#!/usr/bin/env python # ---------------------------------------------------------------------------------------------------- import os,math import Tkinter from Tkinter import * import Pmw from PmwFileDialog import * import traceback import pymol # ---------------------------------------------------------------------------------------------------- # SimTk modules import BaseObjectSimTk import UtilitiesSimTk import LogSimTk from IsimDisplayWidgetsSimTk import * # ---------------------------------------------------------------------------------------------------- # ---------------------------------------------------------------------------------------------------- class IsimDisplayInterfaceSimTk( BaseObjectSimTk.BaseObjectSimTk ): # { # ------------------------------------------------------------------------------------------------- def __init__( self, app, isimDisplay=None ): # { """Constructor for IsimDisplayInterfaceSimTk""" BaseObjectSimTk.BaseObjectSimTk.__init__( self ) # attributes self._workingDirectoryName = None self._parent = None self._mainDialog = None self._advancedDialog = None self._topLabel = None self._notebook = None self._isimDisplay = isimDisplay self._meshSurfaceInterface = None self._molecularSurfaceInterface = None self._helpDialog = None self._advancedHelpDialog = None self._app = app self._updateMain = 0 self._updateAdvanced = 0 # lets go # self.createTestDialog( ) self.createMainDialog( app ) # self.createAdvancedDialog( app ) # } end of constructor # ------------------------------------------------------------------------------------------------- def createTestDialog( self ): # { """Test dialog""" self._parent = Tkinter._default_root self._testDialog = Pmw.Dialog( self._parent, buttons = ( 'Exit', ), title = 'Isim Pymol Test Display' ) # this call is needed to keep window on top of Pymol windows self._testDialog.wait_visibility( ) self._testDialog.tkraise( ) self._testDialog.show( ) # } end of createTestDialog # ------------------------------------------------------------------------------------------------- def createMainDialog( self, app ): # { """Main dialog""" if app is None: self._parent = Tkinter._default_root else: self._parent = app.root self._mainDialog = Pmw.Dialog( self._parent, buttons = ( 'Advanced', 'Exit', 'Help' ), title = 'Isim Pymol Display', command = self._executeSimpleInterfaceCallback ) # this call is needed to keep window on top of Pymol windows # if windows os, then skip wait_visibility() and tkraise() -- system crashes # for unknown reason logReference = self._isimDisplay.getLogReference() if logReference is not None: logReference.info( 'createMainDialog: sys.platform=<' + str( sys.platform ) + '>' ) if sys.platform != 'win32': if logReference is not None: logReference.info( 'createMainDialog: wait_visibility() is being set.' ) self._mainDialog.wait_visibility( ) else: if logReference is not None: logReference.info( 'createMainDialog: wait_visibility() is not being set.' ) # simple dialog self._simpleInterface = IsimSimpleInterface( self._mainDialog.interior() ) returnValue = self._simpleInterface.initialize( self.getIsimDisplay() ) if returnValue is not None: self._simpleInterface.pack( fill = 'both', expand = 1, padx = 10, pady = 5 ) # the setGeometryAndDeiconify() command will place the window # to the right of the Pymol window # needed to prevent overlap w/ Pymol dialog geometry = '+%d+%d' % (900, 10) Pmw.setgeometryanddeiconify( self._mainDialog, geometry ) # 'lift' is aliased to 'tkraise' # threading bug (Warren's inference) in Windows prevents # call to tkraise() if sys.platform != 'win32': self._mainDialog.tkraise( ) self._mainDialog.show( ) self._simpleInterface.update() # self._mainDialog.deactivate() # self._mainDialog.activate( globalMode = 'nograb' ) # } end of createMainDialog # ------------------------------------------------------------------------------------------------- def createAdvancedDialog( self, app ): # { """Main dialog""" if app is None: self._parent = Tkinter._default_root else: self._parent = app.root self._advancedDialog = Pmw.Dialog( self._parent, buttons = ( 'Update', 'Print', 'Exit', 'Help' ), title = 'Isim Pymol Display', command = self._executeCallback ) self._advancedDialog.withdraw() Pmw.setbusycursorattributes( self._advancedDialog.component('hull') ) # self._topLabel = Tkinter.Label( self._advancedDialog.interior(), # text = 'Isim Display', background = 'black', foreground = 'white' ) # self._topLabel.pack( expand = 1, fill = 'both', padx = 4, pady = 4 ) self._notebook = Pmw.NoteBook( self._advancedDialog.interior() ) self._notebook.pack( fill='both', expand=1, padx=10, pady=10 ) # Create interface sheets # molecular surface sheet = self._notebook.add( 'Observables at the Molecular Surface' ) self._molecularSurfaceInterface = IsimMolecularSurfaceInterface( sheet ) self._molecularSurfaceInterface.initialize( self.getIsimDisplay() ) self._molecularSurfaceInterface.pack(fill = 'both', expand = 1, padx = 10, pady = 5) # mesh surfaces sheet = self._notebook.add( 'Observable IsoSurfaces' ) self._meshSurfaceInterface = IsimMeshSurfaceInterface( sheet ) self._meshSurfaceInterface.initialize( self.getIsimDisplay() ) self._meshSurfaceInterface.pack( fill = 'both', expand = 1, padx = 10, pady = 5 ) self._notebook.setnaturalsize() self.showAppModal() # } end of createAdvancedDialog # ------------------------------------------------------------------------------------------------- # accessors for IsimDisplay def setIsimDisplay( self, isimDisplay ): # { """Set accessor for IsimDisplay """ self._isimDisplay = isimDisplay # } end of setIsimDisplay def getIsimDisplay( self ): # { """Get accessor for IsimDisplay """ return self._isimDisplay; # } end of getIsimDisplay # ------------------------------------------------------------------------------------------------- def showAppModal( self ): # { self._advancedDialog.show() # } end of showAppModal # ------------------------------------------------------------------------------------------------- def update( self ): # { clear = 0 update = 0 if self._simpleInterface is not None: if clear: self._simpleInterface.clear() if self._updateMain: update += self._simpleInterface.update() if self._molecularSurfaceInterface is not None: if clear: self._molecularSurfaceInterface.clear() if self._updateAdvanced: update += self._molecularSurfaceInterface.update() if self._meshSurfaceInterface is not None: if clear: self._meshSurfaceInterface.clear() if self._updateAdvanced: update += self._meshSurfaceInterface.update() if update: pymol.cmd.refresh() pymol.cmd.recolor() # } end of update # ------------------------------------------------------------------------------------------------- def clear( self, clearFlag = 0 ): # { if self._simpleInterface is not None: self._simpleInterface.clear( clearFlag ) if self._molecularSurfaceInterface is not None: self._molecularSurfaceInterface.clear( clearFlag ) if self._meshSurfaceInterface is not None: self._meshSurfaceInterface.clear( clearFlag ) pymol.cmd.refresh() pymol.cmd.recolor() # } end of clear # ------------------------------------------------------------------------------------------------- def _executeCallback( self, result ): # { if result == 'Update': self.clear( 0 ) self._updateAdvanced = 1 self.update() self._updateAdvanced = 0 elif result == 'Clear': self.clear( 1 ) elif result == 'Print': self.printPng() elif result == 'Exit': if __name__ == '__main__': self.parent.destroy() else: self._advancedDialog.withdraw() elif result == 'Help': # Create help dialog if self._advancedHelpDialog is None: useMessageDialog = 0 if useMessageDialog: self._advancedHelpDialog = Pmw.MessageDialog( self._notebook.interior(), title = 'Help', message_text = self.getHelpText(), command = self.quitHelp, buttons = ( 'Ok', ) ) else: self._advancedHelpDialog = Pmw.TextDialog( self._notebook.interior(), title = 'Help' ) self._advancedHelpDialog.insert( 'end', self.getHelpText() ) self._advancedHelpDialog.configure( text_state = 'disabled' ) self._advancedHelpDialog.withdraw() self._advancedHelpDialog.activate() # } end of _executeCallback # ------------------------------------------------------------------------------------------------- def _executeSimpleInterfaceCallback( self, result ): # { if result == 'Update': self.clear( 0 ) self._updateMain = 1 self.update() self._updateMain = 0 elif result == 'Advanced': # lets go self.clear( 0 ) if self._simpleInterface is not None: self._simpleInterface.toggleButtons( ) self.createAdvancedDialog( self._app ) elif result == 'Clear': self.clear( 1 ) elif result == 'Print': self.printPng() elif result == 'Exit': if __name__ == '__main__': self.parent.destroy() else: if self._mainDialog is not None: self._mainDialog.withdraw() elif result == 'Help': # Create help dialog if self._helpDialog is None: useMessageDialog = 0 if useMessageDialog: self._helpDialog = Pmw.MessageDialog( self._mainDialog.interior(), title = 'Help', message_text = self.getSimpleInterfaceHelpText(), command = self.quitHelp, buttons = ( 'Ok', ) ) else: self._helpDialog = Pmw.TextDialog( self._mainDialog.interior(), title = 'Help' ) self._helpDialog.insert( 'end', self.getSimpleInterfaceHelpText() ) self._helpDialog.configure( text_state = 'disabled' ) self._helpDialog.withdraw() self._helpDialog.activate() # } end of _executeSimpleInterfaceCallback # ------------------------------------------------------------------------------------------------- def quitHelp( self, callerButton ): # { self._helpDialog.destroy() # } end of quitHelp # ------------------------------------------------------------------------------------------------- def getSimpleInterfaceHelpText( self ): # { message = 'The interface to Pymol allows the user to view \n\n' message += ' (1) the macromolecule,\n' message += ' (2) the electrostatic potential at the surface of the macromolecule\n' message += ' arising from the molecular charges and the average distribution\n' message += ' of the ions,\n' message += ' (3) the averaged number densities for each ion species.\n\n' message += 'The levels for each of the observables are selected based on statistics\n' message += 'collected at grid points near the surface of the molecule and\n' message += "in the 'near' bulk. Here 'near' bulk is the region within approximately\n" message += "15A of the surface of the molecule.\n\n" message += "The color scheme used in the display of the surface electrostatic potential is\n" message += "based on the Pymol surface color ramp ('ramp_new' command). The range used for the color\n" message += "ramp is [ -int( sdTrimmed ) - 1, 0, int( sdTrimmed ) + 1 ], where sdTrimmed is the\n" message += "standard deviation of the 'trimmed' potential distribution at the surface of the molecule.\n" message += "Here the 'trimmed' distribution potential is the set of potential values obtained\n" message += "by deleting the electrostatic potential values less than the 5-percentile level\n" message += "and greater than the 95-percentile level from the collection. The statistics obtained\n" message += "from this truncated distribution are more robust to outliers that may occur.\n\n" message += "The number density isosurface meshes are color coded according to whether the ion\n" message += "is positively charged (warmer colors) or negatively charged ((cooler colors).\n" message += "The level that is displayed is the 90% percentile of the 'near' bulk distribution\n" message += "of number density values. However, if the this level is less than 1.0e-05, then\n" message += "the program looks at the high-end tail of the distribution of values and chooses\n" message += "the highest level such that the number of grid points with values above this level\n" message += "is greater than 100. If no value can be found that satisifies this criterion, then\n" message += "program defaults to a level of 1.0e-04. The actual level used is printed in the\n" message += "interface.\n\n" message += "" message += "The above schemes for selecting the levels to display the observables should work for\n" message += "most cases. However, the user can adjust the displayedlevels by using the Advanced menu.\n" message += "See the Help text available in the Advanced dialog on how to set the levels\n" message += "and obtain statistics of the distribution of values." return message # } end of getSimpleInterfaceHelpText # ------------------------------------------------------------------------------------------------- def getHelpText( self ): # { message = '' message += '\n\n\n----------------------------- Help for Molecular Surface worksheet -----------------------------\n\n' message += 'The Molecular Surface worksheet allows the user to plot the\n' message += 'observables (electrostatic potential, charge density and ion\n' message += 'number densities) at the surface of the macromolecule.\n\n' message += 'In contrast the Isosurfaces worksheet allows the user to plot the\n' message += 'isosurfaces of the different observables at various levels in the solvent.\n\n' message += 'The widgets in the Molecular Surface worksheet are first discussed\n' message += 'followed by a similar description for the Isosurfaces display.\n\n' message += 'The checkbox on the far left of the Molecular Surface worksheet\n' message += 'toggles the observables that are displayed; only one observable\n' message += 'can be plotted at a time. The ability to chose from among 3 possible\n' message += 'observables/settings but with only one active at any given time was\n' message += 'allows the user to quickly switch between different\n' message += 'views.\n\n' message += self.getObservableHelpText() message += "The color scheme used in the display of the observables at the molecular surface\n" message += "is based on the Pymol surface color ramp ('ramp_new' command). This command requires\n" message += "three thresholds, referred to in the interface as low, medium and high.\n" message += "The color ramp interpolates the colors from red to white for the low-medium range and\n" message += "from white to blue for the medium-high range.\n\n" message += self.getUmitsPullDownHelpText() message += "The Surface pulldown menu specifies whether the surface to be mapped to is the molecular\n" message += "or the solvent-accessible surface. This feature is implemented by setting the Pymol\n" message += "'surface_solvent' value to 0 (molecular surface) or 1 (solvent-accessible surface) and \n" message += "'surface_ramp_above_mode' value to 1 (molecular surface) or 0 (solvent-accessible surface).\n\n" message += self.getStatButtonHelpText(); # ------------------------------------------------------------------------------------------------- # mesh surface message += '\n\n\n----------------------------- Help for Isosurface worksheet -----------------------------\n\n' message += 'The checkbox on the far left in the Isosurface worksheet\n' message += 'toggles the observables that are displayed; multiple observables/surface levels\n' message += 'can be plotted simultaneously.\n\n' message += self.getObservableHelpText() message += "The level text box specifies the isosurface contour; for a guide to the distribution\n" message += "for a level see the results from the Stat button\n" message += self.getUmitsPullDownHelpText() message += "The color pulldown allows the user to specify the color of the isosurface.\n" message += "The Surface pulldown menu specifies whether the surface contour is to be displayed\n" message += "as a solid, a mesh or closely-spaced dots. These are implemented by the Pymol\n" message += "isosurface(), isomesh(), and isodot() commands.\n" message += self.getStatButtonHelpText(); return message # } end of getHelpText # ------------------------------------------------------------------------------------------------- def getObservableHelpText( self ): # { message = '' message += 'The observables include the following:\n' message += ' (1) the APBS electrostatic potential that is an input to the ISIM calculation;\n' message += ' this is the potential arising from just the macromolecule charges (no ions).\n' message += ' the Monte Carlo step is 0 since the potential is input to the program and is fixed\n' message += ' throughout the calculation.\n' message += ' (2) the averaged ISIM electrostatic potential\n' message += ' (3) the averaged ISIM number density for each ion species\n' message += ' (4) the avergaed ISIM charge density\n' message += "For all all observables except the APBS electrostatic potential, the running average\n" message += "at regularly spaced Monte Carlo (MC) steps is available; the default MC step\n" message += "is the last available step in the simulation.\n\n" return message # } end of getObservableHelpText # ------------------------------------------------------------------------------------------------- def getUmitsPullDownHelpText( self ): # { message = "" message += "The Units pulldown menu allows the user to specifiy whether the thresholds in the\n" message += "are to be interpreted as absolute thresholds or as units of standard deviation.\n" message += "The standard deviation is calculated from a trimmed distribution of the observable\n" message += "to be displayed: only values between the 5-95th percentil are included in the calculation\n" message += "of the standard deviation -- this removes distortions that may arise from outliers.\n\n" return message # } end of getUmitsPullDownHelpText # ------------------------------------------------------------------------------------------------- def getStatButtonHelpText( self ): # { message = "" message += "The Stat button displays the statistics collected for the current selection/observable.\n" message += "The statistics include the mean, standard deviation, median, min, max for the observables, both\n" message += "on/near the surface of the molecule and in the near bulk (grid points within 15A of the molecule).\n" message += "A histogram of the values is also included. See the text included in the output presented for\n" message += "more details. These statistics can guide the user on how to set the levels for the different observables." return message # } end of getStatButtonHelpText # ------------------------------------------------------------------------------------------------- def printPng( self ): # { # ------------------------------------------------------------------------------------------------- # Create the dialog. self._printDialog = Pmw.Dialog( self._notebook.interior(), buttons = ('OK', 'Cancel', 'Help'), defaultbutton = 'OK', title = 'Print Png', command = self._printDialogCallback) # ------------------------------------------------------------------------------------------------- # Add file chooser self._printPngFile = Pmw.EntryField( self._printDialog.interior(), labelpos='e', label_pyclass = FileDialogButtonClassFactory.get( self.setPngFileName,'*.png'), label_text='Png file:', ) self._printPngFile.pack( fill='both', expand=1, padx=10, pady=10 ) # ------------------------------------------------------------------------------------------------- # ray trace self._rayTrace = IntVar() self._rayTrace.set( 1 ) self._rayTraceCheckButton = Checkbutton( self._printDialog.interior(), anchor='w',indicatoron=True, text='Ray Trace', variable = self._rayTrace ) self._rayTraceCheckButton.pack( fill='both', expand=1, padx=10, pady=10 ) # ------------------------------------------------------------------------------------------------- # pixel width/height self._widthPngFile = Pmw.EntryField( self._printDialog.interior(), labelpos='e', value=2400, label_text='Pixel Width', validate = {'validator' : 'real' }, entry_width = 8,) self._widthPngFile.pack( fill='both', expand=1, padx=10, pady=10 ) self._heightPngFile = Pmw.EntryField( self._printDialog.interior(), labelpos='e', value=2400, label_text='Pixel Height', validate = {'validator' : 'real' }, entry_width = 8,) self._heightPngFile.pack( fill='both', expand=1, padx=10, pady=10 ) # ------------------------------------------------------------------------------------------------- self._printDialog.withdraw() self._printDialog.show() return # } end of printPng # ------------------------------------------------------------------------------------------------- def setPngFileName( self, fileName ): # { fileName = self.addPngFileSuffix( fileName ) self._printPngFile.setvalue(fileName) # } end of setPngFileName # ------------------------------------------------------------------------------------------------- def getPngFileName( self ): # { fileName = self._printPngFile.getvalue() pngSuffix = re.compile( '.png$' ) if pngSuffix.search( fileName ) is None: fileName += '.png' return fileName # } end of getPngFileName # ------------------------------------------------------------------------------------------------- def addPngFileSuffix( self, fileName ): # { pngSuffix = re.compile( '.png$' ) if pngSuffix.search( fileName ) is None: fileName += '.png' return fileName # } end of addPngFileSuffix # ------------------------------------------------------------------------------------------------- def _printDialogCallback( self, request ): # { if request == 'OK': # diagnostics print 'Print File=' + self.getPngFileName() print 'Ray=' + str( self._rayTrace.get() ) print 'Width=' + str( self._widthPngFile.getvalue() ) print 'Height=' + str( self._heightPngFile.getvalue() ) # set parameters for png file print pymol.cmd.bg_color( color='white' ) pymol.cmd.set( 'antialias', 1 ) pymol.cmd.set( 'orthoscopic', 1 ) if self._rayTrace.get(): pymol.cmd.ray( self._widthPngFile.getvalue(), self._heightPngFile.getvalue() ) pymol.cmd.png( self.getPngFileName() ) # pymol.cmd.bg_color( color='black' ) pymol.cmd.set( 'antialias', 0 ) pymol.cmd.set( 'orthoscopic', 0 ) else: print 'Print dialog request=' + request + " ignored." self._printDialog.destroy() return # } end of _printDialogCallback # ---------------------------------------------------------------------------------------------------- # } end of class IsimDisplayInterfaceSimTk