def get_unit_length(phi, psi):
    """
    Calculate a length of single amino acid in particular
    secondary conformation.
    """
    # All unit length values obtained via measurements by me.
    # Fixes bug 2959. --Mark 2008-12-23
    if phi == -57.0 and psi == -47.0:
        unit_length = 1.5 # Alpha helix
    elif phi == -135.0 and psi == 135.0:
        unit_length = 3.4 # Beta strand
    elif phi == -55.0 and psi == -70.0:
        unit_length = 1.05 # Pi helix
    elif phi == -49.0 and psi == -26.0:
        unit_length = 1.95 # 3_10 helix
    elif phi == -75.0 and psi == 150.0:
        unit_length = 3.14 # Polyproline-II helix
    elif phi == -180.0 and psi == 180.0:
        unit_length = 3.6 # Fully extended
    else:
        # User chose "Custom" conformation option in the Insert Peptide PM
        # which lets the user set any phi-psi angle values.
        # We need a formula to estimate the proper unit_length given the
        # conformational angles phi and psi. It would also be a good idea
        # to check these values to confirm they are an allowed combination.
        # For more info, do a google search for "Ramachandran plot".
        # For now, I'm setting the unit length to 1.5. --Mark 2008-12-23
        unit_length = 1.5
        msg = "\nUser selected custom conformational angles: "\
            "phi=%.2f, psi=%.2f.\nSetting unit_length=%.2f\n" % \
            (phi, psi, unit_length)
        print_compact_stack(msg)

    return unit_length

 def careful_widget_setter(self, value):
     # Note: for some time we used self.widget_setter rather than this method,
     # by mistake, and it apparently worked fine. We'll still use this method
     # as a precaution; also it might be truly needed if the widget quantizes
     # the value, unless the widget refrains from sending signals when
     # programmatically set. [bruce 070815]
     if self.debug:
         print "\n_changes__debug_print: %r setting %r to %r using %r" % \
               ( self, self.widget, value, self.widget_setter )
     self.disconnect() # avoid possible recursion
     try:
         self.widget_setter(value)
     except:
         print_compact_traceback("bug: ignoring exception setting value of %r to %r: " % (self, value))
         print_compact_stack(" fyi: prior exception came from: ")
         self.destroy() #bruce 080930
             # this seems to be safe, but debug output implies it fails to stop formula
             # from continuing to call setter! but that seems unlikely... nevermind for now.
             # Review: do we want subsequent use of self
             # to be silently ok, smaller message, or error? If this destroy worked
             # then I think it should be silently ok, but might not be now,
             # depending on how refs to self continue to be used.
         pass
     else:
         self.connect()
         ### WARNING: .connect is slow, since it runs our Python code to set up an undo wrapper
         # around the slot! We should revise this to tell Qt to block the signals instead.
         # [We can use: bool QObject::blockSignals ( bool block ) ==> returns prior value of signalsBlocked,
         #  now used in a helper function setValue_with_signals_blocked]
         # This will matter for performance when this is used for state which changes during a drag.
         # Note: avoiding the slot call is needed not only for recursion, but to avoid the
         # Undo checkpoint in the wrapper.
         # [bruce comments 071015; see also bug 2564 in other code]
     return

    def getStrands(self):
        """
        Returns a list of strands inside a DnaGroup object

        @return: A list containing all the strand objects
                 within self.
        @rtype: list

        @see: B{BuildDna_PropertyManager.updateStrandListWidget()}
        @see: B{BuildDna_PropertyManager._currentSelectionParams}
        """

        #TO BE REVISED. As of 2008-01-17, it uses isinstance check for
        #Chunk and some additional things to find out a list of strands inside
        # a DnaGroup -- Ninad 2008-01-17

        if self.assy is None:
            #This is to avoid possible bugs if group gets deleted. But print
            #traceback so that we know about this bug. This could happen due to
            #insufficient command sequencer stack. Temporary fix for bug 2699
            print_compact_stack("bug: self.assy is None for DnaGroup %s."%self)
            return ()

        strandList = []

        def filterStrands(node):
            if isinstance(node, self.assy.DnaStrand) and not node.isEmpty():
                strandList.append(node)
            elif isinstance(node, self.assy.Chunk) and node.isStrandChunk():
                if node.parent_node_of_class(self.assy.DnaStrand) is None:
                    strandList.append(node)

        self.apply2all(filterStrands)

        return strandList

    def getAxisChunks(self):
        """
        Returns a list of Axis chunks inside a DnaGroup object

        @return: A list containing all the axis chunks
                 within self.
        @rtype: list
        """
        if self.assy is None:
            #This is to avoid possible bugs if group gets deleted. But print
            #traceback so that we know about this bug. This could happen due to
            #insufficient command sequencer stack. Temporary fix for bug 2699
            print_compact_stack("bug: self.assy is None for DnaGroup %s."%self)
            return ()

        #TO BE REVISED. It uses isinstance check for
        #Chunk and some additional things to find out a list of strands inside
        # a DnaGroup -- Ninad 2008-02-02

        axisChunkList = []
        def filterAxisChunks(node):
            if isinstance(node, self.assy.Chunk) and node.isAxisChunk():
                axisChunkList.append(node)

        self.apply2all(filterAxisChunks)

        return axisChunkList

def get_image_path(name, print_errors = True):
    """
    Return the full path given an image/icon path name.

    @param name: The image path name provided by the user. The path should start
           with 'ui/' directory inside the src directory.
    @type  name: str

    @param print_errors: whether to report errors for missing icon files
                         when atom_debug is set. True by default.
    @type print_errors: boolean

    @return: full path of the image.
    @rtype:  str
    """

    root, ext = os.path.splitext(name)

    if not ext:
        if name: # 'name' can be an empty string. See docstring for details.
            msg = "Warning: No '.png' extension passed to get_image_path for [%s]. " \
                "\nPlease add the .png suffix in the source code to remove this warning.\n" % name
            print_compact_stack(msg)
        name = name + '.png'

    iconPath = os.path.join(image_directory(), name)
    iconPath = os.path.normpath(iconPath)

    if not os.path.exists(iconPath):
        if debug_flags.atom_debug and print_errors:
            print "icon path %s doesn't exist." % (iconPath,)

    return iconPath

    def _get_mode(self):
        """
        Old code is trying to get self.mode,
        which it might want for either the Command API (self.currentCommand)
        or GraphicsMode API (self.graphicsMode). We don't know which it wants.
        (TODO, if worthwhile: deduce which, print a map of code line vs
         which one of these to change it to.)

        This can only be supported if the currentCommand is also old, so that
        it handles both APIs.
        Print a warning if not (or assert 0?), and return the currentCommand
        in either case (but don't wrap it with an API enforcer).
        """
        # Note: when we think there are not many uses of this left,
        # we'll make every use print_compact_stack to aid in finding the rest
        # and replacing them with one or the other of currentCommand and
        # graphicsMode. Or we might print a once-per-line-number message when
        # it's called... ### TODO
        #
        # hmm, this is true now! [bruce 071011]
        print_compact_stack("fyi: this old code still accesses glpane.mode " \
                            "by that deprecated name: ")
        
        raw_currentCommand = self._raw_currentCommand
        graphicsMode = self._raw_currentCommand.graphicsMode
        if raw_currentCommand is not graphicsMode:
            print "old code warning: %r is not %r and we don't know " \
                  "which one %r.mode should return" % \
                  (raw_currentCommand, graphicsMode, self)
            # TODO: print_compact_stack?
        return raw_currentCommand

    def _leftDown_preparation_for_dragging(self, objectUnderMouse, event):
        """
        Handle left down event. Preparation for rotation and/or selection
        This method is called inside of self.leftDown.
        @param event: The mouse left down event.
        @type  event: QMouseEvent instance
        @see: self.leftDown
        @see: self.leftDragRotation
        Overrides _superclass._leftDown_preparation_for_dragging
        """

        _superclass._leftDown_preparation_for_dragging(self, objectUnderMouse, event)
        self.o.SaveMouse(event)
        self.picking = True
        self.dragdist = 0.0
        # delta for constrained rotations.
        self.rotDelta = 0

        if self.rotateOption == "ROTATEDEFAULT":
            self.o.trackball.start(self.o.MousePos[0], self.o.MousePos[1])
        else:
            if self.rotateOption == "ROTATEX":
                ma = V(1, 0, 0)  # X Axis
                self.axis = "X"
            elif self.rotateOption == "ROTATEY":
                ma = V(0, 1, 0)  # Y Axis
                self.axis = "Y"
            elif self.rotateOption == "ROTATEZ":
                ma = V(0, 0, 1)  # Z Axis
                self.axis = "Z"
            elif self.rotateOption == "ROT_TRANS_ALONG_AXIS":
                # The method 'self._leftDown_preparation_for_dragging should
                # never be reached if self.rotateOption is 'ROT_TRANS_ALONG_AXIS'
                # If this code is reached, it indicates a bug. So fail gracefully
                # by calling self.leftADown()
                if debug_flags.atom_debug:
                    print_compact_stack(
                        "bug: _leftDown_preparation_for_dragging" " called for rotate option" "'ROT_TRANS_ALONG_AXIS'"
                    )

                self.leftADown(objectUnderMouse, event)
                return

            else:
                print "Move_Command: Error - unknown rotateOption value =", self.rotateOption
                return

            ma = norm(V(dot(ma, self.o.right), dot(ma, self.o.up)))
            # When in the front view, right = 1,0,0 and up = 0,1,0, so ma will
            # be computed as 0,0.This creates a special case problem when the
            # user wants to constrain rotation around the Z axis because Zmat
            # will be zero.  So we have to test for this case (ma = 0,0) and
            # fix ma to -1,0.  This was needed to fix bug 537.  Mark 050420
            if ma[0] == 0.0 and ma[1] == 0.0:
                ma = [-1.0, 0.0]
            self.Zmat = A([ma, [-ma[1], ma[0]]])

        self.leftDownType = "ROTATE"

        return

def _master_model_updater( warn_if_needed = False ):
    """
    This should be called at the end of every user event which might have
    changed anything in any loaded model which defers some updates to this
    function.

    This can also be called at the beginning of user events, such as redraws
    or saves, which want to protect themselves from event-processors which
    should have called this at the end, but forgot to. Those callers should
    pass warn_if_needed = True, to cause a debug-only warning to be emitted
    if the call was necessary. (This function is designed
    to be very fast when called more times than necessary.)

    This should also be called before taking Undo checkpoints, to make sure
    they correspond to legal structures, and so this function's side effects
    (and the effect of assy.changed, done by this function as of 060126(?))
    are treated as part of the same undoable operation as the changes that
    required them to be made. As of 060127 this is done by those checkpoints
    calling update_parts, which indirectly calls this function.

    In practice, as of 071115, we have not yet tried to put in calls
    to this function at the end of user event handlers, so we rely on the
    other calls mentioned above, and none of them pass warn_if_needed.
    """

    # 0. Don't run while mmp file is being read [###FIX, use one global flag]
    if 1:
        # KLUGE; the changedicts and updater should really be per-assy...
        # this is a temporary scheme for detecting the unanticipated
        # running of this in the middle of loading an mmp file, and for
        # preventing errors from that,
        # but it only works for the main assy -- not e.g. for a partlib
        # assy. I don't yet know if this is needed. [bruce 080117]
        #update 080319: just in case, I'm fixing the mmpread code
        # to also use the global assy to store this.
        kluge_main_assy = env.mainwindow().assy
        if not kluge_main_assy.assy_valid:
            global_model_changedicts.status_of_last_dna_updater_run = LAST_RUN_DIDNT_HAPPEN
            msg = "deferring _master_model_updater(warn_if_needed = %r) " \
                  "since not %r.assy_valid" % (warn_if_needed, kluge_main_assy)
            print_compact_stack(msg + ": ") # soon change to print...
            return
        pass

    env.history.emit_all_deferred_summary_messages() #bruce 080212 (3 places)

    _run_dna_updater()

    env.history.emit_all_deferred_summary_messages()

    _run_bond_updater( warn_if_needed = warn_if_needed)

    env.history.emit_all_deferred_summary_messages()

    _autodelete_empty_groups(kluge_main_assy)

    env.history.emit_all_deferred_summary_messages()

    return # from _master_model_updater

 def connect_or_disconnect_signals(self, isConnect): 
     """
     Connect or disconnect widget signals sent to their slot methods.
     @param isConnect: If True the widget will send the signals to the slot 
                       method. 
     @type  isConnect: boolean
     @see: L{BuildAtoms_Command.connect_or_disconnect_signals} where this is called
     """
             
     if isConnect and self.isAlreadyConnected:
         if debug_flags.atom_debug:
             print_compact_stack("warning: attempt to connect widgets"\
                                 "in this PM that are already connected." )
         return 
     
     if not isConnect and self.isAlreadyDisconnected:
         if debug_flags.atom_debug:
             print_compact_stack("warning: attempt to disconnect widgets"\
                                 "in this PM that are already disconnected.")
         return
     
     self.isAlreadyConnected = isConnect
     self.isAlreadyDisconnected = not isConnect
     
     if isConnect:
         change_connect = self.w.connect
     else:
         change_connect = self.w.disconnect
     
     change_connect(self.atomChooserComboBox, 
                  SIGNAL("currentIndexChanged(int)"), 
                  self._updateAtomChooserGroupBoxes)
     
   
     change_connect(self.selectionFilterCheckBox,
                    SIGNAL("stateChanged(int)"),
                    self.set_selection_filter)
     
     change_connect(self.showSelectedAtomInfoCheckBox,
                    SIGNAL("stateChanged(int)"),
                    self.toggle_selectedAtomPosGroupBox)        
     
     change_connect(self.xCoordOfSelectedAtom,
                  SIGNAL("valueChanged(double)"), 
                  self._moveSelectedAtom)
     
     change_connect(self.yCoordOfSelectedAtom,
                  SIGNAL("valueChanged(double)"), 
                  self._moveSelectedAtom)
     
     change_connect(self.zCoordOfSelectedAtom,
                  SIGNAL("valueChanged(double)"), 
                  self._moveSelectedAtom)
     
     connect_checkbox_with_boolean_pref(self.waterCheckBox,
                                            buildModeWaterEnabled_prefs_key)                   
     
     connect_checkbox_with_boolean_pref(self.highlightingCheckBox, 
                                        buildModeHighlightingEnabled_prefs_key)

 def _e_eval_lval(self, env, ipath):  # 070119 also print _e_eval_lval calls [maybe untested]
     assert env
     the_expr = self._e_args[0]
     res = the_expr._e_eval_lval(env, ipath)
     print_compact_stack(
         "debug_evals_of_Expr(%r) eval-lvals it to %r at: " % (the_expr, res)
     )  # k does this ever happen?
     return res

def _do_whycode_reenable( reasons_list_val, whycode):
    """
    [private helper function for maintaining whycode,whymsg lists]
    """
    res = filter( lambda (code, msg): code != whycode , reasons_list_val ) # zap items with same whycode
    if len(res) == len(reasons_list_val) and env.debug():
        print_compact_stack("debug fyi: redundant call of _do_whycode_reenable, whycode %r, remaining reasons %r" % \
                            ( whycode, res ) )
    return res

 def _reverse_neighbor_baseatoms(self):
     self.neighbor_baseatoms = list(self.neighbor_baseatoms)
     self.neighbor_baseatoms.reverse()
     if DEBUG_NEIGHBOR_BASEATOMS:
         if self.neighbor_baseatoms[0] != -1 or \
            self.neighbor_baseatoms[1] != -1:
             msg = "reversed %r.neighbor_baseatoms to get %r" % (self, self.neighbor_baseatoms)
             print_compact_stack( "\n" + msg + ": ")
     return

    def _modifyStructure_NEW_SEGMENT_RESIZE(self, params): #@ NOT FIXED
        """
        This resizes without recreating whole nanotube 
        Overrides EditCommand._modifystructure.
        @attention: is not implemented.
        """        

        #@TODO: - rename this method from _modifyStructure_NEW_SEGMENT_RESIZE
        #to self._modifyStructure, after more testing
        #This method is used for debug prefence: 
        #'Nanotube Segment: resize without recreating whole nanotube'
        #see also self.modifyStructure_NEW_SEGMENT_RESIZE

        assert self.struct      

        from utilities.debug import print_compact_stack
        print_compact_stack("_modifyStructure_NEW_SEGMENT_RESIZE() not fixed!" )
        print "Params =", params

        self.nanotube = params #@

        length_diff =  self._determine_how_to_change_length() #@

        if length_diff == 0:
            print_compact_stack("BUG: length_diff is always ZERO." )
            return
        elif length_diff > 0:
            print "Nanotube longer by ", length_diff, ", angstroms."
        else:
            print "Nanotube shorter by ", length_diff, ", angstroms."

        return

        if numberOfBasePairsToAddOrRemove != 0:   #@@@@ Not reached.

            resizeEnd_final_position = self._get_resizeEnd_final_position(
                ladderEndAxisAtom, 
                abs(numberOfBasePairsToAddOrRemove),
                nanotubeRise )

            self.nanotube.modify(self.struct,
                                 length_diff,
                                 ladderEndAxisAtom.posn(),
                                 resizeEnd_final_position)

        #Find new end points of structure parameters after modification 
        #and set these values in the propMgr. 
        new_end1 , new_end2 = self.struct.nanotube.getEndPoints() #@

        params_to_set_in_propMgr = (new_end1,
                                    new_end2)

        #TODO: Need to set these params in the PM 
        #and then self.previousParams = params_to_set_in_propMgr

        self.previousParams = params
        return  

 def __init__(self):
     print_compact_stack(
         "warning: fake_Part_drawing_frame is being instantiated: " )
     # done in superclass: self.repeated_bonds_dict = None
         # This is necessary to remove any chance of self surviving
         # for more than one draw of one object (since using an actual
         # dict then would make bonds sometimes fail to be drawn).
         # Client code must tolerate this value.
     return

def _do_whycode_disable( reasons_list_val, whycode, whymsg):
    """
    [private helper function for maintaining whycode,whymsg lists]
    """
    res = filter( lambda (code, msg): code != whycode , reasons_list_val ) # zap items with same whycode
    if len(res) < len(reasons_list_val) and env.debug():
        print_compact_stack("debug fyi: redundant call of _do_whycode_disable, whycode %r msg %r, preserved reasons %r" % \
                            ( whycode, whymsg, res ) )
    res.append( (whycode, whymsg) ) # put the changed one at the end (#k good??)
    return res

    def insertSeparator(self):
        """
        This method overrides QToolBar's method. It does nothing since the
        normal behavior will screw things up.

        @note: If you need this method, please code it! Mark 2008-02-29.
        """
        print_compact_stack("insertSeparator() not supported. " \
            "Use addSeparator() instead or implement insertSeparator()")
        return

 def atom_ok(self, atom):
     # note: this can include Pl atoms in PAM5,
     # but the wrapper class filters them out of
     # the atom list it stores.
     if not atom.molecule:
         print_compact_stack( "bug: strand_bond_chain_analyzer skipping %r with no .molecule: " % atom)
         return False
     if atom._dna_updater__error:
         return False
     return atom.element.role == 'strand' and not atom.molecule.in_a_valid_ladder()

    def connect_or_disconnect_signals(self, isConnect):
        """
        Connect or disconnect widget signals sent to their slot methods.
        This can be overridden in subclasses. By default it does nothing.
        @param isConnect: If True the widget will send the signals to the slot
                          method.
        @type  isConnect: boolean
        """
        #TODO: This is a temporary fix for a bug. When you invoke a temporary
        # mode Entering such a temporary mode keeps the signals of
        #PM from the previous mode connected (
        #but while exiting that temporary mode and reentering the
        #previous mode, it atucally reconnects the signal! This gives rise to
        #lots  of bugs. This needs more general fix in Temporary mode API.
        # -- Ninad 2008-01-09 (similar comment exists in MovePropertyManager.py

        if isConnect and self.isAlreadyConnected:
            if debug_flags.atom_debug:
                print_compact_stack("warning: attempt to connect widgets"\
                                    "in this PM that are already connected." )
            return

        if not isConnect and self.isAlreadyDisconnected:
            if debug_flags.atom_debug:
                print_compact_stack("warning: attempt to disconnect widgets"\
                                    "in this PM that are already disconnected.")
            return

        self.isAlreadyConnected = isConnect
        self.isAlreadyDisconnected = not isConnect

        if isConnect:
            change_connect = self.win.connect
        else:
            change_connect = self.win.disconnect


        if self.sequenceEditor:
            self.sequenceEditor.connect_or_disconnect_signals(isConnect)

        _superclass.connect_or_disconnect_signals(self, isConnect)


        change_connect(self.disableStructHighlightingCheckbox,
                       SIGNAL('stateChanged(int)'),
                       self.change_struct_highlightPolicy)

        change_connect(self.showCursorTextCheckBox,
                       SIGNAL('stateChanged(int)'),
                       self._update_state_of_cursorTextGroupBox)

        change_connect(self.nameLineEdit,
                       SIGNAL("editingFinished()"),
                       self._nameChanged)
        return

 def _loadServerList(self):
     """Return the list of servers available, otherwise, create a default one. """
     if os.path.isfile(self.serverFile):
         try:
             file = open(self.serverFile, "rb")
             return pickle.load(file)
         except:
             print_compact_stack("Unpickle exception.")
             return [SimServer()]
     else:
         return [SimServer()]

 def _set_mode(self, new_mode):
     """
     Old code is trying to set self.mode.
     Assume it wants to set _raw_currentCommand, and do that, after complaining.
     Soon, this will be illegal.
     """
     # TODO: a search for 'self.mode =' reveals no remaining calls,
     # so make it an assert 0 soon
     print_compact_stack("bug: old code is trying to set glpane.mode directly: ")
     self._raw_currentCommand = new_mode
     return