Renamed class PeptideLineMode to PeptideLine_GraphicsMode. Cleaned up code docstrings and variable names. Also added more comments that were sorely needed.

author: Mark Sims <mark@nanorex.com> 2008-12-23 21:24:51 +0000
committer: Mark Sims <mark@nanorex.com> 2008-12-23 21:24:51 +0000
commit: 7704e22b57466a1f51294169bd5828457999ad7a (patch)
tree: aa8c0739777387bfebe62b69fdc417fc6a73e23b
parent: 798c3f541ec33c797c3cf80945b952f68af531ed (diff)
download: nanoengineer-theirix-7704e22b57466a1f51294169bd5828457999ad7a.tar.gz
nanoengineer-theirix-7704e22b57466a1f51294169bd5828457999ad7a.zip
4 files changed, 128 insertions, 103 deletions
diff --git a/cad/src/graphics/drawing/drawPeptideTrace.py b/cad/src/graphics/drawing/drawPeptideTrace.py
index 188f62f9e..d4718b97c 100644
--- a/cad/src/graphics/drawing/drawPeptideTrace.py
+++ b/cad/src/graphics/drawing/drawPeptideTrace.py
@@ -28,35 +28,49 @@ from utilities.constants import blue, gray
 
 from protein.commands.InsertPeptide.PeptideGenerator import get_unit_length
 
-def drawPeptideTrace_new(mol):
-
-    if mol and \
-       mol.atoms:
+def drawPeptideTrace(alphaCarbonProteinChunk):
+    """
+    Draws a protein backbone trace using atoms stored in 
+    I{alphaCarbonProteinChunk}.
+    
+    @param alphaCarbonProteinChunk: a special (temporary) chunk that contains 
+                                    only the alpha carbon atoms in the peptide 
+                                    backbone
+    @param alphaCarbonProteinChunk: Chunk
+    
+    @see PeptideLine_GraphicsMode.Draw(), PeptideGenerator.make_aligned()
+    """
 
+    if alphaCarbonProteinChunk and alphaCarbonProteinChunk.atoms:
         last_pos = None
-    
-        atomitems = mol.atoms.items()
-        
+        atomitems = alphaCarbonProteinChunk.atoms.items()
         atomitems.sort() 
-        atlist = [atom for (key, atom) in atomitems] 
+        alphaCarbonAtomsList = [atom for (key, atom) in atomitems] 
         
-        for atom in atlist:
+        for atom in alphaCarbonAtomsList:
             drawsphere(blue, atom.posn(), 0.2, 1)
             if last_pos:
                 drawline(gray, last_pos, atom.posn(), width=2)
             last_pos = atom.posn()
-
-def drawPeptideTrace(endCenter1,  
-                     endCenter2,
-                     phi, 
-                     psi,
-                     glpaneScale,
-                     lineOfSightVector,
-                     beamThickness = 2.0,
-                     beam1Color = None, 
-                     beam2Color = None,
-                     stepColor = None
-                     ):
+            pass
+        pass
+    return
+
+# drawPeptideTrace_orig is the original function for drawing a peptide
+# trace. This function is deprecated and marked for removal. I'm keeping it
+# here for reference for the time being.
+# --Mark 2008-12-23
+def drawPeptideTrace_orig(endCenter1,  
+                          endCenter2,
+                          phi, 
+                          psi,
+                          glpaneScale,
+                          lineOfSightVector,
+                          beamThickness = 2.0,
+                          beam1Color = None, 
+                          beam2Color = None,
+                          stepColor  = None
+                          ):
     """
     Draws the Peptide in a schematic display.
     
@@ -88,6 +102,7 @@ def drawPeptideTrace(endCenter1,
     @see: B{DnaLineMode.Draw } (where it is used) for comments on color 
           convention
 
+    @deprecated: Use drawPeptideTrace() instead.
     """   
 
     ladderWidth = 3.0
@@ -172,3 +187,4 @@ def drawPeptideTrace(endCenter1,
                                 
     glPopMatrix()
     glEnable(GL_LIGHTING)
+    return
diff --git a/cad/src/protein/commands/InsertPeptide/InsertPeptide_EditCommand.py b/cad/src/protein/commands/InsertPeptide/InsertPeptide_EditCommand.py
index 881e17e1a..cc93183f6 100644
--- a/cad/src/protein/commands/InsertPeptide/InsertPeptide_EditCommand.py
+++ b/cad/src/protein/commands/InsertPeptide/InsertPeptide_EditCommand.py
@@ -15,7 +15,7 @@ from command_support.EditCommand import EditCommand
 from protein.commands.InsertPeptide.PeptideGenerator import PeptideGenerator
 from utilities.constants import gensym
 from commands.SelectChunks.SelectChunks_GraphicsMode import SelectChunks_GraphicsMode
-from protein.temporary_commands.PeptideLineMode import PeptideLine_GM
+from protein.temporary_commands.PeptideLine_GraphicsMode import PeptideLine_GraphicsMode
 from utilities.debug import print_compact_stack, print_compact_traceback
 
 import foundation.env as env
@@ -24,10 +24,8 @@ from utilities.prefs_constants import cursorTextColor_prefs_key
 from protein.commands.BuildProtein.BuildProtein_Command import BuildProtein_Command
 from protein.commands.InsertPeptide.InsertPeptide_PropertyManager import InsertPeptide_PropertyManager
 
-#_superclass = BuildProtein_Command
 _superclass = EditCommand
 class InsertPeptide_EditCommand(EditCommand):
-#class InsertPeptide_EditCommand(BuildProtein_Command):
 
     PM_class = InsertPeptide_PropertyManager
     
@@ -43,10 +41,8 @@ class InsertPeptide_EditCommand(EditCommand):
 
     create_name_from_prefix  =  True 
     
-    #GraphicsMode_class = SelectChunks_GraphicsMode
-    #Graphics Mode set to Peptide graphics mode
-    GraphicsMode_class = PeptideLine_GM
-    #required by NanotubeLine_GM
+    GraphicsMode_class = PeptideLine_GraphicsMode
+    #required by PeptideLine_GraphicsMode
     mouseClickPoints = []
     
     structGenerator = PeptideGenerator()
@@ -58,10 +54,10 @@ class InsertPeptide_EditCommand(EditCommand):
         """
         Constructor for InsertPeptide_EditCommand
         """
-
         _superclass.__init__(self, commandSequencer)        
-        #Maintain a list of peptide segments created while this command was running. 
-        self._segmentList = []
+        #Maintain a list of peptides created while this command is running. 
+        self._peptideList = []
+        return
         
     def command_entered(self):
         """
@@ -71,26 +67,27 @@ class InsertPeptide_EditCommand(EditCommand):
         _superclass.command_entered(self)
         #NOTE: Following code was copied from self.init_gui() that existed 
         #in old command API -- Ninad 2008-09-18
-        if isinstance(self.graphicsMode, PeptideLine_GM):            
+        if isinstance(self.graphicsMode, PeptideLine_GraphicsMode):            
             self._setParamsForPeptideLineGraphicsMode()
             self.mouseClickPoints = []
-        #Clear the segmentList as it may still be maintaining a list of segments
+        #Clear the peptideList as it may still be maintaining a list of peptides
         #from the previous run of the command. 
-        self._segmentList = []                    
+        self._peptideList = []                    
         ss_idx, self.phi, self.psi, aa_type = self._gatherParameters()
+        return
         
     def command_will_exit(self):
         """
         Extends superclass method. 
         @see: basecommand.command_will_exit() for documentation
         """
-        if isinstance(self.graphicsMode, PeptideLine_GM):
+        if isinstance(self.graphicsMode, PeptideLine_GraphicsMode):
                 self.mouseClickPoints = []    
         self.graphicsMode.resetVariables()   
-        self._segmentList = []
+        self._peptideList = []
         
         _superclass.command_will_exit(self)
-            
+        return
     
     def _getFlyoutToolBarActionAndParentCommand(self):
         """
@@ -115,7 +112,6 @@ class InsertPeptide_EditCommand(EditCommand):
 
         bool_keep = _superclass.keep_empty_group(self, group)
         return bool_keep
-
         
     def _gatherParameters(self):
         """
@@ -128,6 +124,7 @@ class InsertPeptide_EditCommand(EditCommand):
         Overrides EditCommand.runCommand
         """
         self.struct = None
+        return
     
     def _createStructure(self):        
         """
@@ -157,8 +154,12 @@ class InsertPeptide_EditCommand(EditCommand):
                                            -self.win.glpane.pov)
         """                                   
         from geometry.VQT import V
-        pos1 = V(self.mouseClickPoints[0][0], self.mouseClickPoints[0][1], self.mouseClickPoints[0][2])
-        pos2 = V(self.mouseClickPoints[1][0], self.mouseClickPoints[1][1], self.mouseClickPoints[1][2])
+        pos1 = V(self.mouseClickPoints[0][0], \
+                 self.mouseClickPoints[0][1], \
+                 self.mouseClickPoints[0][2])
+        pos2 = V(self.mouseClickPoints[1][0], \
+                 self.mouseClickPoints[1][1], \
+                 self.mouseClickPoints[1][2])
         struct = self.structGenerator.make_aligned(self.win.assy, 
                                                    name, 
                                                    aa_type, 
@@ -166,8 +167,8 @@ class InsertPeptide_EditCommand(EditCommand):
                                                    self.psi, 
                                                    pos1, 
                                                    pos2, 
-                                                   fake_chain=False, 
-                                                   secondary=self.secondary)
+                                                   fake_chain = False, 
+                                                   secondary = self.secondary)
         
         self.win.assy.part.topnode.addmember(struct)
         self.win.win_update()
@@ -191,36 +192,35 @@ class InsertPeptide_EditCommand(EditCommand):
         self.previousParams = params
 
         self.struct = self._createStructure()
-    
+        return
     
     def cancelStructure(self):
         """
-        Overrides Editcommand.cancelStructure ..calls _removeSegments which 
-        deletes all the segments created while this command was running
+        Overrides Editcommand.cancelStructure. Calls _removePeptides which 
+        deletes all the peptides created while this command was running.
         @see: B{EditCommand.cancelStructure}
         """
         _superclass.cancelStructure(self)
-        self._removeSegments()
+        self._removePeptides()
+        return
 
-    def _removeSegments(self):
+    def _removePeptides(self):
         """
-        Remove the segments created while in this command 
-
-        This deletes all the segments created while this command was running
+        Deletes all the peptides created while this command was running
         @see: L{self.cancelStructure}
         """
-        segmentList = self._segmentList
+        peptideList = self._peptideList
 
-        #for segment in segmentList: 
-            #can segment be None?  Lets add this condition to be on the safer 
+        #for peptide in peptideList: 
+            #can peptide be None?  Lets add this condition to be on the safer 
             #side.
-        #    if segment is not None: 
-        #        segment.kill_with_contents()
+        #    if peptide is not None: 
+        #        peptide.kill_with_contents()
         #    self._revertNumber()
 
-
-        self._segmentList = []	
-        self.win.win_update()    
+        self._peptideList = []	
+        self.win.win_update()
+        return
     
     def createStructure(self):
         """
@@ -240,8 +240,8 @@ class InsertPeptide_EditCommand(EditCommand):
 
         self.preview_or_finalize_structure(previewing = True)
 
-        #Now append this ntSegment  to self._segmentList 
-        self._segmentList.append(self.struct)
+        #Now append this peptide to self._peptideList 
+        self._peptideList.append(self.struct)
 
         #clear the mouseClickPoints list
         self.mouseClickPoints = [] 
@@ -290,7 +290,7 @@ class InsertPeptide_EditCommand(EditCommand):
     def getCursorText(self, endPoint1, endPoint2):
         """
         This is used as a callback method in PeptideLineLine mode 
-        @see: PeptideLineMode.setParams, PeptideLineMode_GM.Draw
+        @see: PeptideLine_GraphicsMode.setParams, PeptideLine_GraphicsMode.Draw
         """
         
         text = ''
diff --git a/cad/src/protein/commands/InsertPeptide/PeptideGenerator.py b/cad/src/protein/commands/InsertPeptide/PeptideGenerator.py
index def5bc767..00fd47dc8 100755
--- a/cad/src/protein/commands/InsertPeptide/PeptideGenerator.py
+++ b/cad/src/protein/commands/InsertPeptide/PeptideGenerator.py
@@ -615,7 +615,9 @@ class PeptideGenerator:
         # structure which is aligned along the Z axis.
         bLine = pt2 - pt1
         bLength = vlen(bLine)
-        b = bLine/bLength
+        if bLength == 0:
+            return
+        b = bLine / bLength
         # <b> is the unit vector parallel to the line (i.e. pt1, pt2).
         axis = cross(a, b)
         # <axis> is the axis of rotation.
@@ -639,7 +641,8 @@ class PeptideGenerator:
         
         # Bruce suggested I add this. It works here, but not if its 
         # before move() and rot() above. Mark 2008-04-11
-        chunk.full_inval_and_update()         
+        chunk.full_inval_and_update()
+        return
         
     def get_number_of_res(self, pos1, pos2, phi, psi):
         """
@@ -654,9 +657,15 @@ class PeptideGenerator:
         """
         return 1 + int(vlen(pos2 - pos1) / get_unit_length(phi, psi))
     
-    def make_aligned(self, assy, name, aa_idx, phi, psi, 
-                     pos1, pos2, secondary=SS_COIL, 
-                     fake_chain=False, length=None):
+    def make_aligned(self, 
+                     assy, 
+                     name, 
+                     aa_idx, 
+                     phi, psi, 
+                     pos1, pos2, 
+                     secondary = SS_COIL, 
+                     fake_chain = False, 
+                     length = None):
         """
         Build and return a chunk that is a homo-peptide aligned to 
         a pos2-pos1 vector.
@@ -679,7 +688,7 @@ class PeptideGenerator:
         
         @param fake_chain: if True, create only C-alpha atoms. used for drawing
         peptide trace image during interactive peptide placement (used by
-        PeptideLineMode.py)
+        PeptideLine_GraphicsMode.py)
         @type fake_chain: boolean
         
         @param length: optional peptide length (number of amino acids), if 
diff --git a/cad/src/protein/temporary_commands/PeptideLineMode.py b/cad/src/protein/temporary_commands/PeptideLine_GraphicsMode.py
index 606ad747d..48bb1ade5 100644
--- a/cad/src/protein/temporary_commands/PeptideLineMode.py
+++ b/cad/src/protein/temporary_commands/PeptideLine_GraphicsMode.py
@@ -1,18 +1,15 @@
 # Copyright 2007-2008 Nanorex, Inc.  See LICENSE file for details. 
 """
-@author:    Urmi
+@author:    Urmi, Mark
 @copyright: 2008 Nanorex, Inc.  See LICENSE file for details.
 @version:   $Id$
 @license:   GPL
-
-
 """
 
-
 from temporary_commands.LineMode.Line_Command import Line_Command
 from temporary_commands.LineMode.Line_GraphicsMode import Line_GraphicsMode
 
-from graphics.drawing.drawPeptideTrace import drawPeptideTrace, drawPeptideTrace_new
+from graphics.drawing.drawPeptideTrace import drawPeptideTrace, drawPeptideTrace_orig
 
 from utilities.constants import gray, black, darkred, blue, white
 
@@ -20,11 +17,11 @@ from protein.commands.InsertPeptide.PeptideGenerator import PeptideGenerator, ge
 
 # == GraphicsMode part
 
-class PeptideLine_GM( Line_GraphicsMode ):
+class PeptideLine_GraphicsMode( Line_GraphicsMode ):
     """
-    Custom GraphicsMode for use as a component of PeptideLineMode.
-    @see: L{PeptideLineMode} for more comments. 
-    @see: InsertPeptide_EditCommand where this is used as a GraphicsMode class.
+    Custom GraphicsMode used while interactively drawing a peptide chain for
+    the "Insert Peptide" command.
+    @see: InsertPeptide_EditCommand where this class is used.
                   
     """    
     # The following valuse are used in drawing the 'sphere' that represent the 
@@ -39,7 +36,7 @@ class PeptideLine_GM( Line_GraphicsMode ):
         
     def leftUp(self, event):
         """
-        Left up method
+        Left up method.
         """
         if  self.command.mouseClickLimit is None:
             if len(self.command.mouseClickPoints) == 2:
@@ -47,7 +44,8 @@ class PeptideLine_GM( Line_GraphicsMode ):
                                 
                 self.command.createStructure()
                 self.glpane.gl_update()            
-            return
+            pass
+        return
     
     def snapLineEndPoint(self):
         """
@@ -73,32 +71,34 @@ class PeptideLine_GM( Line_GraphicsMode ):
         """
         Line_GraphicsMode.Draw(self)        
         if self.endPoint2 is not None and \
-           self.endPoint1 is not None: 
-            #Urmi 20080804: In absence of a better representation, this is a 
-            #placeholder for now. May be Piotr can implement a better representation
-            #for drawing protein secondary structure
-            # Draw the ladder. 
+           self.endPoint1 is not None:
             
-            #print "command = ", self.command
-            #print "phi = ", self.command.phi
+            # Generate a special chunk that contains only alpha carbon atoms
+            # that will be used to draw the peptide backbone trace.
+            alphaCarbonProteinChunk = \
+                                    self.structGenerator.make_aligned(
+                                        self.win.assy, "", 0, 
+                                        self.command.phi, 
+                                        self.command.psi, 
+                                        self.endPoint1, 
+                                        self.endPoint2, 
+                                        fake_chain = True)
             
-            mol = self.structGenerator.make_aligned(self.win.assy, "", 0, 
-                                                    self.command.phi, 
-                                                    self.command.psi, 
-                                                    self.endPoint1, 
-                                                    self.endPoint2, 
-                                                    fake_chain=True)
+            drawPeptideTrace(alphaCarbonProteinChunk)
             
-            drawPeptideTrace_new(mol)
-            
-            """
-            drawPeptideTrace(self.endPoint1,
-                          self.endPoint2, 
-                          135,
-                          -135,
-                          self.glpane.scale,
-                          self.glpane.lineOfSight,
-                          beamThickness = 4.0 
-                          ) 
-            """
+            # The original way of drawing the peptide trace.
+            # This function is deprecated and marked for removal.
+            # --Mark 2008-12-23
+            #drawPeptideTrace_orig(self.endPoint1,
+                                  #self.endPoint2, 
+                                  #135,
+                                  #-135,
+                                  #self.glpane.scale,
+                                  #self.glpane.lineOfSight,
+                                  #beamThickness = 4.0 
+                                  #) 
+
+            pass
+        return
+    pass # end of class PeptideLine_GraphicsMode
author	Mark Sims <mark@nanorex.com>	2008-12-23 21:24:51 +0000
committer	Mark Sims <mark@nanorex.com>	2008-12-23 21:24:51 +0000
commit	7704e22b57466a1f51294169bd5828457999ad7a (patch)
tree	aa8c0739777387bfebe62b69fdc417fc6a73e23b
parent	798c3f541ec33c797c3cf80945b952f68af531ed (diff)
download	nanoengineer-theirix-7704e22b57466a1f51294169bd5828457999ad7a.tar.gz nanoengineer-theirix-7704e22b57466a1f51294169bd5828457999ad7a.zip