry.setvalue("50") self.psr11_entry.setvalue("50") self.psr12_entry.setvalue("100") self.psr21_entry.setvalue("25") self.psr22_entry.setvalue("50") self.psr31_entry.setvalue("0") self.psr32_entry.setvalue("25") #----- FUNCTIONS TRIGGERED BY WIDGETS ON THE --- FOURTH PAGE --- #----- FUNCTIONS TRIGGERED BY WIDGETS ON THE --- FIFTH PAGE --- chimera.dialogs.register(PyRyDialog.name, PyRyDialog) dir, file = os.path.split(__file__) icon = os.path.join(dir, 'ExtensionUI.tiff') chimera.tkgui.app.toolbar.add(icon, lambda d=chimera.dialogs.display, n=PyRyDialog.name: d(n), 'PyRy3D Extension', None)