Better support for the "Compare Proteins" command. Also removed deprecated methods.

author: Mark Sims <mark@nanorex.com> 2008-12-15 08:19:00 +0000
committer: Mark Sims <mark@nanorex.com> 2008-12-15 08:19:00 +0000
commit: 45b38837bab330154258b546ab21c32d3b3118cf (patch)
tree: ffcb27745b7a2f4f8abeed8996ca27e59142de40
parent: d075219cd37628fed2e71a508bd2deea9dc06691 (diff)
download: nanoengineer-theirix-45b38837bab330154258b546ab21c32d3b3118cf.tar.gz
nanoengineer-theirix-45b38837bab330154258b546ab21c32d3b3118cf.zip
8 files changed, 279 insertions, 366 deletions
diff --git a/cad/src/commandSequencer/CommandSequencer.py b/cad/src/commandSequencer/CommandSequencer.py
index 3320c5c7b..a0a8086ca 100644
--- a/cad/src/commandSequencer/CommandSequencer.py
+++ b/cad/src/commandSequencer/CommandSequencer.py
@@ -932,7 +932,7 @@ class CommandSequencer(object):
                  or None if no such command is found.
         @rtype: an active command object, or None
 
-        @param commandName: name of command we're searching for (e.g. 'BUILD_PROTEIN')
+        @param commandName: name of command we're searching for (e.g. 'MODEL_AND_SIMULATE_PROTEIN')
         @type: string
 
         @param starting_from: if provided, start the search at this command
diff --git a/cad/src/model/chunk.py b/cad/src/model/chunk.py
index fc89a16b7..2d7defadf 100755
--- a/cad/src/model/chunk.py
+++ b/cad/src/model/chunk.py
@@ -552,7 +552,7 @@ class Chunk(NodeWithAtomContents, InvalMixin,
             return
         
         #Urmi 20080730: edit properties for protein for context menu in gl pane
-        if command.commandName in ('SELECTMOLS', 'BUILD_PROTEIN'):
+        if command.commandName in ('SELECTMOLS', 'MODEL_AND_SIMULATE_PROTEIN'):
             if self.isProteinChunk():
                 try:
                     protein = self.protein
diff --git a/cad/src/ne1_ui/MWsemantics.py b/cad/src/ne1_ui/MWsemantics.py
index f6be710c4..62f19d223 100755
--- a/cad/src/ne1_ui/MWsemantics.py
+++ b/cad/src/ne1_ui/MWsemantics.py
@@ -1404,7 +1404,7 @@ class MWsemantics(QMainWindow,
         @type otherOptionsText: str
         """
         protein = ""
-        if self.commandSequencer.currentCommand.commandName == 'BUILD_PROTEIN' or \
+        if self.commandSequencer.currentCommand.commandName == 'MODEL_AND_SIMULATE_PROTEIN' or \
            self.commandSequencer.currentCommand.commandName == 'EDIT_ROTAMERS' or \
            self.commandSequencer.currentCommand.commandName == 'EDIT_RESIDUES':
             protein = self.commandSequencer.currentCommand.propMgr.current_protein
diff --git a/cad/src/protein/ProteinSequenceEditor/ProteinSequenceEditor.py b/cad/src/protein/ProteinSequenceEditor/ProteinSequenceEditor.py
index 4a4bcbebb..55cf5fc34 100644
--- a/cad/src/protein/ProteinSequenceEditor/ProteinSequenceEditor.py
+++ b/cad/src/protein/ProteinSequenceEditor/ProteinSequenceEditor.py
@@ -508,7 +508,6 @@ class ProteinSequenceEditor(Ui_ProteinSequenceEditor):
         current_command = self.win.commandSequencer.currentCommand.commandName
         commandSet = ('EDIT_ROTAMERS', \
                       'EDIT_RESIDUES', \
-                      'BUILD_PROTEIN', \
                       'MODEL_AND_SIMULATE_PROTEIN', \
                       'MODEL_PROTEIN', \
                       'SIMULATE_PROTEIN')
diff --git a/cad/src/protein/commands/BuildProtein/BuildProtein_PropertyManager.py b/cad/src/protein/commands/BuildProtein/BuildProtein_PropertyManager.py
index 545b21ea9..062bc7d54 100644
--- a/cad/src/protein/commands/BuildProtein/BuildProtein_PropertyManager.py
+++ b/cad/src/protein/commands/BuildProtein/BuildProtein_PropertyManager.py
@@ -21,6 +21,9 @@ To do list:
 - Special peptide icons for MT and PM list widget.
 - Deprecate set_current_protein_chunk_name() and get_current_protein_chunk_name.
   Use ops_select_Mixin's getSelectedProteinChunk() instead.
+- Bug: Returning from Compare command unselects the two selected protein chunks.
+  The PM list widget shows them as selected and the compare button is enabled,
+  but they are not selected in the graphics area.
 """
 import foundation.env as env
 from PyQt4.Qt import SIGNAL
@@ -34,6 +37,7 @@ from PM.PM_Constants     import PM_DONE_BUTTON
 from PM.PM_Constants     import PM_WHATS_THIS_BUTTON
 from PM.PM_Constants     import PM_CANCEL_BUTTON
 from utilities.Comparison import same_vals
+from protein.model.Protein import getAllProteinChunksInPart
 
 _superclass = EditCommand_PM
 class BuildProtein_PropertyManager(EditCommand_PM):
@@ -57,15 +61,13 @@ class BuildProtein_PropertyManager(EditCommand_PM):
     pmName        =  title
     iconPath      =  "ui/actions/Command Toolbar/BuildProtein/BuildProtein.png"
     
-    current_protein = "" # name of the single selected peptide.
+    current_protein = "" # name of the single selected peptide. To be deprecated soon. --Mark 2008-12-14
 
     def __init__( self, command):
         """
         Constructor for the Build Protein property manager.
         """
         
-        self.sequenceEditor = command.win.createProteinSequenceEditorIfNeeded() 
-        
         #Attributes for self._update_UI_do_updates() to keep track of changes
         #in these , since the last call of that method. These are used to 
         #determine whether certain UI updates are needed. 
@@ -112,6 +114,11 @@ class BuildProtein_PropertyManager(EditCommand_PM):
         change_connect(self.editPeptidePropertiesButton, 
                        SIGNAL("clicked()"),
                        self._editPeptide)
+        
+        change_connect(self.compareProteinsButton, 
+                       SIGNAL("clicked()"),
+                       self._compareProteins)
+        
         return
     
     def enable_or_disable_gui_actions(self, bool_enable = False):
@@ -133,7 +140,7 @@ class BuildProtein_PropertyManager(EditCommand_PM):
         Overrides superclass method. 
         
         @see: Command_PropertyManager._update_UI_do_updates()
-        """                     
+        """
         
         newSelectionParams = self._currentSelectionParams()   
         
@@ -159,7 +166,7 @@ class BuildProtein_PropertyManager(EditCommand_PM):
         #parameters remained unchanged since last call. --- [CONDITION A]
         if selection_params_unchanged and structure_params_unchanged and command_stack_params_unchanged:
             #This second condition above fixes bug 2888
-            print "_update_UI_do_updates(): RETURNING 1"
+            print "Build Protein: _update_UI_do_updates(): DO NOTHING"
             return
         
         self._previousStructureParams = current_struct_params
@@ -188,7 +195,12 @@ class BuildProtein_PropertyManager(EditCommand_PM):
                 self.editPeptidePropertiesButton.setEnabled(True)
             else:
                 self.editPeptidePropertiesButton.setEnabled(False)
-                self.sequenceEditor.hide()
+            
+                # Enable/disable "Compare Proteins" button.
+            if len(selectedProteins) == 2:
+                self.compareProteinsButton.setEnabled(True)
+            else:
+                self.compareProteinsButton.setEnabled(False)
                 
             return
         
@@ -197,11 +209,11 @@ class BuildProtein_PropertyManager(EditCommand_PM):
     
     def _currentCommandStackParams(self):
         """
-        The return value is supposed to be used by BUILD_PROTEIN command PM ONLY
+        The return value is supposed to be used by MODEL_AND_SIMULATE_PROTEIN command PM ONLY
         and NOT by any subclasses.         
         
         Returns a tuple containing current command stack change indicator and 
-        the name of the command 'BUILD_PROTEIN'. These 
+        the name of the command 'MODEL_AND_SIMULATE_PROTEIN'. These 
         parameters are then used to decide whether updating widgets
         in this property manager is needed, when self._update_UI_do_updates()
         is called. 
@@ -219,11 +231,11 @@ class BuildProtein_PropertyManager(EditCommand_PM):
         @see: self._update_UI_do_updates()
         """
         commandStackCounter = self.command.assy.command_stack_change_indicator()
-        #Append 'BUILD_PROTEIN to the tuple to be returned. This is just to remind 
-        #us that this method is meant for BUILD_PROTEIN command PM only. (and not 
+        #Append 'MODEL_AND_SIMULATE_PROTEIN to the tuple to be returned. This is just to remind 
+        #us that this method is meant for MODEL_AND_SIMULATE_PROTEIN command PM only. (and not 
         #by any subclasses) Should we assert this? I think it will slow things 
         #down so this comment is enough -- Ninad 2008-09-30
-        return (commandStackCounter, 'BUILD_PROTEIN')
+        return (commandStackCounter, 'MODEL_AND_SIMULATE_PROTEIN')
                       
     def _currentSelectionParams(self):
         """
@@ -244,7 +256,7 @@ class BuildProtein_PropertyManager(EditCommand_PM):
         if self.command is not None: # and self.command.hasValidStructure():
             selectedPeptides = self.win.assy.getSelectedProteinChunks()          
         
-        print "_currentSelectionParams(): Number of selected peptides:", len(selectedPeptides)
+        #print "_currentSelectionParams(): Number of selected peptides:", len(selectedPeptides)
         return (selectedPeptides)
     
     def _currentStructureParams(self):
@@ -263,7 +275,7 @@ class BuildProtein_PropertyManager(EditCommand_PM):
         
         if self.command: # and self.command.hasValidStructure():
             peptideList = []
-            peptideList = self.getAllProteinChunksInPart()
+            peptideList = getAllProteinChunksInPart(self.win.assy)
             params = len(peptideList)
         
         print "_currentStructureParams(): params:", params
@@ -275,22 +287,23 @@ class BuildProtein_PropertyManager(EditCommand_PM):
         """
         #Clear tags, if any, due to the selection in the self.strandListWidget.
         #self.peptideListWidget.clear()
-        self.sequenceEditor.hide()
         env.history.statusbar_msg("")
         EditCommand_PM.close(self)
         return
     
     def show(self):
         """
-        Show this PM. It also shows the Sequence Editor widget and hides 
-        the history widget.
+        Show the PM. Extends superclass method.
+        @note: _update_UI_do_updates() gets called immediately after this and
+               updates PM widgets with their correct values/settings. 
         """
         
         env.history.statusbar_msg("")
-        self._showPeptideSequenceEditor()
-        
         EditCommand_PM.show(self)
         
+        # NOTE: Think about moving this msg to _update_UI_do_updates() where
+        # custom msgs can be created based on the current selection, etc.
+        # Mark 2008-12-14
         msg = "Select <b>Insert Peptide</b> to create a peptide chain or "\
             "select another modeling tool to modify an existing protein."
         self.updateMessage(msg)
@@ -298,29 +311,23 @@ class BuildProtein_PropertyManager(EditCommand_PM):
     
     def _editPeptide(self):  
         """
-        Opens the sequence editor for the selected peptide.
+        Slot for the "Edit Properties" button. 
         """
         
+        #if not self.command.hasValidStructure():
+        #    return
+        
         peptideChunk = self.getSelectedProteinChunk()
         
         if peptideChunk:
-            sequence = peptideChunk.protein.get_sequence_string()
-            self.sequenceEditor.setSequence(sequence)
-            secStructure = peptideChunk.protein.get_secondary_structure_string()
-            self.sequenceEditor.setSecondaryStructure(secStructure)
-            self.sequenceEditor.setRuler(len(secStructure)) 
-            self.sequenceEditor.show()
+            peptideChunk.protein.edit(self.win)
         return
     
-    def _showPeptideSequenceEditor(self):
+    def _compareProteins(self):
         """
-        Show/hide sequence editor. It is only displayed if there is
-        a single peptide selected. Otherwise it is hidden.
+        Slot for the "Compare Proteins" button.
         """
-        if self.getSelectedProteinChunk():
-            self.sequenceEditor.show()
-        else:
-            self.sequenceEditor.hide()
+        self.win.commandSequencer.userEnterCommand('COMPARE_PROTEINS')
         return
     
     def _addWhatsThisText( self ):
@@ -357,15 +364,21 @@ class BuildProtein_PropertyManager(EditCommand_PM):
         
         self.editPeptidePropertiesButton = PM_PushButton(pmGroupBox,
                                                          label = "",
-                                                         text  = "Edit Sequence" )
+                                                         text  = "Edit Properties..." )
         self.editPeptidePropertiesButton.setEnabled(False)
+        
+        self.compareProteinsButton = PM_PushButton(pmGroupBox,
+                                                         label = "",
+                                                         text  = "Compare Proteins..." )
+        self.compareProteinsButton.setEnabled(False)
+        
         return
     
     def updatePeptideListWidget(self):   
         """
         Update the peptide list widget. It shows all peptides in the part.
         """
-        peptideChunkList = self.getAllProteinChunksInPart()
+        peptideChunkList = getAllProteinChunksInPart(self.win.assy)
         
         if peptideChunkList:
             self.peptideListWidget.insertItems(
@@ -427,11 +440,9 @@ class BuildProtein_PropertyManager(EditCommand_PM):
             return None
         return
     
-    # getAllProteinChunksInPart() should eventually be moved to assy or some other class.
-    # This should wait until we have a data model implemented for 
-    # peptides/proteins.
-    # Ask Bruce. Mark 2008-12-12
-    def getAllProteinChunksInPart(self):
+    # getAllProteinChunksInPart() has been moved to Protein.py
+    # Mark 2008-12-14
+    def getAllProteinChunksInPart_MOVED(self):
         """
         Returns a list of all the protein chunks in the current assy.
         
@@ -444,141 +455,4 @@ class BuildProtein_PropertyManager(EditCommand_PM):
                 peptideList.append(mol)
         return peptideList
     
-    # --------------------------------------------------------------------
-    # Deprecated methods to keep until we're certain this is working.
-    # --Mark 2008-12-12.
-    
-    
-    def _editPeptide_DEPRECATED(self):  
-        """
-        Opens the sequence editor for the selected peptide.
-        """
-        
-        selectedPeptideList = self.win.assy.getSelectedProteinChunks()
-        
-        if len(selectedPeptideList) == 1:     
-            peptideChunk = selectedPeptideList[0]
-            sequence = peptideChunk.protein.get_sequence_string()
-            self.sequenceEditor.setSequence(sequence)
-            secStructure = peptideChunk.protein.get_secondary_structure_string()
-            self.sequenceEditor.setSecondaryStructure(secStructure)
-            self.sequenceEditor.setRuler(len(secStructure)) 
-            self.sequenceEditor.show()
-        return
-    
-    def _updateProteinParameters_DEPRECATED(self, index):
-        """
-        Update number of amino acids and sequence editor, as well as set the
-        current protein pdb id which will be used in the child commands and for
-        rosetta simulation from inside the build protein mode.
-        @param index: index of the protein combo box
-        @type index: int
-        """
-        for mol in self.protein_chunk_list:
-            if  mol.name == self.peptideListComboBox.currentText():
-                self._numberOfAA = len(mol.protein.get_sequence_string())
-                self.numberOfAASpinBox.setValue(self._numberOfAA)
-                sequence = mol.protein.get_sequence_string()
-                self.sequenceEditor.setSequence(sequence)
-                secStructure = mol.protein.get_secondary_structure_string()
-                self.sequenceEditor.setSecondaryStructure(secStructure)
-                self.sequenceEditor.setRuler(len(secStructure))
-                break
-        self.set_current_protein_chunk_name(mol.name) 
-        env.history.statusbar_msg("")
-        
-        self._editPeptideSequence() #@@@
-        
-        return
-    
-    def _updateProteinList_DEPRECATED(self):
-        """
-        Update the list of proteins so that the protein name combo box in this 
-        PM can be populated.
-        """
-        self.protein_chunk_list = []
-        self.protein_name_list = []
-        for mol in self.win.assy.molecules:
-            if mol.isProteinChunk():
-                self.protein_chunk_list.append(mol)
-                self.protein_name_list.append(mol.name)
-        return
-    
-    
-    def _showProteinParametersAndSequenceEditor_DEPRECATED(self):
-        """
-        Show/ Hide protein parameters and sequence editor based on if there's
-        any protein in NE-1 part.
-        """
-        part = self.win.assy.part  
-        proteinExists, proteinChunk = checkIfProteinChunkInPart(part)
-        if proteinExists:
-            #check to see if current_protein is still in part, otherwise set 
-            # this to first available protein
-            try:
-                index = self.peptideListComboBox.findText(self.current_protein)
-                index1 = self.protein_name_list.index(self.current_protein)
-            except ValueError:
-                index = 0
-                index1 = 0
-                self.set_current_protein_chunk_name(self.protein_name_list[index1])
-                
-            self.peptideListComboBox.setCurrentIndex(index)
-            proteinChunk = self.protein_chunk_list[index1]            
-            self._numberOfAA = len(proteinChunk.protein.get_sequence_string())
-        else:  
-            #remove all items from the combo box
-            count = self.peptideListComboBox.count()
-            for i in range(count):
-                self.peptideListComboBox.removeItem(0)
-            self._numberOfAA = 0
-            self.set_current_protein_chunk_name("")
-        self.numberOfAASpinBox.setValue(self._numberOfAA)
-        
-        
-        #get the sequence for this protein chunk
-        if proteinExists:
-            sequence = proteinChunk.protein.get_sequence_string()
-            self.sequenceEditor.setSequence(sequence)
-            secStructure = proteinChunk.protein.get_secondary_structure_string()
-            self.sequenceEditor.setSecondaryStructure(secStructure)
-            self.sequenceEditor.setRuler(len(secStructure)) 
-            self.editPropertiesPushButton.setEnabled(True)
-        else:
-            self.editPropertiesPushButton.setEnabled(False)
-        self.sequenceEditor.hide()  
-        return
-    
-    def _updateProteinListForShow_DEPRECATED(self):
-        """
-        Update the list of proteins in the combo box in the PM.
-        """
-        #first remove from combo box all the proteins that do not exist in NE-1
-        #part anymore
-        currentProteinNameList = []
-        for mol in self.win.assy.molecules:
-            currentProteinNameList.append(mol.name)
-         
-        for name in self.protein_name_list:   
-            try:
-                index = currentProteinNameList.index(name) 
-            except ValueError:    
-                #protein does not exist any more, need to remove it
-                i = self.protein_name_list.index(name)
-                self.protein_chunk_list.pop(i)
-                self.protein_name_list.pop(i)
-                j = self.peptideListComboBox.findText(name)
-                self.peptideListComboBox.removeItem(j)
-        
-        for mol in self.win.assy.molecules:
-            #if molecules does not already exist in combo box list, need to add 
-            #them
-            if mol.isProteinChunk(): 
-                try:
-                    self.protein_name_list.index(mol.name)
-                except ValueError:    
-                    self.protein_chunk_list.append(mol)
-                    self.protein_name_list.append(mol.name)
-                    self.peptideListComboBox.addItem(mol.name)
-        return
     
 \ No newline at end of file
diff --git a/cad/src/protein/commands/CompareProteins/CompareProteins_PropertyManager.py b/cad/src/protein/commands/CompareProteins/CompareProteins_PropertyManager.py
index 8540e4370..85a13baf4 100644
--- a/cad/src/protein/commands/CompareProteins/CompareProteins_PropertyManager.py
+++ b/cad/src/protein/commands/CompareProteins/CompareProteins_PropertyManager.py
@@ -10,6 +10,11 @@ Build > Protein mode.
 @version: $Id$ 
 @copyright: 2008 Nanorex, Inc. See LICENSE file for details.
 
+To do:
+- Switch display styles of selected proteins to diPROTEIN (instead of the GDS).
+- fix bug: Leaving Compare command unselects the two selected protein chunks.
+  The "Build Protein" PM list widget shows them as selected and the compare button is enabled,
+  but they are not selected in the graphics area.
 """
 
 import foundation.env as env
@@ -21,18 +26,19 @@ from utilities.constants import yellow
 from PyQt4.Qt import SIGNAL
 from PM.PM_PushButton   import PM_PushButton
 from PM.PM_GroupBox import PM_GroupBox
-from PM.PM_ComboBox import PM_ComboBox
+from PM.PM_LineEdit import PM_LineEdit
 from PM.PM_DoubleSpinBox import PM_DoubleSpinBox
 from PM.PM_Constants import PM_DONE_BUTTON
 from PM.PM_Constants import PM_WHATS_THIS_BUTTON
-
+from protein.model.Protein import getAllProteinChunksInPart
+from utilities.constants import diPROTEIN
+from utilities.Log import redmsg
 
 _superclass = Command_PropertyManager
 class CompareProteins_PropertyManager(Command_PropertyManager):
     """
-    The ProteinDisplayStyle_PropertyManager class provides a Property Manager 
-    for the B{Display Style} command on the flyout toolbar in the 
-    Build > Protein mode. 
+    The CompareProteins_PropertyManager class provides a Property Manager 
+    for the B{Compare Proteins} command on the Build Protein flyout toolbar. 
 
     @ivar title: The title that appears in the property manager header.
     @type title: str
@@ -44,62 +50,82 @@ class CompareProteins_PropertyManager(Command_PropertyManager):
     @ivar iconPath: The relative path to the PNG file that contains a
                     22 x 22 icon image that appears in the PM header.
     @type iconPath: str
+    
+    @ivar proteinChunk1: The first currently selected protein to be compared.
+    @type proteinChunk1: protein chunk
+    
+    @ivar proteinChunk2: The second currently selected protein to be compared.
+    @type proteinChunk2: protein chunk
     """
 
-    title         =  "Compare Proteins"
-    pmName        =  title
-    iconPath      =  "ui/actions/Command Toolbar/BuildProtein/Compare.png"
-
+    title          =  "Compare Proteins"
+    pmName         =  title
+    iconPath       =  "ui/actions/Command Toolbar/BuildProtein/Compare.png"
+    proteinChunk1  =  None
+    proteinChunk2  =  None
     
     def __init__( self, command ):
         """
         Constructor for the property manager.
-        """
-
-                     
-        self.currentWorkingDirectory = env.prefs[workingDirectory_prefs_key]
-        
+        """        
         self.threshold = 10.0
         
         _superclass.__init__(self, command)
 
         self.showTopRowButtons( PM_DONE_BUTTON | \
                                 PM_WHATS_THIS_BUTTON)
-
-        msg = "Select two protein structures to compare."
-        self.updateMessage(msg)
+        return
 
     def connect_or_disconnect_signals(self, isConnect = True):
         
         if isConnect:
             change_connect = self.win.connect
         else:
-            change_connect = self.win.disconnect 
+            change_connect = self.win.disconnect
         
-        #change_connect(self.nextAAPushButton,
-        #               SIGNAL("clicked()"),
-        #               self._expandNextRotamer)
+        change_connect(self.comparePushButton,
+                       SIGNAL("clicked()"),
+                       self._compareProteins)
         
-    #Protein Display methods         
-
-
+        change_connect(self.thresholdDoubleSpinBox,
+                       SIGNAL("valueChanged(double)"),
+                       self._thresholdChanged)
+        
+        change_connect(self.hidePushButton,
+                       SIGNAL("clicked()"),
+                       self._hideDifferences)
+        return
+    
+    def close(self):
+        """
+        Closes the Property Manager. Overrides EditCommand_PM.close()
+        """
+        
+        env.history.statusbar_msg("")
+        self._resetAminoAcids()
+        _superclass.close(self)
+        
+        # Restore the original global display style.
+        self.o.setGlobalDisplayStyle(self.originalDisplayStyle)
+        return
+    
     def show(self):
         """
-        Shows the Property Manager. Extends superclass method. 
+        Show the PM. Extends superclass method.
+        
+        @note: _update_UI_do_updates() gets called immediately after this and
+               updates PM widgets with their correct values/settings.
         """
-        #@REVIEW: Why does it create sequence editor here? Also, is it
-        #required to be done before the superclass.show call? --Ninad 2008-10-02
-        self.sequenceEditor = self.win.createProteinSequenceEditorIfNeeded()
-        self.sequenceEditor.hide()
         _superclass.show(self)
+        env.history.statusbar_msg("")
         
-        self._updateProteinList()
-        self.structure1ComboBox.clear()
-        self.structure1ComboBox.addItems(self.protein_name_list)
-        self.structure2ComboBox.clear()
-        self.structure2ComboBox.addItems(self.protein_name_list)
-        
-   
+        # Force the Global Display Style to "Protein" since this is the only way
+        # to see comparisons. The global display style will be restored when leaving
+        # this command (via self.close()). 
+        self.originalDisplayStyle = self.o.displayMode
+        self.o.setGlobalDisplayStyle(diPROTEIN)
+        return
+    
     def _addGroupBoxes( self ):
         """
         Add the Property Manager group boxes.
@@ -107,6 +133,7 @@ class CompareProteins_PropertyManager(Command_PropertyManager):
         self._pmGroupBox1 = PM_GroupBox( self,
                                          title = "Compare")
         self._loadGroupBox1( self._pmGroupBox1 )
+        return
         
     def _addWhatsThisText( self ):
         """
@@ -120,33 +147,22 @@ class CompareProteins_PropertyManager(Command_PropertyManager):
         """
         pass
     
-
-    def _updateProteinList(self):
-        """
-        """
-        self.protein_chunk_list = []
-        self.protein_name_list = []
-        for mol in self.win.assy.molecules:
-            if mol.isProteinChunk():
-                self.protein_chunk_list.append(mol)
-                self.protein_name_list.append(mol.name)
-        
     def _loadGroupBox1(self, pmGroupBox):
         """
         Load widgets in group box.
         """
         
-        self._updateProteinList()
-        
-        self.structure1ComboBox = PM_ComboBox( pmGroupBox,
-                                 label         =  "First structure:",
-                                 choices       =  self.protein_name_list,
-                                 setAsDefault  =  False)
+        self.structure1LineEdit = \
+            PM_LineEdit( pmGroupBox,
+                         label         =  "First structure:",
+                         setAsDefault  =  False)
+        self.structure1LineEdit.setEnabled(False)
 
-        self.structure2ComboBox = PM_ComboBox( pmGroupBox,
-                                 label         =  "Second structure:",
-                                 choices       =  self.protein_name_list,
-                                 setAsDefault  =  False)
+        self.structure2LineEdit = \
+            PM_LineEdit( pmGroupBox,
+                         label         =  "Second structure:",
+                         setAsDefault  =  False)
+        self.structure2LineEdit.setEnabled(False)
 
         self.thresholdDoubleSpinBox  =  \
             PM_DoubleSpinBox( pmGroupBox,
@@ -159,40 +175,37 @@ class CompareProteins_PropertyManager(Command_PropertyManager):
                               singleStep    =  30.0,
                               suffix        = " deg",
                               spanWidth = False)
-
-        self.win.connect(self.thresholdDoubleSpinBox,
-                         SIGNAL("valueChanged(double)"),
-                         self._thresholdChanged)
         
         self.comparePushButton  = \
             PM_PushButton( pmGroupBox,
                          text         =  "Compare",
                          setAsDefault  =  True)
         
-        self.win.connect(self.comparePushButton,
-                         SIGNAL("clicked()"),
-                         self._compareProteins)
-        
         self.hidePushButton  = \
             PM_PushButton( pmGroupBox,
                          text         =  "Hide differences",
                          setAsDefault  =  True)
-        
-        self.win.connect(self.hidePushButton,
-                         SIGNAL("clicked()"),
-                         self._hideDifferences)
+        return
         
     def _compareProteins(self):
         """
+        Slot for Compare button.
+        
+        Compares two selected proteins of the same length.
+        Amino acids that differ greater than the "threshold" 
+        value are displayed in two colors (red for the first protein 
+        and yellow for the second protein) and are only visible when
+        the two proteins are displayed in the
+        reduced display style.
         """
         from utilities.constants import red, orange, green, cyan
         
-        if len(self.protein_chunk_list) == 0 or \
-           len(self.protein_chunk_list) == 0:
+        if not self.proteinChunk1 or \
+           not self.proteinChunk2:
             return
         
-        protein_1 = self.protein_chunk_list[self.structure1ComboBox.currentIndex()].protein
-        protein_2 = self.protein_chunk_list[self.structure2ComboBox.currentIndex()].protein
+        protein_1 = self.proteinChunk1.protein
+        protein_2 = self.proteinChunk2.protein
         
         if protein_1 and \
            protein_2:
@@ -234,32 +247,119 @@ class CompareProteins_PropertyManager(Command_PropertyManager):
                         
                 self.win.glpane.gl_update()
             else:
-                env.history.redmsg("The lengths of compared proteins are not equal.")
+                msg = "The lengths of compared proteins are not equal."
+                self.updateMessage(msg)
+                env.history.redmsg(msg)
+        return
 
     def _hideDifferences(self):
         """
+        Slot for the "Hide differences" button.
+        
+        Hides amino acids that differ greater than the "threshold" value. 
+        
+        @warning: Untested. Code looks suspicious.
         """
-        if len(self.protein_chunk_list) == 0 or \
-           len(self.protein_chunk_list) == 0:
+        if not self.proteinChunk1 or \
+           not self.proteinChunk2:
             return
         
-        protein_1 = self.protein_chunk_list[self.structure1ComboBox.currentIndex()].protein
-        protein_2 = self.protein_chunk_list[self.structure2ComboBox.currentIndex()].protein
+        protein_1 = self.proteinChunk1.protein
+        protein_2 = self.proteinChunk2.protein
         
         if protein_1 and \
            protein_2:
             aa_list_1 = protein_1.get_amino_acids()
             aa_list_2 = protein_2.get_amino_acids()
             if len(aa_list_1) == len(aa_list_2):
-                protein_1.collapse_all_rotamers()
-                protein_2.collapse_all_rotamers()
+                protein_1.collapse_all_rotamers() #@@@
+                protein_2.collapse_all_rotamers() #@@@
                 for aa1, aa2 in zip (aa_list_1, aa_list_2):
                     aa1.color = None
                     aa2.color = None
                     aa1.collapse()
                     aa2.collapse()
-
+            self.win.glpane.gl_update()
+        return
+    
     def _thresholdChanged(self, value):
+        """
+        Slot for Threshold spinbox.
+        """
         self.threshold = value
         self._compareProteins()
+        return
+    
+    def _resetAminoAcids(self):
+        """
+        Resets the color and collapse all amino acids of all proteins.
+        """
+        
+        proteinChunkList = getAllProteinChunksInPart(self.win.assy)
+        
+        for proteinChunk in proteinChunkList:
+            proteinChunk.protein.collapse_all_rotamers()
+            aa_list = proteinChunk.protein.get_amino_acids()
+            for aa in aa_list:
+                aa.color = None
+                aa.collapse()
+                
+        self.win.glpane.gl_update()
+        return
         
+    def _update_UI_do_updates(self):
+        """
+        Overrides superclass method. 
+        
+        @see: Command_PropertyManager._update_UI_do_updates()
+        """
+        
+        self.proteinChunk1 = None
+        self.proteinChunk2 = None
+        self.comparePushButton.setEnabled(False)
+        self.hidePushButton.setEnabled(False)
+        
+        selectedProteinList = self.win.assy.getSelectedProteinChunks()
+        
+        if len(selectedProteinList) == 0:
+            self.structure1LineEdit.setText("")
+            self.structure2LineEdit.setText("")
+            msg = "Select two structures of the same length in the graphics area, "\
+                "then click the <b>Compare</b> button to compare them."
+        
+        elif len(selectedProteinList) == 1:
+            self.proteinChunk1 = selectedProteinList[0]
+            aa1_count = " (%d)" % self.proteinChunk1.protein.count_amino_acids()
+            self.structure1LineEdit.setText(self.proteinChunk1.name + aa1_count)
+            self.structure2LineEdit.setText("")
+            msg = "Select one more structure in the graphics area that is the same "\
+                "length as <b>" + self.proteinChunk1.name + "</b>. "\
+                "Then click the <b>Compare</b> button to compare them."
+        
+        elif len(selectedProteinList) == 2:
+            self.proteinChunk1 = selectedProteinList[0]
+            aa1_count = " (%d)" % self.proteinChunk1.protein.count_amino_acids()
+            self.structure1LineEdit.setText(self.proteinChunk1.name + aa1_count)
+            
+            self.proteinChunk2 = selectedProteinList[1]
+            aa2_count = " (%d)" % self.proteinChunk2.protein.count_amino_acids()
+            self.structure2LineEdit.setText(self.proteinChunk2.name + aa2_count)
+            
+            if aa1_count == aa2_count:
+                self.comparePushButton.setEnabled(True)
+                self.hidePushButton.setEnabled(True)
+                msg = "Click the <b>Compare</b> button to compare the two selected structures."
+            else:
+                msg = "<b>%s</b> and <b>%s</b> are not the same length." % \
+                    (self.proteinChunk1.name, self.proteinChunk2.name)
+                msg = redmsg(msg)
+                
+        else:
+            self.structure1LineEdit.setText("")
+            self.structure2LineEdit.setText("")
+            msg = redmsg("Too many proteins selected.")
+        
+        self.updateMessage(msg)
+        env.history.redmsg(msg)
+        return
+    
diff --git a/cad/src/protein/commands/EditRotamers/EditRotamers_PropertyManager.py b/cad/src/protein/commands/EditRotamers/EditRotamers_PropertyManager.py
index e50d29101..6c0631526 100644
--- a/cad/src/protein/commands/EditRotamers/EditRotamers_PropertyManager.py
+++ b/cad/src/protein/commands/EditRotamers/EditRotamers_PropertyManager.py
@@ -19,6 +19,7 @@ To do:
 - Add "Number of AA:" field (disabled).
 - Include name of the current peptide in the title of the Sequence Editor.
 - Sync Residue combobox and sequence editor (or remove one or the other).
+- Add wait (hourglass) cursor when changing the display style of proteins.
 """
 import os, time, fnmatch, string
 import foundation.env as env
@@ -156,10 +157,15 @@ class EditRotamers_PropertyManager(Command_PropertyManager):
         aa_list = self.current_protein.protein.get_amino_acid_id_list()
         for j in range(len(aa_list)):
             self.aminoAcidsComboBox.addItem(aa_list[j])
-            
+        
+        # This doesn't generate a signal (only 'activate' is connected to 
+        # slot _aminoAcidChanged).
         self.aminoAcidsComboBox.setCurrentIndex(
             self.current_protein.protein.get_current_amino_acid_index())
         
+        # Call the slot explicitly. This is needed to draw the rotamer
+        # on top of the reduced model of the current protein.
+        # Also see the comments in _update_UI_do_updates().
         self._aminoAcidChanged(
             self.current_protein.protein.get_current_amino_acid_index())
         
@@ -191,16 +197,17 @@ class EditRotamers_PropertyManager(Command_PropertyManager):
         if self.current_protein:
             self.current_protein.setDisplayStyle(self.previous_protein_display_style)
             self.previous_protein = None
-        EditCommand_PM.close(self)
+        _superclass.close(self)
         return
     
     def show(self):
         """
-        Extends superclass method.
+        Show the PM. Extends superclass method.
+        @note: _update_UI_do_updates() gets called immediately after this and
+               updates PM widgets with their correct values/settings.
         """
         _superclass.show(self)
         
-        #self._update_UI_do_updates() #@@@
         self.updateMessage("Edit...")
         self.sequenceEditor.show()
         env.history.statusbar_msg("")
@@ -475,6 +482,7 @@ class EditRotamers_PropertyManager(Command_PropertyManager):
         
     def _aminoAcidChanged(self, index):
         """
+        Slot for the "Current residue" combobox.
         """
         if not self.current_protein:
             return
@@ -548,6 +556,16 @@ class EditRotamers_PropertyManager(Command_PropertyManager):
             print "_update_UI_do_updates(): DO NOTHING."
             return
         
+        # NOTE: Changing the display styles of the protein chunks can take some
+        # time. We should put up the wait (hourglass) cursor here and restore 
+        # before returning.
+        
+        # Update all PM widgets that need to be since something has changed.
+        print "_update_UI_do_updates(): UPDATING the PMGR."
+        self.update_name_field()
+        self.update_sequence_editor()
+        self.update_residue_combobox()
+        
         
         if self.previous_protein:
             self.previous_protein.setDisplayStyle(self.previous_protein_display_style)
@@ -558,104 +576,4 @@ class EditRotamers_PropertyManager(Command_PropertyManager):
             self.previous_protein_display_style = self.current_protein.getDisplayStyle()
             self.current_protein.setDisplayStyle(diPROTEIN)
         
-        # Update all PM widgets that need to be since something has changed.
-        # NOTE: This must happen after the display style has been changed,
-        # or the rotamer doesn't show up on the protein the first time it is
-        # drawn in diPROTEIN.
-        print "_update_UI_do_updates(): UPDATING the PMGR."
-        self.update_name_field()
-        self.update_residue_combobox()        
-        self.update_sequence_editor()
-        return
-    
-    # =========================================================================
-    # Deprecated methods. Keep them below for reference until everything is 
-    # working.
-    
-    def _expandNextRotamer_DEPRECATED(self):
-        """
-        """
-        for chunk in self.win.assy.molecules:
-            #Urmi 20080728: slot method for the current protein from build protein mode
-            if chunk.isProteinChunk() and chunk.name == self.current_protein:
-                chunk.protein.traverse_forward()
-                self._display_and_recenter()
-                self._updateAminoAcidInfo(
-                    chunk.protein.get_current_amino_acid_index())
-                return
-        return
-    
-    def _expandPreviousRotamer_DEPRECATED(self):
-        """
-        """
-        for chunk in self.win.assy.molecules:
-            #Urmi 20080728: slot method for the current protein from build protein mode
-            if chunk.isProteinChunk() and chunk.name == self.current_protein:
-                chunk.protein.traverse_backward()
-                self._display_and_recenter()
-                self._updateAminoAcidInfo(
-                    chunk.protein.get_current_amino_acid_index())
-                return
-        return
-    
-    def _collapseAllRotamers_DEPRECATED(self):
-        """
-        """
-        for chunk in self.win.assy.molecules:
-            #Urmi 20080728: slot method for the current protein from build protein mode
-            if chunk.isProteinChunk() and chunk.name == self.current_protein:
-                chunk.protein.collapse_all_rotamers()
-                self.win.glpane.gl_update()
-                return
-        return
-        
-    def _expandAllRotamers_DEPRECATED(self):
-        """
-        """
-        for chunk in self.win.assy.molecules:
-            #Urmi 20080728: slot method for the current protein from build protein mode
-            if chunk.isProteinChunk() and chunk.name == self.current_protein:
-                chunk.protein.expand_all_rotamers()
-                self.win.glpane.gl_update()
-                return
-        return
-    
-    def _display_and_recenter_DEPRECATED(self):
-        """
-        """
-        for chunk in self.win.assy.molecules:
-            #Urmi 20080728: display and recenter for the current protein 
-            #from build protein mode
-            if chunk.isProteinChunk() and chunk.name == self.current_protein:
-                chunk.protein.collapse_all_rotamers()
-                current_aa = chunk.protein.get_current_amino_acid()
-                if current_aa:
-                    chunk.protein.expand_rotamer(current_aa)
-                    self._update_chi_angles(current_aa)
-                    if self.recenterViewCheckBox.isChecked():
-                        ca_atom = current_aa.get_c_alpha_atom()
-                        if ca_atom:
-                            self.win.glpane.pov = -ca_atom.posn()                            
-                    
-                    self.win.glpane.gl_update()
-        return
-    
-    def _aminoAcidChanged_DEPRECATED(self, index):
-        """
-        """
-        for chunk in self.win.assy.molecules:
-            #Urmi 20080728: slot method for the current protein from build protein mode
-            if chunk.isProteinChunk() and chunk.name == self.current_protein:
-                chunk.protein.set_current_amino_acid_index(index)
-
-                self._display_and_recenter()
-        
-        #Urmi 20080728: change the cursor position in the sequence editor 
-        # when current amino acid in the amino acid combo box is changed
-        cursor = self.sequenceEditor.sequenceTextEdit.textCursor()
-        if index == -1:
-            index = 0
-        cursor.setPosition(index, QTextCursor.MoveAnchor)       
-        cursor.setPosition(index + 1, QTextCursor.KeepAnchor) 
-        self.sequenceEditor.sequenceTextEdit.setTextCursor( cursor )
         return
diff --git a/cad/src/protein/model/Protein.py b/cad/src/protein/model/Protein.py
index f3b82c195..3a9d4cc10 100644
--- a/cad/src/protein/model/Protein.py
+++ b/cad/src/protein/model/Protein.py
@@ -384,6 +384,12 @@ class Protein:
         """
         return self.residues_list
     
+    def count_amino_acids(self):
+        """
+        Returns the number of amino acids.
+        """
+        return len(self.residues_list)
+    
     def assign_helix(self, resId):
         """
         Assign a helical secondary structure to resId.
@@ -625,11 +631,27 @@ class Protein:
                the actual model. Maybe we'll take care of that when we move to the
                new model
         """ 
-        win.commandSequencer.userEnterCommand('MODEL_AND_SIMULATE_PROTEIN')
+        win.commandSequencer.userEnterCommand('EDIT_ROTAMERS')
         return
        
     pass # end of class Protein
 
+
+# Protein helper methods should be located here.
+# Mark 2008-12-14
+def getAllProteinChunksInPart(assy):
+    """
+    Returns a list of all the protein chunks in assy.
+    
+    @return: a list of all the protein chunks in assy.
+    @rtype: list of chunks
+    """
+    proteinChunkList = []
+    for mol in assy.molecules:
+        if mol.isProteinChunk():
+            proteinChunkList.append(mol)
+    return proteinChunkList
+
 # piotr 082008: This and possibly several Rosetta-related methods of the Protein 
 # class should be re-factored and moved to a separate file in simulations/ROSETTA.
author	Mark Sims <mark@nanorex.com>	2008-12-15 08:19:00 +0000
committer	Mark Sims <mark@nanorex.com>	2008-12-15 08:19:00 +0000
commit	45b38837bab330154258b546ab21c32d3b3118cf (patch)
tree	ffcb27745b7a2f4f8abeed8996ca27e59142de40
parent	d075219cd37628fed2e71a508bd2deea9dc06691 (diff)
download	nanoengineer-theirix-45b38837bab330154258b546ab21c32d3b3118cf.tar.gz nanoengineer-theirix-45b38837bab330154258b546ab21c32d3b3118cf.zip