# Autodock/Vina plugin Copyright Notice # ============================ # # The Autodock/Vina plugin source code is copyrighted, but you can freely use and # copy it as long as you don't change or remove any of the copyright # notices. # # ---------------------------------------------------------------------- # Autodock/Vina plugin is Copyright (C) 2009 by Daniel Seeliger # # All Rights Reserved # # Permission to use, copy, modify, distribute, and distribute modified # versions of this software and its documentation for any purpose and # without fee is hereby granted, provided that the above copyright # notice appear in all copies and that both the copyright notice and # this permission notice appear in supporting documentation, and that # the name of Daniel Seeliger not be used in advertising or publicity # pertaining to distribution of the software without specific, written # prior permission. # # DANIEL SEELIGER DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS # SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND # FITNESS. IN NO EVENT SHALL DANIEL SEELIGER BE LIABLE FOR ANY # SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER # RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF # CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN # CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # ---------------------------------------------------------------------- #================================================================ import sys,os,math,re, fnmatch, shutil from os import stat from os.path import abspath from stat import ST_SIZE from time import sleep, time import Tkinter import Tkinter,Pmw from Tkinter import * import tkMessageBox, tkFileDialog import Pmw from threading import Thread from commands import getstatusoutput from pymol import cmd,selector from pymol.cmd import _feedback,fb_module,fb_mask,is_list,_cmd from pymol.cgo import * from pymol import stored from numpy import * import tkColorChooser from pymol.vfont import plain from glob import glob __version__ = "2.1.1" #============================================================================= # # INITIALISE PLUGIN # def __init__(self): self.menuBar.addmenuitem('Plugin', 'command', 'Launch Autodock', label='Autodock/Vina', command = lambda s=self: Autodock(s)) cmd.set("retain_order") # keep atom ordering #============================================================================= # # SOME BASIC THINGIES # intro_text = """ Welcome to the updated version of the PyMOL Autodock Plugin.The current version has been entirely rewritten and extended. Now you can set up a complete docking run from the very beginning, perform the docking runs from within PyMOL and directly load the results into the viewer. The plugin now supports the novel Autodock spawn \"VINA\" which is orders of magnitudes faster than Autodock4. To get this plugin to work properly you should have the mgltools (http://mgltools.scripps.edu/) installed and tell the plugin on this page where to find the scripts (usually somewhere in /python/site-packages/AutoDockTools/Utilities24/ ) and make sure that they work. Additionally you should tell the plugin where to find the autogrid4, autodock4, and vina executables. If you do this once and press the \"Save Configuration File\" button this information is present the next time you use the plugin. A complete setup and execution of a docking run or a virtual screening is basically a walk from the left to the right along the notebook structure if this plugin. Each page is more or less intuitive or contains a description of what to do. The basic workflow is: Load Structure -> Define binding site -> Receptor preparation -> Ligand preparation -> Docking -> Analysis. Have fun and contact me (dseelig@gwdg.de) if you find bugs or have any suggestions for future versions. Daniel Reference: J. Comput.-Aided Mol. Des. 24:417-422 (2010) """ receptor_prep_text = """ Here you can define receptors from PyMOL selections and setup docking runs with flexible sidechains. Pick a selection from the selection list and press the Generate Receptor ->" button to prepare the protein for a docking run. If you want to use flexible sidechains within the binding site just create a PyMOL selection containing the residues you want to be flexible. Then use the "Import Selections" button and andselect the group in the left list. Then press the Select as Flexible->" button. The receptor definition has now changed. You can see which residues are flexible in the right list. (Proline, Glycine and Alanine residues are never defined as flexible)\n""" ligand_prep_text = """ On this page you can prepare ligands for docking.The first way to do so is to load the ligand into PyMOL and select it in the left list (use the "Import Selection" button to synchronize the list with PyMOL). The plugin saves your ligand in as .pdb file and puts it into the ligand list in the middle of the page. If you press the "Generate Ligand" button your ligand will be prepared for docking and appears in the right list. Alternatively to loading a ligand via PyMOL you can choose an entire directory containing compounds in .pdb or .mol2 format. Use the "Import" button to read all compounds in the directory and use the "Generate All" button to prepare each compound for the docking run.\n""" docking_text = """ This is the docking page. You have to select a recetor and whether you want to use flexible sidechains. You may either dock a single ligand from the list above or all ligands you have prepared. If you use Autodock4 you have to calculate a grid before you can start the actual docking run. Just press "Run AutoGrid" and wait until its finished and then press the "Run AutoDock" button. The genrated grid maps can be loaded into PyMOL on the "Grid Maps" page. If you use vina you don't have to calculate a grid. Just press "Run VINA" and wait until it is finished.You can load the generated docking poses into PyMOL on the "View Poses" page\n""" pdb_format="%6s%5d %-4s%1s%3s%2s%4d %11.3f %7.3f %7.3f %5.2f %5.2f" # get a temporary file directory if not sys.platform.startswith('win'): home = os.environ.get('HOME') else: home = os.environ.get('PYMOL_PATH') tmp_dir = os.path.join(home,'.ADplugin') if not os.path.isdir(tmp_dir): os.mkdir(tmp_dir) print "Created temporary files directory: %s" % tmp_dir default_settings = { "grid_spacing" : '0.375', "n_points_X":'60', "n_points_Y":'60', "n_points_Z":'60', "grid_center_selection":'(all)', "grid_center_X":'0', "grid_center_Y":'0', "grid_center_Z":'0', "dx":'1.0', "dy":'1.0', "dz":'1.0', "box_cylinder_size":'0.2', "box_mesh_line_width":'1', "box_mesh_grid_size":'1', "box_file_name":'box.dat', "gpf_file_name":'grid.gpf', "config_file_name":'config.txt', "rank_dat_file_name":'scores.dat', "rank_csv_file_name":'scores.csv', "rank_pose_file_name":'poses.pdb', "dlg_input_file":'docked.pdbqt', "map_input_file":'receptor.C.map', "map_threshold":5. } BOX_AS_BOX = 0 BOX_AS_WIREBOX = 1 GRID_CENTER_FROM_SELECTION = 0 GRID_CENTER_FROM_COORDINATES = 1 #========================================================================== # # THREAD CLASSES FOR SPAWNING DOCKING JOBS class Thread_run(Thread): def __init__ (self,command, previous = None, status_line = None, log_text = None): Thread.__init__(self) self.command = command self.status = -1 self.previous = previous self.status_line = status_line self.log_text = log_text def run(self): if self.previous: self.previous.join() if self.status_line: self.status_line.configure(text = self.log_text) self.status = os.system(self.command) class Thread_log(Thread): def __init__(self, logfile, page): Thread.__init__(self) self.page = page self.logfile = logfile def run(self): if not os.environ.has_key('ADPLUGIN_NO_OUTPUT_REDIRECT'): t = Tail(self.logfile) line = t.nextline() self.page.insert('end',"%s" % line) while line: line = t.nextline() self.page.insert('end',"%s" % line) self.page.yview('moveto', 1.0)#, 'page') else: line = 'LOG FILE OUTPUT NOT REDIRECTED' self.page.insert('end',"%s" % line) self.page.yview('moveto', 1.0)#, 'page') #========================================================================== # # CLASSES FOR HANDLING AUTODOCK FILES class ADModel: """ STORAGE CLASS FOR DOCKED LIGANDS """ def __init__(self, lst = None): self.atomlines = [] self.energy = 0. self.name = '' self.poseN = 0 self.info = '' self.lst = [] self.num = 0 self.as_string = '' if lst is not None: self.from_list(lst) def from_list(self, lst): self.lst = lst for line in lst: self.info+=line if line.startswith('ATOM') or \ line.startswith('HETATM'): self.atomlines.append(line) self.as_string+='ATOM '+line[6:67]+'\n' elif line.startswith('USER'): if 'Free Energy of Binding' in line: entr = line.split('=')[1] self.energy = float(entr.split()[0]) elif line.startswith('REMARK'): if 'VINA RESULT' in line: entr = line.split(':')[1] self.energy = float(entr.split()[0]) def as_pdb_string(self): return self.as_string def info_string(self): return self.info #--------------------------------------------------------------------------- class ADGridMap: """ CLASS FOR HANDLING AUTODOCK GRID MAP FILES""" def __init__(self, fp = None, name = 'map'): self.name = '' self.npts = [0,0,0] self.n = [0,0,0] self.center = [0,0,0] self.origin = [0,0,0] self.nelem = 0 self.spacing = 0. self.values = [] self.datafile = '' self.molecule = '' self.paramfile = '' self.precision = 0.0001 if fp is not None: self.read(fp,name) def read(self,fp,name='map'): self.name = name for i in range(6): line = fp.readline() if i == 0: self.paramfile = line.split()[1] elif i == 1: self.datafile = line.split()[1] elif i == 2: self.molecule = line.split()[1] elif i == 3: self.spacing = float(line.split()[1]) elif i == 4: self.npts = [int(x) for x in line.split()[1:]] elif i == 5: self.center = [float(x) for x in line.split()[1:]] for i in range(3): self.n[i] = self.npts[i]+1 self.nelem=self.n[0]*self.n[1]*self.n[2] i = 0 while i < self.nelem: val = float(fp.readline()) self.values.append(val) i+=1 for i in range(3): self.origin[i] = self.center[i]-self.npts[i]/2*self.spacing def meta(self): s= 'GRID_PARAMETER_FILE %s\n' % self.paramfile + \ 'GRID_DATA_FILE %s\n' % self.datafile +\ 'MACROMOLECULE %s\n' % self.molecule +\ 'SPACING %4.3f\n' % self.spacing +\ 'NELEMENTS %d %d %d\n' % (self.npts[0],self.npts[1],self.npts[2]) +\ 'CENTER %5.3f %5.3f %5.3f\n' % (self.center[0],self.center[1],self.center[2]) return s def write(self,fp): print >>fp, 'GRID_PARAMETER_FILE %s' % self.paramfile print >>fp, 'GRID_DATA_FILE %s' % self.datafile print >>fp, 'MACROMOLECULE %s' % self.molecule print >>fp, 'SPACING %4.3f' % self.spacing print >>fp, 'NELEMENTS %d %d %d' % (self.npts[0],self.npts[1],self.npts[2]) print >>fp, 'CENTER %5.3f %5.3f %5.3f' % (self.center[0],self.center[1],self.center[2]) for x in self.values: if abs(x) < self.precision: print >>fp, '0.' else: print >>fp, '%.3f' % x def writeDX(self,fname): fp = open(fname,'w') nx = self.n[0] ny = self.n[1] nz = self.n[2] ori = self.origin spacing = self.spacing vals = self.values print >>fp,'#==================================' print >>fp,'# AutoGrid Map File: %s' % self.name print >>fp,'# Receptor File Name: %s' % self.molecule print >>fp,'#==================================' print >>fp,'object 1 class gridpositions counts %d %d %d' % (nx,ny,nz) print >>fp,'origin %12.5E %12.5E %12.5E' % (ori[0],ori[1],ori[2]) print >>fp,'delta %12.5E %12.5E %12.5E' % (spacing,0,0) print >>fp,'delta %12.5E %12.5E %12.5E' % (0,spacing,0) print >>fp,'delta %12.5E %12.5E %12.5E' % (0,0,spacing) print >>fp,'object 2 class gridconnections counts %d %d %d' % (nx,ny,nz) print >>fp,'object 3 class array type double rank 0 items %d data follows' % len(vals) for k in range(nz): col=0; for j in range(ny): for i in range(nx): fp.write(" %12.5E" % vals[i*ny*nz + j*nz + k]) col+=1; if col==3: print >>fp col=0 print >>fp,'attribute \"dep\" string \"positions\"' print >>fp,'object \"regular positions regular connections\" class field' print >>fp,'component \"positions\" value 1' print >>fp,'component \"connections\" value 2' print >>fp,'component \"data\" value 3' fp.close() #========================================================================== # # CLASSES FOR INTERNAL HANDLING OF RECEPTORS AND LIGANDS class Receptor: """CONTAINS ALL INFORMATION ABOUT A DEFINED RECEPTOR""" def __init__(self): self.selection = '' self.pdb_file = '' self.receptor_pdbqt = '' self.receptor_rigid = '' self.receptor_flexible = '' self.flexible_residues = {} self.resi_dic = {} def flex_res_string(self): flex_res_str = '' for key, val in self.flexible_residues.items(): s = os.path.basename(self.receptor_pdbqt)[:-6] lst = [] for idx, resname in val: lst.append( resname + str(idx) ) s+=':'+key+':'+'_'.join(lst) flex_res_str+=s return flex_res_str ## lst = [] ## for idx, resname in self.flexible_residues: ## lst.append( resname+str(idx) ) ## return '_'.join(lst) def info(self): s= '#===============================================\n' s+=' > Receptor : "%s"\n' % self.selection s+=' > Generated from pdb file : "%s"\n' % self.pdb_file s+=' > Receptor file : "%s"\n' % self.receptor_pdbqt s+=' > Receptor rigid : "%s"\n' % self.receptor_rigid s+=' > Receptor flexible : "%s"\n' % self.receptor_flexible # s+=' > Number of flex. residues : %d\n' % len(self.flexible_residues) s+='#===============================================\n' return s class Ligand: """CONTAINS ALL INFORMATION ABOUT A LIGAND""" def __init__(self): self.name = '' self.selection = '' self.input_file = '' self.ligand_pdbqt = '' self.outfile_poses = '' def info(self): s= '#=============================================\n' s+=' > Ligand : %s\n' % self.name s+=' > Generated from file : %s\n' % self.input_file s+=' > Ligand pdbqt file : %s\n' % self.ligand_pdbqt s+=' > Poses output file : %s\n' % self.outfile_poses s+='#=============================================\n' return s #========================================================================== # # THE MAJOR, PRETTY BIG PLUGIN CLASS class Autodock: """ THE MAJOR PLUGIN CLASS """ def __init__(self,app): parent = app.root self.parent = parent # receptors and ligands self.receptor_dic = {} self.ligand_dic = {} # directory with ligands self.ligand_dir = StringVar() # box display settings self.box_display_mode = IntVar() self.box_display_mode.set(BOX_AS_BOX) self.box_color = [1.,1.,1.] self.box_is_on_display = False self.box_display_cylinder_size = DoubleVar() self.box_display_cylinder_size.set(default_settings['box_cylinder_size']) self.box_display_line_width = DoubleVar() self.box_display_line_width.set(default_settings['box_mesh_line_width']) self.box_display_mesh_grid = DoubleVar() self.box_display_mesh_grid.set(default_settings['box_mesh_grid_size']) self.box_size = [] # grid definition self.grid_spacing = DoubleVar() self.grid_spacing.set(default_settings['grid_spacing']) self.n_points_X = DoubleVar() self.n_points_X.set(default_settings['n_points_X']) self.n_points_Y = DoubleVar() self.n_points_Y.set(default_settings['n_points_Y']) self.n_points_Z = DoubleVar() self.n_points_Z.set(default_settings['n_points_Z']) self.grid_center = [DoubleVar(), DoubleVar(), DoubleVar()] self.grid_center[0].set(default_settings['grid_center_X']) self.grid_center[1].set(default_settings['grid_center_Y']) self.grid_center[2].set(default_settings['grid_center_Z']) # paths to executables self.config_settings = {} self.autodock_tools_path = StringVar() self.autogrid_exe = StringVar() self.autodock_exe = StringVar() self.vina_exe = StringVar() # ligand display settings self.ligand_display_mode = { 'lines':True, 'sticks':False, 'spheres':False, 'surface':False, 'mesh':False } # keep in mind what threads are running self.current_thread = None # build main window self.dialog = Pmw.Dialog(parent, buttons = ('Exit',), title = 'PyMOL Autodock/Vina Plugin', command = self.button_pressed) self.dialog.withdraw() Pmw.setbusycursorattributes(self.dialog.component('hull')) self.status_line = Label(self.dialog.interior(), relief='sunken', font='helvetica 12', anchor='w',fg='yellow',bg='black') self.status_line.pack(side=BOTTOM,fill='x', expand=1, padx=0, pady=0) self.dialog.geometry('650x780') self.dialog.bind('',self.button_pressed) # the title self.title_label = Tkinter.Label(self.dialog.interior(), text = 'PyMOL Autodock/Vina Plugin\nDaniel Seeliger\n', background = 'navy', foreground = 'white', ) self.title_label.pack(expand = 0, fill = 'both', padx = 4, pady = 4) # the basic notebook self.notebook = Pmw.NoteBook(self.dialog.interior()) self.notebook.pack(fill='both',expand=1,padx=3,pady=3) # build pages self.configuration_page = self.notebook.add('Configuration') self.grid_definition_page = self.notebook.add('Grid Settings') self.receptor_preparation_page = self.notebook.add('Receptor') self.ligand_preparation_page = self.notebook.add('Ligands') self.docking_page = self.notebook.add('Docking') self.pose_viewer_page = self.notebook.add('View Poses') self.rank_page = self.notebook.add('Score/Rank') self.map_viewer_page = self.notebook.add('Grid Maps') #--------------------------------------------------------------- # GRID DEFINITION PAGE self.grid_page_main_group = Pmw.Group(self.grid_definition_page, tag_text='Grid Definition') self.grid_page_main_group.pack(fill = 'both', expand = 0, padx=10, pady=5) # grid parameters on the left self.grid_page_left_side = Pmw.Group(self.grid_page_main_group.interior(),tag_text = 'Parameters') self.grid_page_left_side.pack(side = LEFT, fill = 'both',expand = 0, padx = 10, pady = 3) # grid spacing entry self.grid_spacing_frame = Tkinter.Frame(self.grid_page_left_side.interior()) self.grid_spacing_label = Label(self.grid_spacing_frame, text='Spacing:', width = 10) self.grid_spacing_location = Entry(self.grid_spacing_frame, textvariable= self.grid_spacing, bg='black',fg='green', width = 10) self.grid_spacing_scrollbar = Scrollbar(self.grid_spacing_frame, orient = 'horizontal', command = self.grid_spacing_changed) self.grid_spacing_label.pack(side = LEFT, anchor='w') self.grid_spacing_location.pack(side = LEFT, anchor='w') self.grid_spacing_scrollbar.pack(side = LEFT, anchor='w') self.grid_spacing_frame.pack(fill = 'x', padx = 4, pady=1) # n grid points entries self.n_points_X_frame = Tkinter.Frame(self.grid_page_left_side.interior()) self.n_points_X_label = Label(self.n_points_X_frame, text='X-points:', width = 10) self.n_points_X_location = Entry(self.n_points_X_frame, textvariable= self.n_points_X, bg='black',fg='green', width = 10) self.n_points_X_scrollbar = Scrollbar(self.n_points_X_frame, orient = 'horizontal', command = self.n_points_X_changed) self.n_points_X_label.pack(side = LEFT, anchor='w') self.n_points_X_location.pack(side = LEFT, anchor='w') self.n_points_X_scrollbar.pack(side = LEFT, anchor='w') self.n_points_X_frame.pack(fill = 'x', padx = 4, pady=1) self.n_points_Y_frame = Tkinter.Frame(self.grid_page_left_side.interior()) self.n_points_Y_label = Label(self.n_points_Y_frame, text='Y-points:', width = 10) self.n_points_Y_location = Entry(self.n_points_Y_frame, textvariable= self.n_points_Y, bg='black',fg='green', width = 10) self.n_points_Y_scrollbar = Scrollbar(self.n_points_Y_frame, orient = 'horizontal', command = self.n_points_Y_changed) self.n_points_Y_label.pack(side = LEFT, anchor='w') self.n_points_Y_location.pack(side = LEFT, anchor='w') self.n_points_Y_scrollbar.pack(side = LEFT, anchor='w') self.n_points_Y_frame.pack(fill = 'x', padx = 4, pady=1) self.n_points_Z_frame = Tkinter.Frame(self.grid_page_left_side.interior()) self.n_points_Z_label = Label(self.n_points_Z_frame, text='Z-points:', width = 10) self.n_points_Z_location = Entry(self.n_points_Z_frame, textvariable= self.n_points_Z, bg='black',fg='green', width = 10) self.n_points_Z_scrollbar = Scrollbar(self.n_points_Z_frame, orient = 'horizontal', command = self.n_points_Z_changed) self.n_points_Z_label.pack(side = LEFT, anchor='w') self.n_points_Z_location.pack(side = LEFT, anchor='w') self.n_points_Z_scrollbar.pack(side = LEFT, anchor='w') self.n_points_Z_frame.pack(fill = 'x', padx = 4, pady=1) Pmw.alignlabels( [self.grid_spacing_label, self.n_points_X_label, self.n_points_Y_label, self.n_points_Z_label ]) Pmw.alignlabels( [self.grid_spacing_location, self.n_points_X_location, self.n_points_Y_location, self.n_points_Z_location ]) # display option buttons self.display_button_box = Pmw.ButtonBox(self.grid_page_main_group.interior(), padx=0, pady=1,orient='vertical') self.display_button_box.pack(side=LEFT) self.display_button_box.add('Show Box',command = self.show_box) self.display_button_box.add('Hide Box',command = self.hide_box) self.display_button_box.add('Change Box Color',command = self.change_box_color) # display options on the right self.grid_page_right_side = Pmw.Group(self.grid_page_main_group.interior(), tag_text = 'Display Options') self.grid_page_right_side.pack(side = LEFT, fill = 'both', expand = 0, padx = 10, pady = 3) self.box_display_radiogroups = [] self.box_display_radioframe = Tkinter.Frame(self.grid_page_right_side.interior()) self.box_display_cylinder_frame = Pmw.Group(self.box_display_radioframe, tag_pyclass = Tkinter.Radiobutton, tag_text = 'Cylindric Box', tag_value = 0, tag_variable = self.box_display_mode ) self.box_display_cylinder_frame.pack(fill='x',expand = 1,side=TOP) self.box_display_radiogroups.append(self.box_display_cylinder_frame) self.box_display_cylinder_size_frame = Tkinter.Frame(self.box_display_cylinder_frame.interior()) self.box_display_cylinder_size_label = Label(self.box_display_cylinder_size_frame, text = 'Size:', width=10) self.box_display_cylinder_size_location = Entry(self.box_display_cylinder_size_frame, textvariable = self.box_display_cylinder_size, bg = 'black',fg = 'green', width = 10) self.box_display_cylinder_size_scrollbar = Scrollbar(self.box_display_cylinder_size_frame, orient = 'horizontal',command = self.box_display_cylinder_size_changed) self.box_display_cylinder_size_label.pack(side = LEFT) self.box_display_cylinder_size_location.pack(side = LEFT) self.box_display_cylinder_size_scrollbar.pack(side = LEFT) self.box_display_cylinder_size_frame.pack(fill='x',padx = 4, pady=1) self.box_display_wire_frame = Pmw.Group(self.box_display_radioframe, tag_pyclass = Tkinter.Radiobutton, tag_text = 'Wired Box', tag_value = 1, tag_variable = self.box_display_mode ) self.box_display_wire_frame.pack(fill='x',expand = 1) self.box_display_radiogroups.append(self.box_display_wire_frame) self.box_display_mesh_line_width_frame = Tkinter.Frame(self.box_display_wire_frame.interior()) self.box_display_mesh_line_width_label = Label(self.box_display_mesh_line_width_frame, text = 'Line Width:', width=10) self.box_display_mesh_line_width_location = Entry(self.box_display_mesh_line_width_frame, textvariable = self.box_display_line_width, bg='black', fg='green',width = 10) self.box_display_mesh_line_width_scrollbar = Scrollbar(self.box_display_mesh_line_width_frame, orient = 'horizontal',command = self.box_display_line_width_changed) self.box_display_mesh_line_width_label.pack(side = LEFT) self.box_display_mesh_line_width_location.pack(side = LEFT) self.box_display_mesh_line_width_scrollbar.pack(side = LEFT) self.box_display_mesh_line_width_frame.pack(fill='x',padx=4,pady=1) self.box_display_mesh_grid_frame = Tkinter.Frame(self.box_display_wire_frame.interior()) self.box_display_mesh_grid_label = Label(self.box_display_mesh_grid_frame, text = 'Grid Size:', width=10) self.box_display_mesh_grid_location = Entry(self.box_display_mesh_grid_frame, textvariable = self.box_display_mesh_grid, bg='black', fg='green',width = 10) self.box_display_mesh_grid_scrollbar = Scrollbar(self.box_display_mesh_grid_frame, orient = 'horizontal',command = self.box_display_mesh_grid_changed) self.box_display_mesh_grid_label.pack(side = LEFT) self.box_display_mesh_grid_location.pack(side = LEFT) self.box_display_mesh_grid_scrollbar.pack(side = LEFT) self.box_display_mesh_grid_frame.pack(fill='x',padx=4,pady=1) self.box_display_radioframe.pack(padx = 6, pady = 6, expand='yes', fill='both') Pmw.aligngrouptags( self.box_display_radiogroups ) # grid center definition self.grid_center_radiogroups = [] self.grid_center_selection_mode = IntVar() self.grid_center_selection_mode.set(GRID_CENTER_FROM_SELECTION) self.grid_center_radioframe = Tkinter.Frame(self.grid_definition_page) self.grid_center_radio_button_pymol_selection = Pmw.Group(self.grid_center_radioframe, tag_pyclass = Tkinter.Radiobutton, tag_text = 'Calculate Grid Center by Selection', tag_value = GRID_CENTER_FROM_SELECTION, tag_variable = self.grid_center_selection_mode ) self.grid_center_radio_button_pymol_selection.pack(fill = 'x', expand = 1, side = TOP) self.grid_center_radiogroups.append(self.grid_center_radio_button_pymol_selection) self.grid_center_selection_entry = Pmw.EntryField(self.grid_center_radio_button_pymol_selection.interior(), labelpos = 'w', label_text = 'Selection', value = default_settings['grid_center_selection'], command = self.grid_center_from_selection_changed ) self.grid_center_selection_entry.pack(fill='x',padx=4,pady=1,expand=0) self.grid_center_radio_button_coordinates = Pmw.Group(self.grid_center_radioframe, tag_pyclass = Tkinter.Radiobutton, tag_text = 'Grid Center Coordinates', tag_value = GRID_CENTER_FROM_COORDINATES, tag_variable = self.grid_center_selection_mode ) self.grid_center_radio_button_coordinates.pack(fill = 'x', expand = 1, side = TOP) self.grid_center_radiogroups.append(self.grid_center_radio_button_coordinates) self.grid_center_radioframe.pack(padx = 6, pady = 6, expand='yes', fill='both') Pmw.aligngrouptags(self.grid_center_radiogroups) self.grid_center_X_frame = Tkinter.Frame(self.grid_center_radio_button_coordinates.interior()) self.grid_center_X_label = Label(self.grid_center_X_frame, text = 'X:') self.grid_center_X_location = Entry(self.grid_center_X_frame, textvariable = self.grid_center[0], bg='black', fg='green', width=10) self.grid_center_X_scrollbar = Scrollbar(self.grid_center_X_frame,orient='horizontal',command = self.grid_center_X_changed) self.grid_center_Y_frame = Tkinter.Frame(self.grid_center_radio_button_coordinates.interior()) self.grid_center_Y_label = Label(self.grid_center_Y_frame, text = 'Y:') self.grid_center_Y_location = Entry(self.grid_center_Y_frame, textvariable = self.grid_center[1], bg='black', fg='green', width=10) self.grid_center_Y_scrollbar = Scrollbar(self.grid_center_Y_frame,orient='horizontal',command = self.grid_center_Y_changed) self.grid_center_Z_frame = Tkinter.Frame(self.grid_center_radio_button_coordinates.interior()) self.grid_center_Z_label = Label(self.grid_center_Z_frame, text = 'Z:') self.grid_center_Z_location = Entry(self.grid_center_Z_frame, textvariable = self.grid_center[2], bg='black', fg='green', width=10) self.grid_center_Z_scrollbar = Scrollbar(self.grid_center_Z_frame,orient='horizontal',command = self.grid_center_Z_changed) self.grid_center_X_label.pack(side = LEFT) self.grid_center_X_location.pack(side=LEFT) self.grid_center_X_scrollbar.pack(side=LEFT) self.grid_center_X_frame.pack(side=LEFT,padx=4,pady=1) self.grid_center_Y_label.pack(side = LEFT) self.grid_center_Y_location.pack(side=LEFT) self.grid_center_Y_scrollbar.pack(side=LEFT) self.grid_center_Y_frame.pack(side=LEFT,padx=4,pady=1) self.grid_center_Z_label.pack(side = LEFT) self.grid_center_Z_location.pack(side=LEFT) self.grid_center_Z_scrollbar.pack(side=LEFT) self.grid_center_Z_frame.pack(side=LEFT,padx=4,pady=1) self.select_binding_site_button_box = Pmw.ButtonBox(self.grid_center_radio_button_coordinates.interior(),orient='horizontal', padx=0,pady=0) self.select_binding_site_button_box.add('Select binding site',command = self.select_atoms_within_binding_site) self.select_binding_site_button_box.pack(side=TOP,expand = 1, padx = 3, pady = 3) # load/write gpf self.gpf_file_io = Pmw.Group(self.grid_definition_page, tag_text='GPF File') self.gpf_file_io.pack(side = TOP,expand=1, fill='x') self.gpf_file_location = Pmw.EntryField(self.gpf_file_io.interior(), labelpos = 'w', label_pyclass = FileDialogButtonClassFactory.get(self.set_gpf_filename,mode='w',filter=[("Grid Parameter File","*.gpf")]), validate = {'validator':quickFileValidation,}, value = default_settings['gpf_file_name'], label_text = 'Autodock GPF File:') self.gpf_file_location.pack(side=LEFT,fill = 'x', expand = 1, padx = 1, pady = 5) self.gpf_button_box = Pmw.ButtonBox(self.gpf_file_io.interior(),orient='horizontal', padx=0,pady=0) self.gpf_button_box.add('Load',command = self.load_gpf_file) self.gpf_button_box.add('Save',command = self.save_gpf_file) self.gpf_button_box.pack(side=BOTTOM,expand = 1, padx = 10, pady = 5) # load/write vina config file self.config_file_io = Pmw.Group(self.grid_definition_page, tag_text='Config File') self.config_file_io.pack(side = TOP,expand=1, fill='x') self.config_file_location = Pmw.EntryField(self.config_file_io.interior(), labelpos = 'w', label_pyclass = FileDialogButtonClassFactory.get(self.set_config_filename,mode='w',filter=[("Vina Config File","*.txt")]), validate = {'validator':quickFileValidation,}, value = default_settings['config_file_name'], label_text = 'VINA config File:') self.config_file_location.pack(side=LEFT,fill = 'x', expand = 1, padx = 1, pady = 5) self.config_button_box = Pmw.ButtonBox(self.config_file_io.interior(), padx=0, pady=0,orient='horizontal') self.config_button_box.pack(side=BOTTOM,expand = 1, padx = 10, pady = 5) self.config_button_box.add('Load',command = self.load_config_file) self.config_button_box.add('Save',command = self.save_config_file) #------------------------------------------------------------------ # # PLUGIN CONFIGURATION PAGE self.configuration_top_group = Pmw.Group(self.configuration_page,tag_text='General Notes') self.configuration_top_group.pack(fill = 'both', expand = 0, padx = 10, pady = 5) self.text_field = Tkinter.Label(self.configuration_top_group.interior(), text = intro_text, background = 'black', foreground = 'yellow', justify = LEFT, ) self.text_field.pack(expand = 0, fill = 'both', padx = 4, pady = 4) self.configuration_group = Pmw.Group(self.configuration_page,tag_text='Scripts and Program Paths') self.configuration_group.pack(fill = 'both', expand = 0, padx = 10, pady = 5) self.config_settings = self.read_plugin_config_file() self.autodock_tools_location = Pmw.EntryField(self.configuration_group.interior(), labelpos='w', label_pyclass = DirDialogButtonClassFactory.get(self.set_autodock_tools_path), value = self.config_settings['autodock_tools_path'], label_text = 'AutoDockTools:') self.autogrid_location = Pmw.EntryField(self.configuration_group.interior(), labelpos='w', label_pyclass = FileDialogButtonClassFactory.get(self.set_autogrid_location), value = self.config_settings['autogrid_exe'], label_text = 'autogrid4 executable:') self.autodock_location = Pmw.EntryField(self.configuration_group.interior(), labelpos='w', label_pyclass = FileDialogButtonClassFactory.get(self.set_autodock_location), value = self.config_settings['autodock_exe'], label_text = 'autodock4 executable:') self.vina_location = Pmw.EntryField(self.configuration_group.interior(), labelpos='w', label_pyclass = FileDialogButtonClassFactory.get(self.set_vina_location), value = self.config_settings['vina_exe'], label_text = 'vina executable:') self.work_path_location = Pmw.EntryField(self.configuration_group.interior(), labelpos='w', label_pyclass = DirDialogButtonClassFactory.get(self.set_work_path_location), value = os.path.abspath(os.curdir), label_text = 'Working Directory:') for x in [self.autodock_tools_location, self.autogrid_location, self.autodock_location, self.vina_location, self.work_path_location ]: x.pack(fill = 'both', expand = 1, padx = 10, pady = 5) Pmw.alignlabels( [self.autodock_tools_location, self.autogrid_location, self.autodock_location, self.vina_location, self.work_path_location ] ) self.config_button_box = Pmw.ButtonBox(self.configuration_page, padx=0, pady=0,orient='horizontal') self.config_button_box.pack(side=BOTTOM,expand = 1, padx = 10, pady = 0) self.config_button_box.add('Save Plugin Configuration File',command = self.save_plugin_config_file) #------------------------------------------------------------------ # # RECEPTOR PREPARATION PAGE self.receptor_preparation_top_group = Pmw.Group(self.receptor_preparation_page, tag_text='Selections') self.receptor_preparation_top_group.pack(fill = 'both', expand = 0, padx=10, pady=5) self.receptor_import_selection_button_box = Pmw.ButtonBox(self.receptor_preparation_top_group.interior(),orient='vertical', padx=0,pady=0) self.receptor_import_selection_button_box.add('Import Selections',command = self.import_selections) self.receptor_import_selection_button_box.pack(side=LEFT, fill='x', padx = 0, pady = 3) self.receptor_pdbqt_location = Pmw.EntryField(self.receptor_preparation_top_group.interior(), labelpos = 'w', label_pyclass = FileDialogButtonClassFactory.get(self.set_receptor_pdbqt_location,filter=[("PDBQT File","*.pdbqt")]), validate = {'validator':quickFileValidation,}, value = '', label_text = 'Receptor:') self.receptor_pdbqt_location.pack(side=LEFT,fill = 'x', expand = 1, padx = 1, pady = 5) self.receptor_button_box = Pmw.ButtonBox(self.receptor_preparation_top_group.interior(), padx=0, pady=0,orient='horizontal') self.receptor_button_box.pack(side=BOTTOM,expand = 1, padx = 10, pady = 5) self.receptor_button_box.add('Load',command = self.load_receptor_pdbqt) self.receptor_preparation_center_group = Pmw.Group(self.receptor_preparation_page, tag_text='Receptor Preparation') self.receptor_preparation_center_group.pack(fill = 'both', expand = 0, padx=10, pady=5) self.selection_list = Pmw.ComboBox(self.receptor_preparation_center_group.interior(), scrolledlist_items=cmd.get_names("selections")+cmd.get_names(), labelpos='nw', label_text='PyMOL Selections', listbox_height = 10, selectioncommand=self.selectionCommand, dropdown=False ) self.receptor_list = Pmw.ComboBox(self.receptor_preparation_center_group.interior(), scrolledlist_items=[], labelpos='nw', label_text='Receptors', listbox_height = 10, selectioncommand=self.selected_receptor, dropdown=False ) self.flexible_residues_list = Pmw.ScrolledListBox(self.receptor_preparation_center_group.interior(), items=[], labelpos='nw', label_text='Flexible Residues', listbox_height = 11, selectioncommand=self.delete_residue, ) self.selection_list.pack(side=LEFT, padx=0, anchor='n') self.receptor_conversion_button_box = Pmw.ButtonBox(self.receptor_preparation_center_group.interior(),orient='vertical', padx=0,pady=0) self.receptor_conversion_button_box.add('Generate Receptor ->',command = self.generate_receptor) self.receptor_conversion_button_box.add('Select as Flexible ->',command = self.select_flexible_residues) self.receptor_conversion_button_box.add('Remove Receptor',command = self.remove_receptor) self.receptor_conversion_button_box.add('Remove Flexible',command = self.remove_flexible_residues) self.receptor_conversion_button_box.add('Remove All',command = self.remove_all_receptors) self.receptor_conversion_button_box.pack(side = LEFT, expand = 0, padx = 0, pady = 12, anchor='n') self.receptor_list.pack(side=LEFT, padx=3, anchor='n') self.flexible_residues_list.pack(side=LEFT, padx=3, anchor='n') self.receptor_preparation_bottom_group = Pmw.Group(self.receptor_preparation_page, tag_text='Log') self.receptor_preparation_bottom_group.pack(fill = 'both', expand = 0, padx=10, pady=5) self.receptor_page_log_text = Pmw.ScrolledText(self.receptor_preparation_bottom_group.interior(), borderframe=5, vscrollmode='dynamic', hscrollmode='dynamic', labelpos='n', text_width=150, text_height=15, text_wrap='none', text_background='#000000', text_foreground='green' ) self.receptor_page_log_text.pack(side=LEFT, anchor='n',pady=0) self.receptor_page_log_text.insert('end',receptor_prep_text) #=============================================== # # LIGAND PREPARATION PAGE self.ligand_preparation_top_group = Pmw.Group(self.ligand_preparation_page, tag_text='Selections') self.ligand_preparation_top_group.pack(fill = 'both', expand = 0, padx=10, pady=5) self.ligand_import_selection_button_box = Pmw.ButtonBox(self.ligand_preparation_top_group.interior(),orient='vertical', padx=0,pady=0) self.ligand_import_selection_button_box.add('Import Selections',command = self.import_selections) self.ligand_import_selection_button_box.pack(side=LEFT, fill='x', padx = 0, pady = 3) self.ligand_dir_location = Pmw.EntryField(self.ligand_preparation_top_group.interior(), labelpos = 'w', label_pyclass = DirDialogButtonClassFactory.get(self.set_ligand_dir_location), validate = {'validator':quickFileValidation,}, value = '', label_text = 'Ligands:') self.ligand_dir_location.pack(side=LEFT,fill = 'x', expand = 1, padx = 1, pady = 5) self.ligand_button_box = Pmw.ButtonBox(self.ligand_preparation_top_group.interior(), padx=0, pady=0,orient='horizontal') self.ligand_button_box.pack(side=BOTTOM,expand = 1, padx = 10, pady = 5) self.ligand_button_box.add('Import',command = self.import_ligands) self.ligand_preparation_center_group = Pmw.Group(self.ligand_preparation_page, tag_text='Ligand Preparation') self.ligand_preparation_center_group.pack(fill = 'both', expand = 0, padx=10, pady=5) self.ligand_selection_list = Pmw.ComboBox(self.ligand_preparation_center_group.interior(), scrolledlist_items=cmd.get_names("selections")+cmd.get_names(), labelpos='nw', label_text='PyMOL Selections', listbox_height = 10, selectioncommand=self.save_as_ligand_pdb, dropdown=False # vscrollmode='dynamic', # hscrollmode='dynamic', ) self.ligand_list = Pmw.ComboBox(self.ligand_preparation_center_group.interior(), scrolledlist_items=[], labelpos='nw', label_text='Ligand List', listbox_height = 10, selectioncommand=self.ligand_info, dropdown=False # vscrollmode='dynamic', # hscrollmode='dynamic', ) self.ligand_pdbqt_list = Pmw.ComboBox(self.ligand_preparation_center_group.interior(), scrolledlist_items=[], labelpos='nw', label_text='Prepared Ligands', listbox_height = 10, selectioncommand=self.ligand_info, dropdown=False, # dropdown=False # vscrollmode='dynamic', # hscrollmode='dynamic', ) self.ligand_selection_list.pack(side=LEFT, padx=0, anchor='n') self.ligand_list.pack(side=LEFT, padx=3, anchor='n') self.ligand_conversion_button_box = Pmw.ButtonBox(self.ligand_preparation_center_group.interior(),orient='vertical', padx=0,pady=0) self.ligand_conversion_button_box.add('Generate Ligand ->',command = self.generate_ligand) self.ligand_conversion_button_box.add('Remove Ligand',command = self.remove_ligand) self.ligand_conversion_button_box.add('Display Ligand',command = self.display_ligand) self.ligand_conversion_button_box.add('Generate All',command = self.generate_all_ligands) self.ligand_conversion_button_box.add('Remove All',command = self.remove_all_ligands) self.ligand_conversion_button_box.pack(side = LEFT, expand = 0, padx = 0, pady = 12, anchor='n') self.ligand_pdbqt_list.pack(side=LEFT, padx=3, anchor='n') self.ligand_preparation_bottom_group = Pmw.Group(self.ligand_preparation_page, tag_text='Log') self.ligand_preparation_bottom_group.pack(fill = 'both', expand = 0, padx=10, pady=5) self.ligand_page_log_text = Pmw.ScrolledText(self.ligand_preparation_bottom_group.interior(), borderframe=5, vscrollmode='dynamic', hscrollmode='dynamic', labelpos='n', # label_text='Log', text_width=150, text_height=15, text_wrap='none', text_background='#000000', text_foreground='green' ) self.ligand_page_log_text.pack(side=LEFT, anchor='n',pady=0) self.ligand_page_log_text.insert('end',ligand_prep_text) #------------------------------------------------------------------ # # DOCKING PAGE self.docking_top_group = Pmw.Group(self.docking_page, tag_text='Docking') self.docking_top_group.pack(fill = 'both', expand = 0, padx=10, pady=5) self.docking_receptor_rigid_list = Pmw.ComboBox(self.docking_top_group.interior(), scrolledlist_items=[], labelpos='nw', label_text='Receptor', listbox_height = 10, selectioncommand=self.selectionCommand, dropdown=True ) self.docking_receptor_flexible_list = Pmw.ComboBox(self.docking_top_group.interior(), scrolledlist_items=['No','Yes'], labelpos='nw', label_text='Use flexible sidechains', listbox_height = 2, selectioncommand=self.selectionCommand, dropdown=True ) self.docking_ligand_list = Pmw.ComboBox(self.docking_top_group.interior(), scrolledlist_items=['All'], labelpos='nw', label_text='Ligands', listbox_height = 10, selectioncommand=self.selectionCommand, dropdown=True ) self.docking_nposes_list = Pmw.ComboBox(self.docking_top_group.interior(), scrolledlist_items=range(1,101), labelpos='nw', label_text='# Poses', listbox_height = 10, selectioncommand=self.selectionCommand, dropdown=True ) self.docking_nposes_list.selectitem(9) self.docking_receptor_flexible_list.selectitem('No') self.docking_ligand_list.selectitem('All') self.docking_receptor_rigid_list.pack(side=LEFT, padx=0, anchor='n') self.docking_receptor_flexible_list.pack(side=LEFT, padx=0, anchor='n') self.docking_ligand_list.pack(side=LEFT, padx=0, anchor='n') self.docking_nposes_list.pack(side=LEFT, padx=0, anchor='n') self.docking_center_group = Pmw.Group(self.docking_page, tag_text='AutoDock') self.docking_center_group.pack(fill = 'both', expand = 0, padx=10, pady=5) self.docking_center_group2 = Pmw.Group(self.docking_page, tag_text='VINA') self.docking_center_group2.pack(fill = 'both', expand = 0, padx=10, pady=5) self.docking_button_box = Pmw.ButtonBox(self.docking_center_group.interior(),orient='horizontal', padx=0,pady=0) self.docking_button_box.add('Run AutoGrid',command = self.run_autogrid) self.docking_button_box.add('Run AutoDock',command = self.run_autodock) self.docking_button_box.add('Write AutoDock Input File(s)',command = self.write_autodock_input_files) self.docking_button_box2 = Pmw.ButtonBox(self.docking_center_group2.interior(),orient='horizontal', padx=0,pady=0) self.docking_button_box2.add('Run Vina',command = self.run_vina) self.docking_button_box2.add('Write Vina Input File(s)',command = self.write_vina_input_files) self.docking_button_box.pack(side=LEFT, fill='x', padx = 0, pady = 3) self.docking_button_box2.pack(side=LEFT, fill='x', padx = 0, pady = 3) self.docking_button_box.alignbuttons() self.docking_button_box2.alignbuttons() self.docking_bottom_group = Pmw.Group(self.docking_page, tag_text='Log') self.docking_bottom_group.pack(fill = 'both', expand = 0, padx=10, pady=5) self.docking_page_log_text = Pmw.ScrolledText(self.docking_bottom_group.interior(), borderframe=5, vscrollmode='dynamic', hscrollmode='dynamic', labelpos='n', text_width=150, text_height=25, text_wrap='none', text_background='#000000', text_foreground='green' ) self.docking_page_log_text.pack(side=LEFT, anchor='n',pady=0) self.docking_page_log_text.insert('end',docking_text) #------------------------------------------------------------------ # # POSE VIEWER PAGE self.pose_viewer_page_top_group = Pmw.Group(self.pose_viewer_page,tag_text='File') self.pose_viewer_page_top_group.pack(fill = 'both', expand = 0, padx = 10, pady = 5) self.pose_viewer_page_stucts = Pmw.Group(self.pose_viewer_page,tag_text='Poses') self.pose_viewer_page_stucts.pack(fill = 'both', expand = 1, padx = 10, pady = 0) self.pose_viewer_page_display = Pmw.Group(self.pose_viewer_page,tag_text='Display Options') self.pose_viewer_page_display.pack(fill = 'x', expand = 1, padx = 10, pady = 0) self.pose_viewer_notebook = Pmw.NoteBook(self.pose_viewer_page_stucts.interior()) self.pose_viewer_notebook.pack(fill='both',expand=1,padx=3,pady=3) self.pose_viewer_pages = {} self.pose_viewer_ligand_dic = {} self.pose_file = StringVar() self.pose_file.set(default_settings['dlg_input_file']) self.pose_file_location = Pmw.EntryField(self.pose_viewer_page_top_group.interior(), labelpos='w', label_pyclass = FileDialogButtonClassFactory.get(self.set_pose_filename,filter=[("PDBQT File","*.pdbqt"),("DLG File","*.dlg")]), validate = {'validator':quickFileValidation,}, value = default_settings['dlg_input_file'], label_text = 'Browse:') # self.pose_file_location.pack(fill = 'both', expand = 1, padx = 10, pady = 5) self.pose_file_location.pack(side=LEFT,fill = 'x', expand = 1, padx = 1, pady = 5) self.load_pose_file_buttonbox = Pmw.ButtonBox(self.pose_viewer_page_top_group.interior(), padx=0) self.load_pose_file_buttonbox.pack(side=BOTTOM,expand = 1, padx = 10, pady = 5) self.load_pose_file_buttonbox.add('Load',command=self.load_ligand_file) self.load_pose_file_buttonbox.add('Load All',command=self.load_all_ligand_files) self.pose_viewer_ligand_display_radio = Pmw.RadioSelect(self.pose_viewer_page_display.interior(), selectmode='multiple', buttontype='checkbutton', labelpos='w', label_text='Display mode', orient='horizontal', frame_relief='ridge', command=self.ligand_display_mode_changed) self.pose_viewer_ligand_display_radio.pack(side=TOP, padx=10, anchor='w') for entry in ('lines', 'sticks','spheres','surface','mesh'): self.pose_viewer_ligand_display_radio.add(entry) for entry in ('lines', 'sticks','spheres','surface','mesh'): if self.ligand_display_mode[entry]: self.pose_viewer_ligand_display_radio.invoke(entry) self.pose_viewer_radiobuttons = Pmw.RadioSelect(self.pose_viewer_page_display.interior(), buttontype = 'radiobutton', orient = 'horizontal', labelpos = 'w', ) for text in ('Show Selected', 'Hide Selected'): self.pose_viewer_radiobuttons.add(text) self.pose_viewer_radiobuttons.setvalue('Show Selected') self.pose_viewer_radiobuttons.pack(padx=4,pady=1,side=TOP) self.pose_viewer_ligand_pages = {} #--------------------------------------------------------------- # SCORE/RANK PAGE self.score_table = ScoreTable(self.rank_page) self.score_table.pack(pady=20) self.score_table_radiobuttons = Pmw.RadioSelect(self.rank_page, buttontype = 'radiobutton', orient = 'horizontal', labelpos = 'w', command = self.update_score_table ) for text in ('Show All Poses', 'Show Only Best Pose'): self.score_table_radiobuttons.add(text) self.score_table_radiobuttons.setvalue('Show All Poses') self.score_table_radiobuttons.pack(padx=4,pady=1,side=TOP) self.rank_dat_file_io = Pmw.Group(self.rank_page, tag_text='Export scores as data file') self.rank_dat_file_io.pack(side = TOP,expand=1, fill='x') self.rank_dat_file_location = Pmw.EntryField(self.rank_dat_file_io.interior(), labelpos = 'w', label_pyclass = FileDialogButtonClassFactory.get(self.set_rank_dat_filename,mode='w',filter=[("Data File","*.dat")]), validate = {'validator':quickFileValidation,}, value = default_settings['rank_dat_file_name'], label_text = 'Filename:') self.rank_dat_file_location.pack(side=LEFT,fill = 'x', expand = 1, padx = 1, pady = 0) self.rank_dat_button_box = Pmw.ButtonBox(self.rank_dat_file_io.interior(), padx=0, pady=0,orient='horizontal') self.rank_dat_button_box.pack(side=BOTTOM,expand = 1, padx = 10, pady = 0) self.rank_dat_button_box.add('Export',command = self.export_score_dat_file) self.rank_csv_file_io = Pmw.Group(self.rank_page, tag_text='Export scores as CSV file') self.rank_csv_file_io.pack(side = TOP,expand=1, fill='x') self.rank_pose_file_io = Pmw.Group(self.rank_page, tag_text='Export poses as PDB file') self.rank_pose_file_io.pack(side = TOP,expand=1, fill='x') self.rank_csv_file_location = Pmw.EntryField(self.rank_csv_file_io.interior(), labelpos = 'w', label_pyclass = FileDialogButtonClassFactory.get(self.set_rank_csv_filename,mode='w',filter=[("CSV File","*.csv")]), validate = {'validator':quickFileValidation,}, value = default_settings['rank_csv_file_name'], label_text = 'Filename:') self.rank_csv_file_location.pack(side=LEFT,fill = 'x', expand = 1, padx = 1, pady = 0) self.rank_csv_button_box = Pmw.ButtonBox(self.rank_csv_file_io.interior(), padx=0, pady=0,orient='horizontal') self.rank_csv_button_box.pack(side=BOTTOM,expand = 1, padx = 10, pady = 0) self.rank_csv_button_box.add('Export',command = self.export_score_csv_file) self.rank_pose_file_location = Pmw.EntryField(self.rank_pose_file_io.interior(), labelpos = 'w', label_pyclass = FileDialogButtonClassFactory.get(self.set_rank_pose_filename,mode='w',filter=[("PDB File","*.pdb")]), validate = {'validator':quickFileValidation,}, value = default_settings['rank_pose_file_name'], label_text = 'Filename:') self.rank_pose_file_location.pack(side=LEFT,fill = 'x', expand = 1, padx = 1, pady = 0) self.rank_pose_button_box = Pmw.ButtonBox(self.rank_pose_file_io.interior(), padx=0, pady=0,orient='horizontal') self.rank_pose_button_box.pack(side=BOTTOM,expand = 1, padx = 10, pady = 0) self.rank_pose_button_box.add('Export',command = self.export_score_pose_file) #------------------------------------------------------------------ # # MAP VIEWER PAGE self.map_threshold = {} self.map_meta = {} self.map_viewer_page_top_group = Pmw.Group(self.map_viewer_page,tag_text='Grid Map') self.map_viewer_page_top_group.pack(fill = 'both', expand = 0, padx = 10, pady = 5) # the maps card self.map_viewer_page_center_group = Pmw.Group(self.map_viewer_page,tag_text='Maps') self.map_viewer_page_center_group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) self.map_viewer_notebook = Pmw.NoteBook(self.map_viewer_page_center_group.interior()) self.map_viewer_notebook.pack(fill='both',expand=1,padx=3,pady=3) self.map_pages = {} self.map_dic = {} self.mapfile = StringVar() self.mapfile.set(default_settings['map_input_file']) self.map_file_location = Pmw.EntryField(self.map_viewer_page_top_group.interior(), labelpos='w', label_pyclass = FileDialogButtonClassFactory.get(self.set_mapfilename,filter=[("Autodock Map File","*.map")]), validate = {'validator':quickFileValidation,}, value = default_settings['map_input_file'], label_text = 'Browse:') self.map_file_location.pack(side = LEFT,fill = 'x', expand = 1, padx = 10, pady = 5) self.load_map_buttonbox = Pmw.ButtonBox(self.map_viewer_page_top_group.interior(), padx=0) self.load_map_buttonbox.pack(side=BOTTOM,expand = 1, padx = 10, pady = 5) self.load_map_buttonbox.add('Load',command=self.load_grid_map) #------------------------------------------------------------------ ################################################################## # DONE PAGES self.notebook.setnaturalsize() self.dialog.show() self.status_line.configure(text ="Ready..... (version: %s)" % __version__) #------------------------------------------------------------------ ################################################################## def button_pressed(self, result): if hasattr(result,'keycode'): if result.keycode == 36: if self.notebook.getcurselection()=='Grid Settings': self.show_box() elif self.notebook.getcurselection()=='View Poses': self.load_ligand_file() elif result == 'Exit' or result == None: self.dialog.withdraw() #------------------------------------------------------------------ # grid settings functions def grid_spacing_changed(self, x): val = float(self.grid_spacing.get())+float(x)*0.005 self.grid_spacing.set(val) if self.box_is_on_display: self.grid_center_selection_mode.set(GRID_CENTER_FROM_COORDINATES) def calculate_grid_center(self): if self.grid_center_selection_mode.get() == GRID_CENTER_FROM_SELECTION: sel = self.grid_center_selection_entry.get() if sel: stored.xyz = [] cmd.iterate_state(1,sel,"stored.xyz.append([x,y,z])") xx = average(map(lambda a: a[0], stored.xyz)) yy = average(map(lambda a: a[1], stored.xyz)) zz = average(map(lambda a: a[2], stored.xyz)) self.grid_center[0].set(round(xx,2)) self.grid_center[1].set(round(yy,2)) self.grid_center[2].set(round(zz,2)) else: self.grid_center_selection_mode.set(GRID_CENTER_FROM_COORDINATES) def n_points_X_changed(self, x): val = int(self.n_points_X.get())+int(x) self.n_points_X.set(val) self.grid_center_selection_mode.set(GRID_CENTER_FROM_COORDINATES) self.show_box() def n_points_Y_changed(self, x): val = int(self.n_points_Y.get())+int(x) self.n_points_Y.set(val) self.grid_center_selection_mode.set(GRID_CENTER_FROM_COORDINATES) self.show_box() def n_points_Z_changed(self, x): val = int(self.n_points_Z.get())+int(x) self.n_points_Z.set(val) self.grid_center_selection_mode.set(GRID_CENTER_FROM_COORDINATES) self.show_box() def grid_center_from_selection_changed(self): self.grid_center_selection_mode.set(GRID_CENTER_FROM_SELECTION) self.show_box() self.grid_center_selection_entry.clear() def grid_center_X_changed(self, x): self.grid_center_selection_mode.set(GRID_CENTER_FROM_COORDINATES) val=float(self.grid_center[0].get())+float(x)*1.0 self.grid_center[0].set(val) self.show_box() def grid_center_Y_changed(self, x): self.grid_center_selection_mode.set(GRID_CENTER_FROM_COORDINATES) val=float(self.grid_center[1].get())+float(x)*1.0 self.grid_center[1].set(val) self.show_box() def grid_center_Z_changed(self, x): self.grid_center_selection_mode.set(GRID_CENTER_FROM_COORDINATES) val=float(self.grid_center[2].get())+float(x)*1.0 self.grid_center[2].set(val) self.show_box() def select_atoms_within_binding_site(self): m = cmd.get_model("polymer") xmin, xmax = self.box_coords[0] ymin, ymax = self.box_coords[1] zmin, zmax = self.box_coords[2] lst = filter(lambda a: a.coord[0] >= xmin and \ a.coord[0] <= xmax and \ a.coord[1] >= ymin and \ a.coord[1] <= ymax and \ a.coord[2] >= zmin and \ a.coord[2] <= zmax, m.atom) by_id = map(lambda a: a.id, lst) if len(by_id) > 1: cmd.select("binding_site", "ID %d" % by_id[0]) for idx in by_id[1:]: cmd.select("binding_site", "binding_site or ID %d" % idx) self.status_line.configure(text = "Selector 'binding_site' created with %d atoms" % len(by_id)) self.import_selections() def box_display_cylinder_size_changed(self, x): val=float(self.box_display_cylinder_size.get())+float(x)*0.1 self.box_display_cylinder_size.set(val) self.grid_center_selection_mode.set(GRID_CENTER_FROM_COORDINATES) self.show_box() def box_display_line_width_changed(self, x): val=float(self.box_display_line_width.get())+float(x)*0.1 self.box_display_line_width.set(val) self.grid_center_selection_mode.set(GRID_CENTER_FROM_COORDINATES) self.show_box() def box_display_mesh_grid_changed(self, x): val=float(self.box_display_mesh_grid.get())+float(x)*0.1 self.box_display_mesh_grid.set(val) self.grid_center_selection_mode.set(GRID_CENTER_FROM_COORDINATES) self.show_box() def show_box(self): self.calculate_grid_center() self.show_crisscross() self.calculate_box() def hide_box(self): cmd.delete("box") cmd.delete("wirebox") cmd.delete("grid_center") self.box_is_on_display = False def change_box_color(self): color = tkColorChooser.Chooser( initialcolor='white',title='Choose box color').show() if color[0] is not None: self.box_color = [color[0][0]/100., color[0][1]/100., color[0][2]/100.] self.show_box() def set_box_filename(self, filename): self.box_file_location.setvalue(filename) def set_gpf_filename(self, filename): self.gpf_file_location.setvalue(filename) def set_config_filename(self, filename): self.config_file_location.setvalue(filename) def set_rank_dat_filename(self, filename): self.rank_dat_file_location.setvalue(filename) def set_rank_csv_filename(self, filename): self.rank_csv_file_location.setvalue(filename) def set_rank_pose_filename(self, filename): self.rank_pose_file_location.setvalue(filename) def load_gpf_file(self): filename = self.gpf_file_location.get() fp = self.fileopen(filename,'r') if not fp: return lst = fp.readlines() new = [] for line in lst: if line.strip(): new.append(line.strip()) lst = new for line in lst: entr = line.split() if entr[0] == 'npts': n_points_X = int(entr[1]) n_points_Y = int(entr[2]) n_points_Z = int(entr[3]) self.n_points_X.set(n_points_X) self.n_points_Y.set(n_points_Y) self.n_points_Z.set(n_points_Z) elif entr[0] == 'spacing': spacing = float(entr[1]) self.grid_spacing.set(spacing) elif entr[0] == 'gridcenter': if entr[1]!='auto': grid_X = float(entr[1]) grid_Y = float(entr[2]) grid_Z = float(entr[3]) self.grid_center[0].set(grid_X) self.grid_center[1].set(grid_Y) self.grid_center[2].set(grid_Z) self.status_line.configure(text= 'Reading box info from %s' % filename) self.grid_center_selection_mode.set(GRID_CENTER_FROM_COORDINATES) self.calculate_box() def save_gpf_file(self): filename = self.gpf_file_location.get() fp = self.fileopen(filename,'w') if not fp: return n_points_X = self.n_points_X.get() n_points_Y = self.n_points_Y.get() n_points_Z = self.n_points_Z.get() spacing = self.grid_spacing.get() center_X = self.grid_center[0].get() center_Y = self.grid_center[1].get() center_Z = self.grid_center[2].get() print >>fp, 'npts %d %d %d' % (n_points_X, n_points_Y, n_points_Z) print >>fp, 'spacing %5.3f' % spacing print >>fp, 'gridcenter %8.3f %8.3f %8.3f' % (center_X, center_Y, center_Z) fp.close() self.status_line.configure(text= 'Wrote box info to %s' % filename) def load_config_file(self): filename = self.config_file_location.get() fp = self.fileopen(filename,'r') spacing = self.grid_spacing.get() if not fp: return lst = fp.readlines() new = [] for line in lst: if line.strip(): new.append(line.strip()) lst = new for line in lst: entr = line.split() if entr[0] == 'center_x': center_x = float(entr[2]) self.grid_center[0].set(center_x) elif entr[0] == 'center_y': center_y = float(entr[2]) self.grid_center[1].set(center_y) elif entr[0] == 'center_z': center_z = float(entr[2]) self.grid_center[2].set(center_z) elif entr[0] == 'size_x': size_x = float(entr[2]) n_points_X = size_x/spacing self.n_points_X.set(n_points_X) elif entr[0] == 'size_y': size_y = float(entr[2]) n_points_Y = size_y/spacing self.n_points_Y.set(n_points_Y) elif entr[0] == 'size_z': size_z = float(entr[2]) n_points_Z = size_z/spacing self.n_points_Z.set(n_points_Z) self.status_line.configure(text= 'Reading box info from %s' % filename) self.grid_center_selection_mode.set(GRID_CENTER_FROM_COORDINATES) self.calculate_box() def save_config_file(self): filename = self.config_file_location.get() fp = self.fileopen(filename,'w') if not fp: return n_points_X = self.n_points_X.get() n_points_Y = self.n_points_Y.get() n_points_Z = self.n_points_Z.get() spacing = self.grid_spacing.get() size_x = n_points_X*spacing size_y = n_points_Y*spacing size_z = n_points_Z*spacing center_x = self.grid_center[0].get() center_y = self.grid_center[1].get() center_z = self.grid_center[2].get() print >>fp, "size_x = %6.2f" % size_x print >>fp, "size_y = %6.2f" % size_y print >>fp, "size_z = %6.2f" % size_z print >>fp, "center_x = %6.2f" % center_x print >>fp, "center_y = %6.2f" % center_y print >>fp, "center_z = %6.2f" % center_z fp.close() self.status_line.configure(text= 'Wrote box info to %s' % filename) def show_crisscross(self): center = [float(self.grid_center[0].get()), float(self.grid_center[1].get()), float(self.grid_center[2].get()) ] cmd.delete("grid_center") self.crisscross(center[0], center[1], center[2], 0.5, "grid_center") def crisscross(self,x,y,z,d,name="crisscross"): obj = [ LINEWIDTH, 3, BEGIN, LINE_STRIP, VERTEX, float(x-d), float(y), float(z), VERTEX, float(x+d), float(y), float(z), END, BEGIN, LINE_STRIP, VERTEX, float(x), float(y-d), float(z), VERTEX, float(x), float(y+d), float(z), END, BEGIN, LINE_STRIP, VERTEX, float(x), float(y), float(z-d), VERTEX, float(x), float(y), float(z+d), END ] view = cmd.get_view() cmd.load_cgo(obj,name) cmd.set_view(view) def calculate_box(self): x = float(self.grid_center[0].get()) y = float(self.grid_center[1].get()) z = float(self.grid_center[2].get()) xpts = int(self.n_points_X.get()) ypts = int(self.n_points_Y.get()) zpts = int(self.n_points_Z.get()) spacing = float(self.grid_spacing.get()) cylinder_size = float(self.box_display_cylinder_size.get()) size = [xpts*spacing, ypts*spacing, zpts*spacing] xmax = x + size[0]/2. xmin = x - size[0]/2. ymax = y + size[1]/2. ymin = y - size[1]/2. zmax = z + size[2]/2. zmin = z - size[2]/2. box_edge_x = [xmin,xmax] box_edge_y = [ymin,ymax] box_edge_z = [zmin,zmax] self.box_coords = [box_edge_x,box_edge_y,box_edge_z] cmd.delete('box') if self.box_display_mode.get()==BOX_AS_BOX: self.display_box(self.box_coords,cylinder_size) elif self.box_display_mode.get()==BOX_AS_WIREBOX: self.display_wire_box(self.box_coords) self.box_is_on_display = True def display_box(self, box, cylinder_size): view = cmd.get_view() name = "box" obj = [] # build cgo object color = self.box_color for i in range(2): for k in range (2): for j in range(2): if i != 1: obj.append(CYLINDER) obj.extend([box[0][i],box[1][j],box[2][k]]) obj.extend([box[0][i+1],box[1][j],box[2][k]]) obj.append(cylinder_size) obj.extend(color) obj.extend(color) obj.append(COLOR) obj.extend(color) obj.append(SPHERE) obj.extend([box[0][i],box[1][j],box[2][k],cylinder_size]) if j != 1: obj.append(CYLINDER) obj.extend([box[0][i],box[1][j],box[2][k]]) obj.extend([box[0][i],box[1][j+1],box[2][k]]) obj.append(cylinder_size) obj.extend(color) obj.extend(color) obj.append(COLOR) obj.extend(color) obj.append(SPHERE) obj.extend([box[0][i],box[1][j+1],box[2][k],cylinder_size]) if k != 1: obj.append(CYLINDER) obj.extend([box[0][i],box[1][j],box[2][k]]) obj.extend([box[0][i],box[1][j],box[2][k+1]]) obj.append(cylinder_size) obj.extend(color) obj.extend(color) obj.append(COLOR) obj.extend(color) obj.append(SPHERE) obj.extend([box[0][i],box[1][j],box[2][k+1],cylinder_size]) axes = [[2.0,0.0,0.0],[0.0,2.0,0.0],[0.0,0.0,2.0]] xpos = [box[0][1]+(box[0][1]-box[0][0])/5.,box[1][0],box[2][0]] cyl_text(obj,plain,xpos,'X',0.10,axes=axes) ypos = [box[0][0],box[1][1]+(box[1][1]-box[1][0])/5,box[2][0]] cyl_text(obj,plain,ypos,'Y',0.10,axes=axes) zpos = [box[0][0],box[1][0],box[2][1]+(box[2][1]-box[2][0])/5] cyl_text(obj,plain,zpos,'Z',0.10,axes=axes) cmd.load_cgo(obj,name) cmd.set_view(view) def display_wire_box(self, box): cmd.delete("wirebox") color = self.box_color view = cmd.get_view() spacing = float(self.box_display_mesh_grid.get()) lwidth = float(self.box_display_line_width.get()) xpts = int(round((box[0][1]-box[0][0])/spacing))+1 ypts = int(round((box[1][1]-box[1][0])/spacing))+1 zpts = int(round((box[2][1]-box[2][0])/spacing))+1 obj = [] for i in range(xpts): for k in range (ypts): obj.append(BEGIN) obj.append(LINE_STRIP) obj.append(COLOR) obj.extend(color) for j in range(zpts): obj.append(VERTEX) obj.extend([box[0][0]+spacing*i,box[1][0]+spacing*k,\ box[2][0]+spacing*j]) obj.append(END) for i in range(xpts): for j in range (zpts): obj.append(BEGIN) obj.append(LINE_STRIP) obj.append(COLOR) obj.extend(color) for k in range(ypts): obj.append(VERTEX) obj.extend([box[0][0]+spacing*i,box[1][0]+spacing*k,\ box[2][0]+spacing*j]) obj.append(END) for j in range(zpts): for i in range (xpts): obj.append(BEGIN) obj.append(LINE_STRIP) obj.append(COLOR) obj.extend(color) for k in range(ypts): obj.append(VERTEX) obj.extend([box[0][0]+spacing*i,box[1][0]+spacing*k,\ box[2][0]+spacing*j]) obj.append(END) for j in range(zpts): for k in range (ypts): obj.append(BEGIN) obj.append(LINE_STRIP) obj.append(COLOR) obj.extend(color) for i in range(xpts): obj.append(VERTEX) obj.extend([box[0][0]+spacing*i,box[1][0]+spacing*k,\ box[2][0]+spacing*j]) obj.append(END) cmd.load_cgo(obj,"wirebox") cmd.set("cgo_line_width",lwidth) cmd.set_view(view) #--------------------------------------------------------------------- # config functions def set_autodock_tools_path(self, dirname): self.autodock_tools_location.setvalue(dirname) self.autodock_tools_path.set(dirname) self.config_settings['autodock_tools_path'] = dirname def set_autogrid_location(self, filename): self.autogrid_location.setvalue(filename) self.autogrid_exe.set(filename) self.config_settings['autogrid_exe'] = filename def set_autodock_location(self, filename): self.autodock_location.setvalue(filename) self.autodock_exe.set(filename) self.config_settings['autodock_exe'] = filename def set_vina_location(self, filename): self.vina_location.setvalue(filename) self.vina_exe.set(filename) self.config_settings['vina_exe'] = filename def set_work_path_location(self, dirname): self.work_path_location.setvalue(dirname) def work_dir(self): return self.work_path_location.getvalue() def read_plugin_config_file(self): config_file_name = os.path.join(tmp_dir,"pymol_autodock_plugin.conf") self.config_settings = {} self.config_settings['autodock_tools_path'] = '' self.config_settings['autogrid_exe'] = '' self.config_settings['autodock_exe'] = '' self.config_settings['vina_exe'] = '' if os.path.isfile(config_file_name): self.status_line.configure(text = 'Reading configuration file: %s' % config_file_name) lst = self.fileopen(config_file_name,'r').readlines() for line in lst: if line[0]!='#': entr = line.split('=') self.config_settings[entr[0].strip()] = entr[1].strip() self.autogrid_exe.set(self.config_settings['autogrid_exe']) self.autodock_exe.set(self.config_settings['autodock_exe']) self.vina_exe.set(self.config_settings['vina_exe']) self.autodock_tools_path.set(self.config_settings['autodock_tools_path']) else: self.status_line.configure(text = 'Configuration file not found') return self.config_settings def save_plugin_config_file(self): config_file_name = os.path.join(tmp_dir,"pymol_autodock_plugin.conf") fp = self.fileopen(config_file_name,'w') print >>fp, '#========================================' print >>fp, '# Autodock/Vina Plugin configuration file' self.config_settings['autogrid_exe'] = self.autogrid_location.getvalue() self.config_settings['autodock_exe'] = self.autodock_location.getvalue() self.config_settings['vina_exe'] = self.vina_location.getvalue() self.config_settings['autodock_tools_path'] = self.autodock_tools_location.getvalue() print 'ADDD', self.autodock_location.getvalue() for key, val in self.config_settings.items(): print >>fp, key, '=', val fp.close() self.status_line.configure(text = 'Wrote configuration file %s' % config_file_name) def ligand_display_mode_changed(self, button_name, pressed): if pressed: self.ligand_display_mode[button_name] = True action = 'Enabled' else: self.ligand_display_mode[button_name] = False action = 'Disabled' txt = action+' ligand display mode <'+button_name+'>' self.status_line.configure(text=txt) #---------------------------------------------------------------------------- # receptors def delete_residue(self): sel = self.flexible_residues_list.getcurselection() def selectionCommand(self, value): sels = self.selection_list.getcurselection() ## if len(sels) == 0: ## print 'No selection' ## else: ## print 'Selection:', sels[0] def selected_receptor(self, value): sel = self.receptor_list.get() receptor_object = self.receptor_dic[sel] lst = [] for key, val in receptor_object.flexible_residues.items(): for resn, resi in val: lst.append("%s:%4d %s" % (key, resn, resi)) self.flexible_residues_list.setlist(lst) self.receptor_page_log_text.insert('end',receptor_object.info()) self.receptor_page_log_text.yview('moveto',1.0) self.docking_receptor_rigid_list.selectitem(value) def import_selections(self): lst = cmd.get_names("selections")+cmd.get_names() if 'grid_center' in lst: lst.remove('grid_center') if 'box' in lst: lst.remove('box') self.selection_list.setlist(lst) self.ligand_selection_list.setlist(lst) def generate_receptor(self): print self.work_dir() sel = self.selection_list.getcurselection() tmp_rec_pdb = os.path.join(self.work_dir(),"receptor.%s.pdb" % sel[0]) print tmp_rec_pdb cmd.save(tmp_rec_pdb,sel[0]) util_program = os.path.join(self.autodock_tools_path.get(),"prepare_receptor4.py") outfilename = os.path.join(self.work_dir(), "receptor.%s.pdbqt" % sel[0]) command = "%s -r %s -o %s -A checkhydrogens" % (util_program,tmp_rec_pdb,outfilename) self.receptor_page_log_text.insert('end',"Batch: %s\n" % command) self.receptor_page_log_text.yview('moveto',1.0) result, output = getstatusoutput(command) if result == 0: self.receptor_list.insert('end',sel[0]) self.status_line.configure(text="Successfully generated receptor file receptor.%s.pdbqt" % sel[0]) #self.receptor_page_log_text.insert('end',"Successfully generated receptor file receptor.%s.pdbqt\n" % sel[0]) self.receptor_page_log_text.insert('end',output) self.receptor_page_log_text.yview('moveto',1.0) r = Receptor() r.selection = sel[0] r.pdb_file = tmp_rec_pdb r.receptor_pdbqt = outfilename stored.list = [] cmd.iterate(sel[0]+' and name ca',"stored.list.append([resi,resn])") for resi, resn in stored.list: r.resi_dic[int(resi)] = resn self.receptor_dic[sel[0]] = r self.receptor_list.selectitem(-1) self.docking_receptor_rigid_list.insert('end',sel[0]) self.docking_receptor_rigid_list.selectitem(-1) else: self.status_line.configure(text="An error occured while preparing receptor from selection %s" % sel[0]) self.receptor_page_log_text.insert('end',output) def select_flexible_residues(self): sel = self.selection_list.get() rec = self.receptor_list.get() stored.list = [] cmd.iterate(sel+' and name ca',"stored.list.append([chain, resn,resi])") receptor_object = self.receptor_dic[rec] receptor_object.flexible_residues = [] chains = {} for chain, resn, resi in stored.list: if resn not in ['ALA','GLY','PRO']: if chains.has_key(chain): chains[chain].append([int(resi), resn]) else: chains[chain] = [ [int(resi), resn] ] receptor_object.flexible_residues = chains # receptor_object.flexible_residues.append( [int(resi), resn] ) # self.status_line.configure(text = "Selected %d flexible residues for receptor %s" \ # % (len(receptor_object.flexible_residues), rec)) util_program = os.path.join(self.autodock_tools_path.get(),"prepare_flexreceptor4.py") flex_res_string = receptor_object.flex_res_string() receptor_filename = receptor_object.receptor_pdbqt rec_rigid = receptor_filename[:-6]+'.rigid.pdbqt' rec_flexible = receptor_filename[:-6]+'.flexible.pdbqt' command = "%s -r %s -s %s -g %s -x %s" % \ (util_program, receptor_filename, flex_res_string, rec_rigid, rec_flexible) self.receptor_page_log_text.insert('end',"Batch: %s\n" % command) self.receptor_page_log_text.yview('moveto',1.0) # result = os.system(command) result, output = getstatusoutput(command) if result == 0: receptor_object.receptor_rigid = rec_rigid receptor_object.receptor_flexible = rec_flexible self.status_line.configure(text="Successfully generated flexible receptor files for %s(%s)" % (rec,sel)) # self.receptor_page_log_text.insert('end',"Successfully generated flexible receptor files for %s(%s)\n" % (rec,sel)) self.receptor_page_log_text.insert('end',output) self.selected_receptor(rec) self.docking_receptor_flexible_list.selectitem('Yes') else: self.status_line.configure(text="An error occured while preparing a flexible receptor from selection %s" % sel) self.receptor_page_log_text.insert('end',output) self.receptor_page_log_text.yview('moveto',1.0) def set_receptor_pdbqt_location(self, filename): self.receptor_pdbqt_location.setvalue(filename) def load_receptor_pdbqt(self): fn = self.receptor_pdbqt_location.getvalue() outfile = os.path.join(self.work_dir(), os.path.basename(fn).split('.')[0]+'_pdb.pdb') util_program = os.path.join(self.autodock_tools_path.get(),"pdbqt_to_pdb.py") command = "%s -f %s -o %s " % (util_program, fn, outfile) self.receptor_page_log_text.insert('end',"Batch: %s\n" % command) self.receptor_page_log_text.yview('moveto',1.0) result, output = getstatusoutput(command) if result == 0: self.status_line.configure(text = "Loading receptor %s" % fn) self.receptor_page_log_text.insert('end',output) self.receptor_page_log_text.yview('moveto',1.0) name = os.path.basename(fn).split('.')[0] cmd.load(outfile,name) r = Receptor() r.selection = name r.pdb_file = outfile r.receptor_pdbqt = os.path.abspath(fn) stored.list = [] cmd.iterate(name+' and name ca',"stored.list.append([resi,resn])") for resi, resn in stored.list: r.resi_dic[int(resi)] = resn self.receptor_dic[name] = r self.receptor_list.insert('end',name) self.receptor_list.selectitem(-1) self.docking_receptor_rigid_list.insert('end',name) self.docking_receptor_rigid_list.selectitem(-1) else: self.status_line.configure(text="An error occured while loading receptor %s" % fn) self.receptor_page_log_text.insert('end',output) def remove_receptor(self): rec = self.receptor_list.get() del self.receptor_dic[rec] self.status_line.configure(text="Removed receptor %s" % rec) index = list(self.receptor_list.get(0, 'end')).index(rec) self.receptor_list.delete(index) self.docking_receptor_list.delete(index) try: self.receptor_list.selectitem(0) self.docking_receptor_list.selectitem(0) except: self.receptor_list.clear() self.docking_receptor_list.clear() def remove_flexible_residues(self): rec = self.receptor_list.get() rec_object = self.receptor_dic[rec] rec_object.flexible_residues = [] rec_object.receptor_rigid = "" rec_object.receptor_flexible = "" self.status_line.configure(text="Removed flexible residues from receptor %s" % rec) self.selected_receptor(rec) def remove_all_receptors(self): self.receptor_dic = {} self.status_line.configure(text="Deleted all receptor objects") self.receptor_list.clear() self.flexible_residues_list.clear() #------------------------------------------------------------------------------ # ligands def save_as_ligand_pdb(self, name): pdb_name = os.path.join(self.work_dir(), name+'.ligand.pdb') cmd.save(pdb_name, name) self.status_line.configure(text="Saving ligand pdb file %s from selection %s" % (pdb_name, name)) self.ligand_list.insert('end',name) l = Ligand() l.input_file = pdb_name l.selection = name l.name = name self.ligand_dic[name] = l self.ligand_list.selectitem(-1) def generate_ligand(self): sel = self.ligand_list.get() filename = self.ligand_dic[sel].input_file outfile = os.path.join(self.work_dir(), os.path.basename(filename).split('.')[0]+'.pdbqt') util_program = os.path.join(self.autodock_tools_path.get(),"prepare_ligand4.py") command = "%s -l %s -o %s -A checkhydrogens" % (util_program,filename,outfile) self.ligand_page_log_text.insert('end',"Batch: %s\n" % command) # result = os.system(command) result, output = getstatusoutput(command) if result == 0: self.ligand_pdbqt_list.insert('end',sel) self.docking_ligand_list.insert('end',sel) self.docking_ligand_list.selectitem(-1) self.status_line.configure(text="Successfully generated ligand file %s" % outfile) #self.ligand_page_log_text.insert('end',"Successfully generated ligand file %s\n" % outfile) self.ligand_page_log_text.insert('end',output) self.ligand_pdbqt_list.selectitem(-1) self.ligand_dic[sel].ligand_pdbqt = outfile else: self.status_line.configure(text="An error occured while preparing ligand file from %s" % sel) self.ligand_page_log_text.insert('end',output) self.ligand_page_log_text.yview('moveto',1.0) def ligand_info(self, sel): try: sel = self.ligand_pdbqt_list.getcurselection()[0] except: sel = self.ligand_list.getcurselection()[0] self.ligand_page_log_text.insert('end',self.ligand_dic[sel].info()) self.ligand_page_log_text.yview('moveto',1.0) def remove_ligand(self): lig = self.ligand_pdbqt_list.get() try: del self.ligand_dic[lig] except: lig = self.ligand_list.get() del self.ligand_dic[lig] try: index = list(self.ligand_pdbqt_list.get(0, 'end')).index(lig) self.ligand_pdbqt_list.delete(index) self.docking_ligand_list.delete(index+1) except: pass index = list(self.ligand_list.get(0, 'end')).index(lig) self.ligand_list.delete(index) self.status_line.configure(text="Removed ligand %s" % lig) try: self.ligand_list.selectitem(0) except: self.ligand_list.clear() try: self.ligand_pdbqt_list.selectitem(0) except: self.ligand_pdbqt_list.clear() try: self.docking_ligand_list.selectitem(0) except: self.docking_ligand_list.clear() def display_ligand(self): lig = self.ligand_list.get() ligand_input = self.ligand_dic[lig].input_file string = open(ligand_input).read() cmd.load(ligand_input) self.ligand_page_log_text.insert('end',string) self.ligand_page_log_text.yview('moveto',1.0) def remove_all_ligands(self): self.ligand_dic = {} self.status_line.configure(text="Deleted all ligand objects") self.ligand_list.clear() self.ligand_pdbqt_list.clear() def set_ligand_dir_location(self, dirname): pth = self.ligand_dir_location.setvalue(dirname) self.ligand_dir.set(dirname) def import_ligands(self): pth = self.ligand_dir.get() lst = glob(os.path.join(pth,"*.pdb"))\ +glob(os.path.join(pth,"*.mol2"))\ +glob(os.path.join(pth,"*.pdbqt")) self.ligand_dic['VS_DIR'] = pth self.multiple_ligands = True for f in lst: l = Ligand() l.input_file = f name = os.path.basename(f).split('.')[0] filetype = os.path.basename(f).split('.')[1] if filetype == 'pdbqt': if os.path.abspath(os.path.dirname(f)) != os.path.dirname('.'): os.symlink(f,os.path.basename(f)) l.ligand_pdbqt = os.path.basename(f) else: l.ligand_pdbqt = f self.ligand_pdbqt_list.insert('end',name) self.docking_ligand_list.insert('end',name) self.docking_ligand_list.selectitem(-1) self.ligand_pdbqt_list.selectitem(-1) self.ligand_dic[name] = l self.ligand_dic[name].name = name self.ligand_page_log_text.insert('end',"Importing ligand %s\n" % f) self.ligand_page_log_text.yview('moveto',1.0) self.ligand_list.insert('end',name) self.status_line.configure(text="Loaded %d ligands" % len(lst)) def generate_all_ligands(self): self.multiple_ligands = True for key, ligand in self.ligand_dic.items(): if key !='VS_DIR': self.ligand_list.selectitem(key) self.generate_ligand() self.docking_ligand_list.selectitem(0) #------------------------------------------------------------------- # docking def run_autogrid(self): rec = self.docking_receptor_rigid_list.get() use_flex = self.docking_receptor_flexible_list.get() receptor_object = self.receptor_dic[rec] if use_flex == 'No': rigid_receptor_file = receptor_object.receptor_pdbqt flex_receptor_file = None elif use_flex == 'Yes': if receptor_object.receptor_flexible: rigid_receptor_file = receptor_object.receptor_rigid flex_receptor_file = receptor_object.receptor_flexible else: self.status_line.configure(text="No flexible receptor defined! Cannot do flexible docking!") return self.docking_page_log_text.insert('end','#---------------------------------------\n') self.docking_page_log_text.insert('end','# SETTING UP GRID CALCULATION\n') self.docking_page_log_text.insert('end',' > RECEPTOR RIGID : %s\n' % rigid_receptor_file) self.docking_page_log_text.insert('end',' > RECEPTOR FLEXIBLE : %s\n' % flex_receptor_file) ligands = self.docking_ligand_list.get() if ligands == 'All': pth = self.ligand_dic['VS_DIR'] else: lig_pdbqt = self.ligand_dic[ligands].ligand_pdbqt self.docking_page_log_text.insert('end',' > LIGAND(s) : %s\n' % ligands) if ligands == 'All': self.docking_page_log_text.insert('end',' > LIGAND VS-DIR : %s\n' % pth) n_points_X = self.n_points_X.get() n_points_Y = self.n_points_Y.get() n_points_Z = self.n_points_Z.get() spacing = self.grid_spacing.get() center_X = self.grid_center[0].get() center_Y = self.grid_center[1].get() center_Z = self.grid_center[2].get() self.docking_page_log_text.insert('end',' > GRID POINTS : %d %d %d\n' % (n_points_X, n_points_Y, n_points_Z)) self.docking_page_log_text.insert('end',' > GRID CENTER : %8.3f %8.3f %8.3f\n' % (center_X, center_Y, center_Z)) self.docking_page_log_text.insert('end',' > GRID SPACING : %8.3f \n' % spacing) template_gpf = os.path.join(self.work_dir(),'template.gpf') outfile_gpf = rec+'.gpf' fp = self.fileopen(template_gpf,'w') print >>fp, 'npts %d %d %d' % (n_points_X, n_points_Y, n_points_Z) print >>fp, 'spacing %5.3f' % spacing print >>fp, 'gridcenter %8.3f %8.3f %8.3f' % (center_X, center_Y, center_Z) fp.close() util_program = os.path.join(self.autodock_tools_path.get(),"prepare_gpf4.py") command = "%s -r %s -i %s -o %s" % (util_program, rigid_receptor_file, template_gpf, outfile_gpf) if flex_receptor_file is not None: command+=' -x %s' % flex_receptor_file if hasattr(self, "multiple_ligands"): command+=' -d %s' % self.ligand_dic['VS_DIR'] else: command+=' -l %s' % lig_pdbqt self.docking_page_log_text.insert('end',"Batch: %s\n" % command) self.docking_page_log_text.yview('moveto',1.0) result, output = getstatusoutput(command) if result == 0: self.status_line.configure(text="Successfully generated AutoGrid input file") self.docking_page_log_text.insert('end',output) self.docking_page_log_text.insert('end',"Running AutoGrid.....\n") autogrid = self.autogrid_exe.get() outfile_log = outfile_gpf.split('.')[0]+'.glg' receptor_object.autogrid_gpf = outfile_gpf receptor_object.autogrid_log = outfile_log command = '%s -p %s -l %s' % (autogrid, outfile_gpf, outfile_log) self.status_line.configure(text="Running AutoGrid....") # dirty if os.path.isfile(outfile_log): shutil.move(outfile_log,outfile_log+'~') os.system('touch %s' % outfile_log) r = Thread_run(command) r.start() sleep(1) ll = Thread_log(outfile_log, self.docking_page_log_text) ll.start() else: self.status_line.configure(text="An error occured while trying to run Autogrid....") self.docking_page_log_text.insert('end',output) self.docking_page_log_text.yview('moveto',1.0) def run_autodock(self, write_only = False): rec = self.docking_receptor_rigid_list.get() use_flex = self.docking_receptor_flexible_list.get() receptor_object = self.receptor_dic[rec] if use_flex == 'No': rigid_receptor_file = receptor_object.receptor_pdbqt flex_receptor_file = None elif use_flex == 'Yes': if receptor_object.receptor_flexible: rigid_receptor_file = receptor_object.receptor_rigid flex_receptor_file = receptor_object.receptor_flexible else: self.status_line.configure(text="No flexible receptor defined! Cannot do flexible docking!") return self.docking_page_log_text.insert('end','#---------------------------------------\n') self.docking_page_log_text.insert('end','# SETTING UP DOCKING RUN\n') self.docking_page_log_text.insert('end',' > RECEPTOR RIGID : %s\n' % rigid_receptor_file) self.docking_page_log_text.insert('end',' > RECEPTOR FLEXIBLE : %s\n' % flex_receptor_file) ligands = self.docking_ligand_list.get() if ligands == 'All': pth = self.ligand_dic['VS_DIR'] else: lig_pdbqt = self.ligand_dic[ligands].ligand_pdbqt self.docking_page_log_text.insert('end',' > LIGAND(s) : %s\n' % ligands) if ligands == 'All': self.docking_page_log_text.insert('end',' > LIGAND VS-DIR : %s\n' % pth) nposes = int(self.docking_nposes_list.get()) self.docking_page_log_text.insert('end',' > # POSES : %d \n' % nposes) template_dpf = os.path.join(self.work_dir(),'template.dpf') fp = self.fileopen(template_dpf,'w') print >>fp, 'ga_run %d ' % (nposes) fp.close() util_program = os.path.join(self.autodock_tools_path.get(),"prepare_dpf4.py") if ligands!='All': outfile_dpf = ligands+'.dpf' command = "%s -r %s -i %s -o %s " % (util_program, rigid_receptor_file, template_dpf, outfile_dpf) if flex_receptor_file is not None: command+=' -x %s' % flex_receptor_file else: command+=' -l %s' % lig_pdbqt self.docking_page_log_text.insert('end',"Batch: %s\n" % command) self.docking_page_log_text.yview('moveto', 1.0) result, output = getstatusoutput(command) if result == 0: self.status_line.configure(text="Wrote AutoDock input file for ligand: %s" % ligands) # self.docking_page_log_text.insert('end',"Running AutoDock.....\n") self.docking_page_log_text.insert('end',output) self.docking_page_log_text.yview('moveto', 1.0) if write_only: return autodock = self.autodock_exe.get() outfile_poses = outfile_dpf.split('.')[0]+'.dlg' self.ligand_dic[ligands].outfile_poses = outfile_poses command = '%s -p %s -l %s' % (autodock, outfile_dpf, outfile_poses) # self.status_line.configure(text="Now docking ligand: %s...." % ligands) if os.path.isfile(outfile_poses): shutil.move(outfile_poses,outfile_poses+'~') os.system('touch %s' % outfile_poses) r = Thread_run(command, self.current_thread, self.status_line, "Now docking ligand: %s...." % ligands) r.start() self.current_thread = r ll = Thread_log(outfile_poses, self.docking_page_log_text) ll.start() else: self.status_line.configure(text="Error while generating run input file for ligand: %s" % ligands) self.docking_page_log_text.insert('end',output) self.docking_page_log_text.yview('moveto', 1.0) else: ligand_list = [] for lig in self.ligand_dic.values(): if hasattr(lig,"ligand_pdbqt") and lig.ligand_pdbqt!='': ligand_list.append(lig) for idx in range(len(ligand_list)): self.docking_ligand_list.selectitem(idx+1) self.run_autodock(write_only = write_only) def run_vina(self, write_only = False): rec = self.docking_receptor_rigid_list.get() use_flex = self.docking_receptor_flexible_list.get() receptor_object = self.receptor_dic[rec] if use_flex == 'No': rigid_receptor_file = receptor_object.receptor_pdbqt flex_receptor_file = None elif use_flex == 'Yes': if receptor_object.receptor_flexible: rigid_receptor_file = receptor_object.receptor_rigid flex_receptor_file = receptor_object.receptor_flexible else: self.status_line.configure(text="No flexible receptor defined! Cannot do flexible docking!") return self.docking_page_log_text.insert('end','#---------------------------------------\n') self.docking_page_log_text.insert('end','# SETTING UP VINA RUN\n') self.docking_page_log_text.insert('end',' > RECEPTOR RIGID : %s\n' % rigid_receptor_file) self.docking_page_log_text.insert('end',' > RECEPTOR FLEXIBLE : %s\n' % flex_receptor_file) n_points_X = self.n_points_X.get() n_points_Y = self.n_points_Y.get() n_points_Z = self.n_points_Z.get() spacing = self.grid_spacing.get() center_X = self.grid_center[0].get() center_Y = self.grid_center[1].get() center_Z = self.grid_center[2].get() size_X = n_points_X*spacing size_Y = n_points_Y*spacing size_Z = n_points_Z*spacing self.docking_page_log_text.insert('end',' > CENTER X : %s\n' % center_X) self.docking_page_log_text.insert('end',' > CENTER Y : %s\n' % center_Y) self.docking_page_log_text.insert('end',' > CENTER Z : %s\n' % center_Z) self.docking_page_log_text.insert('end',' > SIZE X : %s\n' % str(size_X)) self.docking_page_log_text.insert('end',' > SIZE Y : %s\n' % str(size_Y)) self.docking_page_log_text.insert('end',' > SIZE Z : %s\n' % str(size_Z)) ligands = self.docking_ligand_list.get() if ligands == 'All': pth = self.ligand_dic['VS_DIR'] else: lig_pdbqt = self.ligand_dic[ligands].ligand_pdbqt self.docking_page_log_text.insert('end',' > LIGAND(s) : %s\n' % ligands) if ligands == 'All': self.docking_page_log_text.insert('end',' > LIGAND VS-DIR : %s\n' % pth) nposes = int(self.docking_nposes_list.get()) self.docking_page_log_text.insert('end',' > # POSES : %d \n' % nposes) self.docking_page_log_text.yview('moveto', 1.0) if ligands!='All': outfile_conf = os.path.join(self.work_dir(), ligands+'.vina_config.txt') outfile_log = os.path.join(self.work_dir(),ligands+'.vina.log') outfile_poses = os.path.join(self.work_dir(),ligands+'.docked.pdbqt') self.ligand_dic[ligands].outfile_poses = outfile_poses self.ligand_dic[ligands].outfile_log = outfile_log self.ligand_dic[ligands].vina_conf = outfile_conf fp = self.fileopen(outfile_conf,'w') print >>fp, "receptor = %s" % rigid_receptor_file if flex_receptor_file is not None: print >>fp, "flex = %s" % flex_receptor_file print >>fp, "ligand = %s" % lig_pdbqt print >>fp, "center_x = %s" % center_X print >>fp, "center_y = %s" % center_Y print >>fp, "center_z = %s" % center_Z print >>fp, "size_x = %6.2f" % size_X print >>fp, "size_y = %6.2f" % size_Y print >>fp, "size_z = %6.2f" % size_Z print >>fp, "out = %s" % outfile_poses print >>fp, "log = %s" % outfile_log print >>fp, "num_modes = %d" % nposes fp.close() self.status_line.configure(text="Wrote VINA input file for ligand: %s" % ligands) # self.docking_page_log_text.insert('end',"Running VINA.....\n") self.docking_page_log_text.yview('moveto', 1.0) if write_only: return vina = self.vina_exe.get() command = '%s --config %s' % (vina, outfile_conf) # self.status_line.configure(text="Now docking ligand: %s...." % ligands) if os.path.isfile(outfile_log): shutil.move(outfile_log,outfile_log+'~') os.system('touch %s' % outfile_log) r = Thread_run(command, self.current_thread, self.status_line, "Now docking ligand: %s...." % ligands) r.start() self.current_thread = r ll = Thread_log(outfile_log, self.docking_page_log_text) ll.start() else: ligand_list = [] for lig in self.ligand_dic.values(): if hasattr(lig,"ligand_pdbqt") and lig.ligand_pdbqt!='': ligand_list.append(lig) for idx in range(len(ligand_list)): self.docking_ligand_list.selectitem(idx+1) self.run_vina(write_only = write_only) def write_autodock_input_files(self): self.run_autodock(write_only = True) def write_vina_input_files(self): self.run_vina(write_only = True) #------------------------------------------------------------------- # view poses def set_pose_filename(self, filename): self.pose_file_location.setvalue(filename) def load_ligand_file(self, update = True): filename = self.pose_file_location.get() ext = os.path.basename(filename).split('.')[-1] if ext == 'pdbqt': #print 'loading pdbqt' self.load_pdbqt(filename) elif ext == 'dlg': self.load_dlg(filename) if update: self.make_complete_ligand_list() self.score_table.clearTable() self.score_table.updateView(self.all_ligands) def load_all_ligand_files(self): lst = [] for name, ligand in self.ligand_dic.items(): if name != 'VS_DIR' and ligand.outfile_poses!='': lst.append(ligand.outfile_poses) for f in lst: self.pose_file_location.setvalue(f) self.load_ligand_file(update=False) self.make_complete_ligand_list() self.score_table.clearTable() self.score_table.updateView(self.all_ligands) def load_dlg(self, filename): # print 'loading dlg file' name = '.'.join(os.path.basename(filename).split('.')[:-1]) lst = self.fileopen(filename,'r').readlines() filt = [] for line in lst: if line.startswith('DOCKED:'): filt.append(line[8:]) modlist = [] for i, line in enumerate(filt): if line.startswith('MODEL'): newmod = [] for k, line2 in enumerate(filt[i:]): if not line2.startswith('ENDMDL'): newmod.append(line2) else: modlist.append(newmod) break pose_list = [] for m in modlist: model = ADModel(lst = m) model.name = name pose_list.append(model) pose_list.sort(lambda a, b: cmp(a.energy, b.energy)) self.pose_viewer_ligand_dic[name] = {} for i in range(len(pose_list)): pose_list[i].poseN = i+1 self.pose_viewer_ligand_dic[name].update({name+'::%d'%(i+1):pose_list[i]}) self.update_combo(name) def load_pdbqt(self, filename): lst = self.fileopen(filename,'r').readlines() name = '.'.join(os.path.basename(filename).split('.')[:-1]) modlist = [] for i, line in enumerate(lst): if line.startswith('MODEL'): newmod = [] for k, line2 in enumerate(lst[i:]): if not line2.startswith('ENDMDL'): newmod.append(line2) else: modlist.append(newmod) break pose_list = [] for m in modlist: model = ADModel(lst = m) model.name = name # print model.energy pose_list.append(model) # print 'done pose list' pose_list.sort(lambda a, b: cmp(a.energy, b.energy)) self.pose_viewer_ligand_dic[name] = {} for i in range(len(pose_list)): pose_list[i].poseN = i+1 self.pose_viewer_ligand_dic[name].update({name+'::%d'%(i+1):pose_list[i]}) self.update_combo(name) def update_combo(self,name): try: self.pose_viewer_notebook.delete(name) except: pass self.pose_viewer_ligand_pages[name] = {'name':self.pose_viewer_notebook.add(name)} pose_list = self.pose_viewer_ligand_dic[name].keys() pose_list.sort(lambda a,b: cmp(int(a.split('::')[1]), int(b.split('::')[1]))) self.pose_viewer_ligand_pages[name].update( {'poses':pose_list} ) self.pose_viewer_buttonbox = Pmw.ButtonBox(self.pose_viewer_ligand_pages[name]['name'], padx=3) self.pose_viewer_buttonbox.add('Show best 10' ,command=self.show_best_poses) self.pose_viewer_buttonbox.add('Show all' ,command=self.show_all_poses) self.pose_viewer_buttonbox.add('Hide all' ,command=self.hide_all_poses) self.pose_viewer_buttonbox.add('Delete',command=self.delete_ligand) self.pose_viewer_buttonbox.pack(fill='x',side=TOP) self.pose_viewer_buttonbox.alignbuttons() self.pose_viewer_ligand_pages[name]['combo'] = Pmw.ComboBox(self.pose_viewer_ligand_pages[name]['name'], label_text='Docked', labelpos='nw', scrolledlist_items= pose_list, selectioncommand=self.ligand_combo_box_selected, listbox_height=10, listbox_width=1, dropdown=False) self.pose_viewer_ligand_pages[name]['combo'].pack(side='left', padx=3, anchor='n') self.pose_viewer_ligand_pages[name]['text'] = Pmw.ScrolledText(self.pose_viewer_ligand_pages[name]['name'], borderframe=5, vscrollmode='dynamic', hscrollmode='dynamic', labelpos='n', label_text=name, text_width=150, text_height=15, text_wrap='none', text_background='#000000', text_foreground='green' ) self.pose_viewer_ligand_pages[name]['text'].pack() self.pose_viewer_notebook.selectpage(name) self.status_line.configure(text ='Loading %s' % name) def ligand_combo_box_selected(self, value): name = value.split('::')[0] if self.pose_viewer_radiobuttons.getvalue()=='Show Selected': view = cmd.get_view() ligand = self.pose_viewer_ligand_dic[name][str(value)] cmd.read_pdbstr(ligand.as_pdb_string(),str(value)) pmlname = value.replace(' ','_').replace('::','_') for key, val in self.ligand_display_mode.items(): # print key, val if val == True: cmd.show(key,pmlname) else: cmd.hide(key,pmlname) cmd.set_view(view) # cmd.zoom(str(value)) text = 'Docked Energy: %8.2f kcal/mol' % ligand.energy self.status_line.configure(text=text) self.pose_viewer_ligand_pages[name]['text'].clear() self.pose_viewer_ligand_pages[name]['text'].insert('end',ligand.info_string()) else: pmlname = value.replace(' ','_').replace('::','_') cmd.delete(pmlname) self.pose_viewer_ligand_pages[name]['text'].clear() self.status_line.configure(text='') def show_all_poses(self): name = self.pose_viewer_notebook.getcurselection() for pose in self.pose_viewer_ligand_pages[name]['poses']: self.ligand_combo_box_selected(pose) self.status_line.configure(text = 'Showing all poses %s' % name) def show_best_poses(self): name = self.pose_viewer_notebook.getcurselection() for pose in self.pose_viewer_ligand_pages[name]['poses'][:10]: self.ligand_combo_box_selected(pose) self.status_line.configure(text = 'Showing best 10 poses %s' % name) def hide_all_poses(self): name = self.pose_viewer_notebook.getcurselection() # pmlname = name.replace(' ','_') # cmd.delete(pmlname+'.*') cmd.delete(name+'_*') self.status_line.configure(text = 'Deleted all poses %s' % name) def delete_ligand(self): name = self.pose_viewer_notebook.getcurselection() cmd.delete(name+'_*') self.pose_viewer_notebook.delete(name) del self.pose_viewer_ligand_pages[name] del self.pose_viewer_ligand_dic[name] self.status_line.configure(text = 'Deleted %s' % name) how = self.score_table_radiobuttons.getvalue() self.update_score_table(how) def make_complete_ligand_list(self): self.all_ligands = [] for key, val in self.pose_viewer_ligand_dic.items(): self.all_ligands.extend(val.values()) self.sort_complete_ligand_list() def sort_complete_ligand_list(self): self.all_ligands.sort(lambda a, b: cmp(a.energy, b.energy)) def select_best_poses(self): self.sort_complete_ligand_list() self.best_ligand_list = [] done = [] for ligand in self.all_ligands: if ligand.name not in done: self.best_ligand_list.append(ligand) done.append(ligand.name) def update_score_table(self, value): if value=='Show All Poses': self.make_complete_ligand_list() self.score_table.resetTable() self.score_table.updateView(self.all_ligands) elif value=='Show Only Best Pose': self.select_best_poses() self.score_table.resetTable() self.score_table.updateView(self.best_ligand_list) def export_score_dat_file(self): what = self.score_table_radiobuttons.getvalue() filename = self.rank_dat_file_location.getvalue() fp = self.fileopen(filename,'w') if what == 'Show All Poses': ligand_list = self.all_ligands elif what == 'Show Only Best Pose': ligand_list = self.best_ligand_list print >>fp,"# RANK NAME POSE # SCORE" for i, ligand in enumerate(ligand_list): print >>fp, "%8d %20s %5d %8.3f" % \ (i+1, ligand.name, ligand.poseN, ligand.energy) self.status_line.configure(text="Exported docking results to %s" % filename) def export_score_csv_file(self): what = self.score_table_radiobuttons.getvalue() filename = self.rank_csv_file_location.getvalue() fp = self.fileopen(filename,'w') if what == 'Show All Poses': ligand_list = self.all_ligands elif what == 'Show Only Best Pose': ligand_list = self.best_ligand_list print >>fp, "RANK, NAME, POSE, SCORE" for i, ligand in enumerate(ligand_list): print >>fp, "%8d, %20s, %5d, %8.3f" % \ (i+1, ligand.name, ligand.poseN, ligand.energy) self.status_line.configure(text="Exported docking results to %s" % filename) def export_score_pose_file(self): what = self.score_table_radiobuttons.getvalue() filename = self.rank_pose_file_location.getvalue() fp = self.fileopen(filename,'w') if what == 'Show All Poses': ligand_list = self.all_ligands elif what == 'Show Only Best Pose': ligand_list = self.best_ligand_list print >>fp, "TITLE DOCKING POSES " for i, ligand in enumerate(ligand_list): print >>fp, "MODEL%5d" % (i+1) print >>fp, "REMARK ligand: %s" % ligand.name print >>fp, "REMARK pose #: %d" % ligand.poseN print >>fp, "REMARK energy: %8.3f" % ligand.energy print >>fp, ligand.as_string.rstrip() print >>fp, "ENDMDL" self.status_line.configure(text="Exported docking poses to %s" % filename) #------------------------------------------- # maps def set_mapfilename(self,filename): self.map_file_location.setvalue(filename) def load_grid_map(self): view = cmd.get_view() fn = self.map_file_location.get() fp = self.fileopen(fn,'r') if not fp: return None try: name = fn#.split('.')[-2] except: name = fn mp = ADGridMap(fp,name) fname = os.path.basename(name) self.status_line.configure(text = 'Loading map %s' % fn) tmpn = os.path.join(self.work_dir(),fname+'.dx') mp.writeDX(tmpn) cmd.load(tmpn, fname) self.status_line.configure(text = 'Loading map %s' % tmpn) map_key = fname+'.5.0' self.map_color = [1,0,0] self.map_meta[fname] = mp.meta() self.map_dic[fname] = {map_key:{'color':self.map_color, 'displ':'isosurface', 'thresh':5, 'meta':mp.meta() } } info = '#====================================\n' info+= '# DISPLAY SETTINGS\n' info+= 'THRESHOLD: 5\n' info+= 'COLOR : %4.3f %4.3f %4.3f\n' % (self.map_color[0], self.map_color[1], self.map_color[2]) info+= 'MODE : isosurface\n' info+= '#====================================\n' info+= '# GRID MAP INFO\n' info+= self.map_meta[fname] self.map_meta[map_key] = info self.map_threshold[fname] = DoubleVar() self.map_threshold[fname].set(float(default_settings["map_threshold"])) self.display_map(fname, self.map_dic[fname][map_key]) self.update_mapcombo(fname, self.map_dic[fname]) self.map_pages[fname]['combo'].selectitem(-1) self.status_line.configure(text ='Loading Map %s' % fn) cmd.set_view(view) self.status_mapbox(map_key) def display_map(self,mapname,map_dic): view = cmd.get_view() surfname = mapname+'.'+"%2.1f" % map_dic['thresh'] cmd.delete(surfname) if map_dic['displ'] == 'isosurface': cmd.isosurface(surfname,mapname,map_dic['thresh']) cmd.set_color("mycol_"+surfname,map_dic['color']) cmd.color('mycol_'+surfname,surfname) elif map_dic['displ'] == 'isomesh': cmd.isomesh(surfname,mapname,map_dic['thresh']) cmd.set_color("mycol_"+surfname,map_dic['color']) cmd.color('mycol_'+surfname,surfname) info = '#====================================\n' info+= '# DISPLAY SETTINGS\n' info+= 'THRESHOLD: %4.2f\n' % map_dic['thresh'] info+= 'COLOR : %4.3f %4.3f %4.3f\n' % (map_dic['color'][0], map_dic['color'][1], map_dic['color'][2]) info+= 'MODE : %s\n' % map_dic['displ'] info+= '#====================================\n' info+= '# GRID MAP INFO\n' info+= self.map_meta[mapname] self.map_meta[surfname] = info cmd.set_view(view) def create_surface(self): name = self.map_viewer_notebook.getcurselection() thresh = float(self.map_threshold[name].get()) surfname = name+'.'+str(thresh) cmd.delete(surfname) if self.map_radiobuttons.getvalue()=='isosurface': mode = 'isosurface' elif self.map_radiobuttons.getvalue()=='isomesh': mode = 'isomesh' if self.map_dic[name].has_key(surfname): mmp = self.map_dic[name][surfname] else: self.map_dic[name].update({surfname:{ 'color':self.map_color, 'displ':mode, 'thresh':thresh }}) mmp = self.map_dic[name][surfname] mmp['thresh'] = float(self.map_threshold[name].get()) mmp['color'] = self.map_color self.display_map(name, mmp) self.update_mapcombo(name,self.map_dic[name]) self.map_radiobuttons.setvalue(mode) self.map_pages[name]['combo'].selectitem(-1) self.status_mapbox(surfname) def delete_surface(self): name = self.map_viewer_notebook.getcurselection() s = self.map_pages[name]['combo'].getcurselection() for mp in s: self.status_line.configure(text = "Deleting map %s" % mp) cmd.delete(mp) del self.map_dic[name][mp] self.update_mapcombo(name,self.map_dic[name]) try: self.map_pages[name]['combo'].selectitem(0) except: pass def select_map_color(self): color = tkColorChooser.Chooser( initialcolor='red',title='Choose map color').show() if color[0] is not None: self.map_color = [color[0][0]/255., color[0][1]/255., color[0][2]/255.] def delete_map(self): name = self.map_viewer_notebook.getcurselection() #print name for mp in self.map_dic[name].keys(): cmd.delete(mp) cmd.delete(name+'*') del self.map_pages[name] del self.map_meta[name] del self.map_dic[name] self.map_viewer_notebook.delete(name) def status_mapbox(self,key): name = self.map_viewer_notebook.getcurselection() self.map_pages[name]['text'].clear() self.map_pages[name]['text'].insert('end',self.map_meta[key]) def update_mapcombo(self,name, map_dic): try: self.map_viewer_notebook.delete(name) except: pass self.map_pages[name] = {'name':self.map_viewer_notebook.add(name)} # self.map_pages[name].update({'maps':self.map_dic.keys()}) self.upper_part = Tkinter.Frame(self.map_pages[name]['name']) self.lower_part = Tkinter.Frame(self.map_pages[name]['name']) self.upper_part.pack(side=TOP) self.lower_part.pack(side=BOTTOM) self.upper_part1 = Tkinter.Frame(self.upper_part) self.upper_part2 = Tkinter.Frame(self.upper_part) self.upper_part1.pack(side=TOP, fill='x') self.upper_part2.pack(side=BOTTOM, fill='x') self.map_thresholdfr = Tkinter.Frame(self.upper_part1) labmap_threshold = Label(self.map_thresholdfr,text="Threshold:"); self.map_thresholdloc = Entry(self.map_thresholdfr,textvariable=self.map_threshold[name],bg='black',fg='green',width=15); self.scrmap_threshold=Scrollbar(self.map_thresholdfr,orient="horizontal",command=self.change_map_threshold) labmap_threshold.pack(side=LEFT) self.map_thresholdloc.pack(side=LEFT) self.scrmap_threshold.pack(side=LEFT) self.map_thresholdfr.pack(fill='x',padx=4,pady=3, side=LEFT) # vertical self.map_buttonbox = Pmw.ButtonBox(self.upper_part2, padx=3) self.map_buttonbox.add('Create Surface',command=self.create_surface) self.map_buttonbox.add('Delete Surface',command=self.delete_surface) self.map_buttonbox.add('Color',command=self.select_map_color) self.map_buttonbox.add('Delete Map',command=self.delete_map) self.map_buttonbox.pack(fill='x',side=LEFT,pady=3) self.map_buttonbox.alignbuttons() self.map_pages[name]['combo'] = Pmw.ComboBox(self.lower_part, label_text='Representations', labelpos='nw', scrolledlist_items= self.map_dic[name].keys(), selectioncommand=self.status_mapbox, listbox_height=15, listbox_width=1, dropdown=False) self.map_pages[name]['combo'].pack(side=LEFT, padx=3, anchor='n', fill='y') self.map_pages[name]['text'] = Pmw.ScrolledText(self.lower_part, borderframe=5, vscrollmode='dynamic', hscrollmode='dynamic', labelpos='n', label_text=name, text_width=60, text_height=15, text_wrap='none', text_background='#000000', text_foreground='green' ) self.map_pages[name]['text'].pack(fill='y') self.map_viewer_notebook.selectpage(name) self.map_radiobuttons = Pmw.RadioSelect(self.lower_part, buttontype = 'radiobutton', orient = 'horizontal', labelpos = 'w', ) for text in ('isosurface', 'isomesh'): self.map_radiobuttons.add(text) self.map_radiobuttons.setvalue('isosurface') self.map_radiobuttons.pack(padx=4,pady=1,side='top') def change_map_threshold(self,a): current = self.map_viewer_notebook.getcurselection() val=float(self.map_threshold[current].get())+float(a)*0.2 self.map_threshold[current].set(val) def fileopen(self, filename, mode): if mode=='w' and os.path.isfile(filename): p = os.path.abspath(filename) b = os.path.basename(p) pa,n= p.split(b) tmp = '#'+b+'#' fn = os.path.join(pa,tmp) os.rename(filename,fn) self.status_line.configure(text='Backing up %s to %s' % (filename,fn)) try: fp = open(filename,mode) return fp except: tkMessageBox.showerror('Error','Could not open file %s' % filename) return None #========================================================== # # FOREIGN DIALOG CLASSES # The classes PmwFileDialog and PmwExistingFileDialog and the _errorpop function # are taken from the Pmw contrib directory. The attribution given in that file # is: ################################################################################ # Filename dialogs using Pmw # # (C) Rob W.W. Hooft, Nonius BV, 1998 # # Modifications: # # J. Willem M. Nissink, Cambridge Crystallographic Data Centre, 8/2002 # Added optional information pane at top of dialog; if option # 'info' is specified, the text given will be shown (in blue). # Modified example to show both file and directory-type dialog # # No Guarantees. Distribute Freely. # Please send bug-fixes/patches/features to # ################################################################################ def quickFileValidation(s): if s == '': return Pmw.PARTIAL elif os.path.isfile(s): return Pmw.OK elif os.path.exists(s): return Pmw.PARTIAL else: return Pmw.PARTIAL class FileDialogButtonClassFactory: def get(fn,mode = 'r',filter=[("Executable",'*')]): """This returns a FileDialogButton class that will call the specified function with the resulting file. """ class FileDialogButton(Tkinter.Button): # This is just an ordinary button with special colors. def __init__(self, master=None, cnf={}, **kw): '''when we get a file, we call fn(filename)''' self.fn = fn self.__toggle = 0 apply(Tkinter.Button.__init__, (self, master, cnf), kw) self.configure(command=self.set) def set(self): if mode == 'r': n = MyFileDialog(types = filter).getopenfile() elif mode == 'w': n = MyFileDialog(types = filter).getsavefile() # n = MyFileDialog().get() # fd = PmwFileDialog(self.master,filter=filter) # fd.title('Please choose a file') # n=fd.askfilename() if n is not None: self.fn(n) return FileDialogButton get = staticmethod(get) class DirDialogButtonClassFactory: def get(fn): """This returns a FileDialogButton class that will call the specified function with the resulting file. """ class DirDialogButton(Tkinter.Button): # This is just an ordinary button with special colors. def __init__(self, master=None, cnf={}, **kw): '''when we get a file, we call fn(filename)''' self.fn = fn self.__toggle = 0 apply(Tkinter.Button.__init__, (self, master, cnf), kw) self.configure(command=self.set) def set(self): fd = PmwDirDialog(self.master) fd.title('Please choose a directory') n=fd.askfilename() if n is not None: self.fn(n) return DirDialogButton get = staticmethod(get) class MyFileDialog: def __init__(self,types = [("Executable","*")]): self.types = types def getopenfile(self): result = tkFileDialog.askopenfilename(filetypes=self.types) if result == "": return None else: return result def getsavefile(self): result = tkFileDialog.asksaveasfilename(filetypes=self.types) if result == "": return None else: return result def _errorpop(master,text): d=Pmw.MessageDialog(master, title="Error", message_text=text, buttons=("OK",)) d.component('message').pack(ipadx=15,ipady=15) d.activate() d.destroy() class PmwFileDialog(Pmw.Dialog): """File Dialog using Pmw""" def __init__(self, parent = None, **kw): # Define the megawidget options. optiondefs = ( ('filter', '*', self.newfilter), ('directory', os.getcwd(), self.newdir), ('filename', '', self.newfilename), ('historylen',10, None), ('command', None, None), ('info', None, None), ) self.defineoptions(kw, optiondefs) # Initialise base class (after defining options). Pmw.Dialog.__init__(self, parent) self.withdraw() # Create the components. interior = self.interior() if self['info'] is not None: rowoffset=1 dn = self.infotxt() dn.grid(row=0,column=0,columnspan=2,padx=3,pady=3) else: rowoffset=0 dn = self.mkdn() dn.grid(row=0+rowoffset,column=0,columnspan=2,padx=3,pady=3) del dn # Create the directory list component. dnb = self.mkdnb() dnb.grid(row=1+rowoffset,column=0,sticky='news',padx=3,pady=3) del dnb # Create the filename list component. fnb = self.mkfnb() fnb.grid(row=1+rowoffset,column=1,sticky='news',padx=3,pady=3) del fnb # Create the filter entry ft = self.mkft() ft.grid(row=2+rowoffset,column=0,columnspan=2,padx=3,pady=3) del ft # Create the filename entry fn = self.mkfn() fn.grid(row=3+rowoffset,column=0,columnspan=2,padx=3,pady=3) fn.bind('',self.okbutton) del fn # Buttonbox already exists bb=self.component('buttonbox') bb.add('OK',command=self.okbutton) bb.add('Cancel',command=self.cancelbutton) del bb Pmw.alignlabels([self.component('filename'), self.component('filter'), self.component('dirname')]) def infotxt(self): """ Make information block component at the top """ return self.createcomponent( 'infobox', (), None, Tkinter.Label, (self.interior(),), width=51, relief='groove', foreground='darkblue', justify='left', text=self['info'] ) def mkdn(self): """Make directory name component""" return self.createcomponent( 'dirname', (), None, Pmw.ComboBox, (self.interior(),), entryfield_value=self['directory'], entryfield_entry_width=40, entryfield_validate=self.dirvalidate, selectioncommand=self.setdir, labelpos='w', label_text='Directory:') def mkdnb(self): """Make directory name box""" return self.createcomponent( 'dirnamebox', (), None, Pmw.ScrolledListBox, (self.interior(),), label_text='directories', labelpos='n', hscrollmode='none', dblclickcommand=self.selectdir) def mkft(self): """Make filter""" return self.createcomponent( 'filter', (), None, Pmw.ComboBox, (self.interior(),), entryfield_value=self['filter'], entryfield_entry_width=40, selectioncommand=self.setfilter, labelpos='w', label_text='Filter:') def mkfnb(self): """Make filename list box""" return self.createcomponent( 'filenamebox', (), None, Pmw.ScrolledListBox, (self.interior(),), label_text='files', labelpos='n', hscrollmode='none', selectioncommand=self.singleselectfile, dblclickcommand=self.selectfile) def mkfn(self): """Make file name entry""" return self.createcomponent( 'filename', (), None, Pmw.ComboBox, (self.interior(),), entryfield_value=self['filename'], entryfield_entry_width=40, entryfield_validate=self.filevalidate, selectioncommand=self.setfilename, labelpos='w', label_text='Filename:') def dirvalidate(self,string): if os.path.isdir(string): return Pmw.OK else: return Pmw.PARTIAL def filevalidate(self,string): if string=='': return Pmw.PARTIAL elif os.path.isfile(string): return Pmw.OK elif os.path.exists(string): return Pmw.PARTIAL else: return Pmw.OK def okbutton(self): """OK action: user thinks he has input valid data and wants to proceed. This is also called by in the filename entry""" fn=self.component('filename').get() self.setfilename(fn) if self.validate(fn): self.canceled=0 self.deactivate() def cancelbutton(self): """Cancel the operation""" self.canceled=1 self.deactivate() def tidy(self,w,v): """Insert text v into the entry and at the top of the list of the combobox w, remove duplicates""" if not v: return entry=w.component('entry') entry.delete(0,'end') entry.insert(0,v) list=w.component('scrolledlist') list.insert(0,v) index=1 while indexself['historylen']: list.delete(index) else: index=index+1 w.checkentry() def setfilename(self,value): if not value: return value=os.path.join(self['directory'],value) dir,fil=os.path.split(value) self.configure(directory=dir,filename=value) c=self['command'] if callable(c): c() def newfilename(self): """Make sure a newly set filename makes it into the combobox list""" self.tidy(self.component('filename'),self['filename']) def setfilter(self,value): self.configure(filter=value) def newfilter(self): """Make sure a newly set filter makes it into the combobox list""" self.tidy(self.component('filter'),self['filter']) self.fillit() def setdir(self,value): self.configure(directory=value) def newdir(self): """Make sure a newly set dirname makes it into the combobox list""" self.tidy(self.component('dirname'),self['directory']) self.fillit() def singleselectfile(self): """Single click in file listbox. Move file to "filename" combobox""" cs=self.component('filenamebox').curselection() if cs!=(): value=self.component('filenamebox').get(cs) self.setfilename(value) def selectfile(self): """Take the selected file from the filename, normalize it, and OK""" self.singleselectfile() value=self.component('filename').get() self.setfilename(value) if value: self.okbutton() def selectdir(self): """Take selected directory from the dirnamebox into the dirname""" cs=self.component('dirnamebox').curselection() if cs!=(): value=self.component('dirnamebox').get(cs) dir=self['directory'] if not dir: dir=os.getcwd() if value: if value=='..': dir=os.path.split(dir)[0] else: dir=os.path.join(dir,value) self.configure(directory=dir) self.fillit() def askfilename(self,directory=None,filter=None): """The actual client function. Activates the dialog, and returns only after a valid filename has been entered (return value is that filename) or when canceled (return value is None)""" if directory!=None: self.configure(directory=directory) if filter!=None: self.configure(filter=filter) self.fillit() self.canceled=1 # Needed for when user kills dialog window self.activate() if self.canceled: return None else: return self.component('filename').get() lastdir="" lastfilter=None lasttime=0 def fillit(self): """Get the directory list and show it in the two listboxes""" # Do not run unnecesarily if self.lastdir==self['directory'] and self.lastfilter==self['filter'] and self.lasttime>os.stat(self.lastdir)[8]: return self.lastdir=self['directory'] self.lastfilter=self['filter'] self.lasttime=time() dir=self['directory'] if not dir: dir=os.getcwd() dirs=['..'] files=[] try: fl=os.listdir(dir) fl.sort() except os.error,arg: if arg[0] in (2,20): return raise for f in fl: if os.path.isdir(os.path.join(dir,f)): dirs.append(f) else: filter=self['filter'] if not filter: filter='*' if fnmatch.fnmatch(f,filter): files.append(f) self.component('filenamebox').setlist(files) self.component('dirnamebox').setlist(dirs) def validate(self,filename): """Validation function. Should return 1 if the filename is valid, 0 if invalid. May pop up dialogs to tell user why. Especially suited to subclasses: i.e. only return 1 if the file does/doesn't exist""" return 1 class PmwExistingFileDialog(PmwFileDialog): def filevalidate(self,string): if os.path.isfile(string): return Pmw.OK else: return Pmw.PARTIAL def validate(self,filename): if os.path.isfile(filename): return 1 elif os.path.exists(filename): _errorpop(self.interior(),"This is not a plain file") return 0 else: _errorpop(self.interior(),"Please select an existing file") return 0 class PmwDirDialog(PmwFileDialog): """Directory Dialog using Pmw""" def __init__(self, parent = None, **kw): # Define the megawidget options. optiondefs = ( ('directory', os.getcwd(), self.newdir), ('historylen',10, None), ('command', None, None), ('info', None, None), ) self.defineoptions(kw, optiondefs) # Initialise base class (after defining options). Pmw.Dialog.__init__(self, parent) self.withdraw() # Create the components. interior = self.interior() if self['info'] is not None: rowoffset=1 dn = self.infotxt() dn.grid(row=0,column=0,columnspan=2,padx=3,pady=3) else: rowoffset=0 dn = self.mkdn() dn.grid(row=1+rowoffset,column=0,columnspan=2,padx=3,pady=3) dn.bind('',self.okbutton) del dn # Create the directory list component. dnb = self.mkdnb() dnb.grid(row=0+rowoffset,column=0,columnspan=2,sticky='news',padx=3,pady=3) del dnb # Buttonbox already exists bb=self.component('buttonbox') bb.add('OK',command=self.okbutton) bb.add('Cancel',command=self.cancelbutton) del bb lastdir="" def fillit(self): """Get the directory list and show it in the two listboxes""" # Do not run unnecesarily if self.lastdir==self['directory']: return self.lastdir=self['directory'] dir=self['directory'] if not dir: dir=os.getcwd() dirs=['..'] try: fl=os.listdir(dir) fl.sort() except os.error,arg: if arg[0] in (2,20): return raise for f in fl: if os.path.isdir(os.path.join(dir,f)): dirs.append(f) self.component('dirnamebox').setlist(dirs) def okbutton(self): """OK action: user thinks he has input valid data and wants to proceed. This is also called by in the dirname entry""" fn=self.component('dirname').get() self.configure(directory=fn) if self.validate(fn): self.canceled=0 self.deactivate() def askfilename(self,directory=None): """The actual client function. Activates the dialog, and returns only after a valid filename has been entered (return value is that filename) or when canceled (return value is None)""" if directory!=None: self.configure(directory=directory) self.fillit() self.activate() if self.canceled: return None else: return self.component('dirname').get() def dirvalidate(self,string): if os.path.isdir(string): return Pmw.OK elif os.path.exists(string): return Pmw.PARTIAL else: return Pmw.OK def validate(self,filename): """Validation function. Should return 1 if the filename is valid, 0 if invalid. May pop up dialogs to tell user why. Especially suited to subclasses: i.e. only return 1 if the file does/doesn't exist""" if filename=='': _errorpop(self.interior(),"Empty filename") return 0 if os.path.isdir(filename) or not os.path.exists(filename): return 1 else: _errorpop(self.interior(),"This is not a directory") return 0 class Tail(object): """The Tail monitor object.""" def __init__(self, path, only_new = False, min_sleep = 1, sleep_interval = 1, max_sleep = 60): """Initialize a tail monitor. path: filename to open only_new: By default, the tail monitor will start reading from the beginning of the file when first opened. Set only_new to True to have it skip to the end when it first opens, so that you only get the new additions that arrive after you start monitoring. min_sleep: Shortest interval in seconds to sleep when waiting for more input to arrive. Defaults to 1.0 second. sleep_interval: The tail monitor will dynamically recompute an appropriate sleep interval based on a sliding window of data arrival rate. You can set sleep_interval here to seed it initially if the default of 1.0 second doesn't work for you and you don't want to wait for it to converge. max_sleep: Maximum interval in seconds to sleep when waiting for more input to arrive. Also, if this many seconds have elapsed without getting any new data, the tail monitor will check to see if the log got truncated (rotated) and will quietly reopen itself if this was the case. Defaults to 60.0 seconds. """ # remember path to file in case I need to reopen self.path = abspath(path) self.f = open(self.path,"r") self.min_sleep = min_sleep * 1.0 self.sleep_interval = sleep_interval * 1.0 self.max_sleep = max_sleep * 1.0 if only_new: # seek to current end of file file_len = stat(path)[ST_SIZE] self.f.seek(file_len) self.pos = self.f.tell() # where am I in the file? self.last_read = time() # when did I last get some data? self.queue = [] # queue of lines that are ready self.window = [] # sliding window for dynamically # adjusting the sleep_interval def _recompute_rate(self, n, start, stop): """Internal function for recomputing the sleep interval. I get called with a number of lines that appeared between the start and stop times; this will get added to a sliding window, and I will recompute the average interarrival rate over the last window. """ self.window.append((n, start, stop)) purge_idx = -1 # index of the highest old record tot_n = 0 # total arrivals in the window tot_start = stop # earliest time in the window tot_stop = start # latest time in the window for i, record in enumerate(self.window): (i_n, i_start, i_stop) = record if i_stop < start - self.max_sleep: # window size is based on self.max_sleep; this record has # fallen out of the window purge_idx = i else: tot_n += i_n if i_start < tot_start: tot_start = i_start if i_stop > tot_stop: tot_stop = i_stop if purge_idx >= 0: # clean the old records out of the window (slide the window) self.window = self.window[purge_idx+1:] if tot_n > 0: # recompute; stay within bounds self.sleep_interval = (tot_stop - tot_start) / tot_n if self.sleep_interval > self.max_sleep: self.sleep_interval = self.max_sleep if self.sleep_interval < self.min_sleep: self.sleep_interval = self.min_sleep def _fill_cache(self): """Internal method for grabbing as much data out of the file as is available and caching it for future calls to nextline(). Returns the number of lines just read. """ old_len = len(self.queue) line = self.f.readline() while line != "": self.queue.append(line) line = self.f.readline() # how many did we just get? num_read = len(self.queue) - old_len if num_read > 0: self.pos = self.f.tell() now = time() self._recompute_rate(num_read, self.last_read, now) self.last_read = now return num_read def _dequeue(self): """Internal method; returns the first available line out of the cache, if any.""" if len(self.queue) > 0: line = self.queue[0] self.queue = self.queue[1:] return line else: return None def _reset(self): """Internal method; reopen the internal file handle (probably because the log file got rotated/truncated).""" self.f.close() self.f = open(self.path, "r") self.pos = self.f.tell() self.last_read = time() def nextline(self): """Return the next line from the file. Blocks if there are no lines immediately available.""" # see if we have any lines cached from the last file read line = self._dequeue() if line: return line # ok, we are out of cache; let's get some lines from the file if self._fill_cache() > 0: # got some return self._dequeue() # hmm, still no input available while True: sleep(self.sleep_interval) if self._fill_cache() > 0: return self._dequeue() now = time() if (now - self.last_read > self.max_sleep): # maybe the log got rotated out from under us? if stat(self.path)[ST_SIZE] < self.pos: # file got truncated and/or re-created self._reset() if self._fill_cache() > 0: return self._dequeue() def close(self): """Close the tail monitor, discarding any remaining input.""" self.f.close() self.f = None self.queue = [] self.window = [] def __iter__(self): """Iterator interface, so you can do: for line in filetail.Tail('log.txt'): # do stuff pass """ return self def next(self): """Kick the iterator interface. Used under the covers to support: for line in filetail.Tail('log.txt'): # do stuff pass """ return self.nextline() class TableCell( Label ): params = {"relief":RIDGE, "bd":2, "bg":"#ffffff", "anchor":W,"font":("Helvetica",12), "width":1} def __init__(self, *args, **kwargs): apply(Label.__init__,((self,)+args), self.params) self.bind("", self.on_enter) self.bind("", self.on_leave) self.bind("", self.on_clicked) self.table = kwargs["command"] self.entry = kwargs["entry"] self.row = kwargs["row"] self.col = kwargs["col"] self.HIGHLIGHT = "#ccccff" self.SELECTED = "#bbccdd" self.UNSELECTED = "#ffffff" def on_enter(self, event): event.widget["bg"] = self.HIGHLIGHT def on_leave(self, event): if self.table.selected != self.row: event.widget["bg"] = self.UNSELECTED else: event.widget["bg"] = self.SELECTED def on_clicked(self, event): for col in xrange(0,len(ScoreTable.fields)): self.entry[self.row][col]["bg"] = self.SELECTED if self.table.selected != -1: self.entry[self.table.selected][col]["bg"] = self.UNSELECTED self.table.on_select(self.row) class ScoreTable(Frame): fields = {0:"Rank",1:"Ligand",2:"Pose #",3:"Score"} width = [10,30,10,20] def __init__(self, parent, rows=16, cols = len(fields), command = None): Frame.__init__(self, parent, relief=SUNKEN, bd=2) self.windowSize = rows self.cols = cols self.rows = rows self.command = command self.table = Frame(self, relief=FLAT, bd=0) self.table.pack(side=LEFT, expand = YES, fill=BOTH) self.yscrollbar = Scrollbar(self, jump=0, command = self.on_scroll) self.yscrollbar.pack(side=RIGHT, fill=Y) self.clearTable() self.entry={} self.createTable(rows, cols) def clearTable(self): self.data = {} self.selected = -1 self.rows = 0 self.firstVisible = 0 self.lastVisible = self.windowSize - 1 self.yscrollbar.set(0.0,1.0) # self.createTable(self.rows, self.cols) def updateScrollbar(self): top = float(self.firstVisible)/float(self.rows) bottom = float(self.lastVisible+1)/float(self.rows) self.yscrollbar.set(top, bottom) def createTable(self, rows, cols): for col in xrange(0, len(self.fields)): Label(self.table, relief=SUNKEN, bd=2, width=self.width[col], font=("Helvetica",12), text=self.fields[col]).grid(row=0, column=col, sticky=W+E) for row in xrange(0, rows): self.entry[row] = {} for colx in xrange(0, cols): self.entry[row][colx] = TableCell(self.table, row=row, col=colx, entry=self.entry, command=self) self.entry[row][colx].grid(row=row+1,column=colx,sticky=N+W+S+E) def updateScreen(self, firstVisible): if firstVisible < 0: firstVisible = 0 self.firstVisible = firstVisible self.lastVisible = firstVisible+self.windowSize-1 if self.lastVisible < len(self.data.values()): for row in xrange(0, self.windowSize): for col in xrange(0, self.cols): try: self.entry[row][col]["text"] = self.data[row+firstVisible][col] except: pass self.updateScrollbar() def on_scroll(self, *args): if args[0] == "moveto": self.updateScreen(int(float(args[1])*self.rows)) elif args[0] == "scroll": offset = int(args[1]) if args[2] == "pages": offset*=self.windowSize newFirstVisible = self.firstVisible + offset if newFirstVisible < 0: newFirstVisible = 0 if newFirstVisible > self.rows - self.windowSize: newFirstVisible = self.rows - self.windowSize self.updateScreen(newFirstVisible) def on_select(self, row): self.selected = row def append_row(self, header = None): self.data[self.rows] = {} self.rows+=1 self.updateScrollbar() def set_cell_value(self, row, col, text): self.data[row][col] = str(text) if row<=self.lastVisible: self.entry[row-self.firstVisible][col]["text"] = text def add_ligand(self, ligand, rank): self.append_row() self.set_cell_value(self.rows-1, 0, rank) self.set_cell_value(self.rows-1, 1, ligand.name) self.set_cell_value(self.rows-1, 2, ligand.poseN) self.set_cell_value(self.rows-1, 3, ligand.energy) def updateView(self, ligand_list): for i, ligand in enumerate(ligand_list): self.add_ligand(ligand, i+1) def resetTable(self): for i in range(self.rows): for k in range(4): self.set_cell_value(i,k,"") self.clearTable()