class EditNanotube_EditCommand(State_preMixin, EditCommand):
"""
Command to edit a NanotubeSegment (nanotube).
"""
# class constants
GraphicsMode_class = EditNanotube_GraphicsMode
PM_class = EditNanotube_PropertyManager
commandName = 'EDIT_NANOTUBE'
featurename = "Edit Nanotube"
from utilities.constants import CL_SUBCOMMAND
command_level = CL_SUBCOMMAND
command_parent = 'BUILD_NANOTUBE'
command_should_resume_prevMode = True
command_has_its_own_PM = True
flyoutToolbar = None
call_makeMenus_for_each_event = True
handlePoint1 = State( Point, ORIGIN)
handlePoint2 = State( Point, ORIGIN)
#The minimum 'stopper'length used for resize handles
#@see: self._update_resizeHandle_stopper_length for details.
_resizeHandle_stopper_length = State(Width, -100000)
rotationHandleBasePoint1 = State( Point, ORIGIN)
rotationHandleBasePoint2 = State( Point, ORIGIN)
#See self._update_resizeHandle_radius where this gets changed.
#also see EditNanotube_ResizeHandle to see how its implemented.
handleSphereRadius1 = State(Width, HANDLE_RADIUS_DEFAULT_VALUE)
handleSphereRadius2 = State(Width, HANDLE_RADIUS_DEFAULT_VALUE)
cylinderWidth = State(Width, CYLINDER_WIDTH_DEFAULT_VALUE)
cylinderWidth2 = State(Width, CYLINDER_WIDTH_DEFAULT_VALUE)
#@TODO: modify the 'State params for rotation_distance
rotation_distance1 = State(Width, CYLINDER_WIDTH_DEFAULT_VALUE)
rotation_distance2 = State(Width, CYLINDER_WIDTH_DEFAULT_VALUE)
leftHandle = Instance(
EditNanotube_ResizeHandle(
command = _self,
height_ref = call_Expr( ObjAttr_StateRef, _self, 'cylinderWidth'),
origin = handlePoint1,
fixedEndOfStructure = handlePoint2,
direction = norm_Expr(handlePoint1 - handlePoint2),
sphereRadius = handleSphereRadius1,
range = (_resizeHandle_stopper_length, 10000)
))
rightHandle = Instance(
EditNanotube_ResizeHandle(
command = _self,
height_ref = call_Expr( ObjAttr_StateRef, _self, 'cylinderWidth2'),
origin = handlePoint2,
fixedEndOfStructure = handlePoint1,
direction = norm_Expr(handlePoint2 - handlePoint1),
sphereRadius = handleSphereRadius2,
range = (_resizeHandle_stopper_length, 10000)
))
rotationHandle1 = Instance(
RotationHandle(
command = _self,
rotationDistanceRef = call_Expr( ObjAttr_StateRef,
_self,
'rotation_distance1'),
center = handlePoint1,
axis = norm_Expr(handlePoint1 - handlePoint2),
origin = rotationHandleBasePoint1,
radiusVector = norm_Expr(rotationHandleBasePoint1 - handlePoint1)
))
rotationHandle2 = Instance(
RotationHandle(
command = _self,
rotationDistanceRef = call_Expr( ObjAttr_StateRef,
_self,
'rotation_distance2'),
center = handlePoint2,
axis = norm_Expr(handlePoint2 - handlePoint1),
origin = rotationHandleBasePoint2,
radiusVector = norm_Expr(rotationHandleBasePoint2 - handlePoint2)
))
def __init__(self, commandSequencer):
"""
Constructor for InsertDna_EditCommand
"""
glpane = commandSequencer.assy.glpane
State_preMixin.__init__(self, glpane)
EditCommand.__init__(self, commandSequencer)
#Graphics handles for editing the structure .
self.handles = []
self.grabbedHandle = None
#Initialize DEBUG preference
pref_nt_segment_resize_by_recreating_nanotube()
return
def editStructure(self, struct = None):
EditCommand.editStructure(self, struct)
if self.hasValidStructure():
#TODO 2008-03-25: better to get all parameters from self.struct and
#set it in propMgr? This will mostly work except that reverse is
#not true. i.e. we can not specify same set of params for
#self.struct.setProps ...because endPoint1 and endPoint2 are derived.
#by the structure when needed.
self.propMgr.setParameters(self.struct.getProps())
#Store the previous parameters. Important to set it after you
#set nanotube attrs in the propMgr.
#self.previousParams is used in self._previewStructure and
#self._finalizeStructure to check if self.struct changed.
self.previousParams = self._gatherParameters()
self._updateHandleList()
self.updateHandlePositions()
return
def hasValidStructure(self):
"""
Tells the caller if this edit command has a valid structure.
Overrides EditCommand.hasValidStructure()
"""
#(By Bruce 2008-02-13)
isValid = EditCommand.hasValidStructure(self)
if not isValid:
return isValid
# would like to check here whether it's empty of axis chunks;
# instead, this will do for now (probably too slow, though):
p1, p2 = self.struct.nanotube.getEndPoints()
return (p1 is not None)
def _getStructureType(self):
"""
Subclasses override this method to define their own structure type.
Returns the type of the structure this editCommand supports.
This is used in isinstance test.
@see: EditCommand._getStructureType() (overridden here)
"""
return self.win.assy.NanotubeSegment
def _updateHandleList(self):
"""
Updates the list of handles (self.handles)
@see: self.editStructure
@see: EditNanotube_GraphicsMode._drawHandles()
"""
# note: if handlePoint1 and/or handlePoint2 can change more often than this
# runs, we'll need to rerun the two assignments above whenever they
# change and before the handle is drawn. An easy way would be to rerun
# these assignments in the draw method of our GM. [bruce 080128]
self.handles = [] # guess, but seems like a good idea [bruce 080128]
self.handles.append(self.leftHandle)
self.handles.append(self.rightHandle)
if DEBUG_ROTATION_HANDLES:
self.handles.append(self.rotationHandle1)
self.handles.append(self.rotationHandle2)
return
def updateHandlePositions(self):
"""
Update handle positions and also update the resize handle radii and
their 'stopper' lengths.
@see: self._update_resizeHandle_radius()
@see: self._update_resizeHandle_stopper_length()
@see: EditNanotube_GraphicsMode._drawHandles()
"""
self.handlePoint1 = None # Needed!
self.handlePoint2 = None
#TODO: Call this method less often by implementing model_changed
#see bug 2729 for a planned optimization
self.cylinderWidth = CYLINDER_WIDTH_DEFAULT_VALUE
self.cylinderWidth2 = CYLINDER_WIDTH_DEFAULT_VALUE
self._update_resizeHandle_radius()
handlePoint1, handlePoint2 = self.struct.nanotube.getEndPoints()
if 0: # Debug prints
print "updateHandlePositions(): handlePoint1=", handlePoint1
print "updateHandlePositions(): handlePoint2=", handlePoint2
if handlePoint1 is not None and handlePoint2 is not None:
# (that condition is bugfix for deleted axis segment, bruce 080213)
self.handlePoint1, self.handlePoint2 = handlePoint1, handlePoint2
#Update the 'stopper' length where the resize handle being dragged
#should stop. See self._update_resizeHandle_stopper_length()
#for more details
self._update_resizeHandle_stopper_length()
if DEBUG_ROTATION_HANDLES:
self.rotation_distance1 = CYLINDER_WIDTH_DEFAULT_VALUE
self.rotation_distance2 = CYLINDER_WIDTH_DEFAULT_VALUE
#Following computes the base points for rotation handles.
#to be revised -- Ninad 2008-02-13
unitVectorAlongAxis = norm(self.handlePoint1 - self.handlePoint2)
v = cross(self.glpane.lineOfSight, unitVectorAlongAxis)
self.rotationHandleBasePoint1 = self.handlePoint1 + norm(v) * 4.0
self.rotationHandleBasePoint2 = self.handlePoint2 + norm(v) * 4.0
return
def _update_resizeHandle_radius(self):
"""
Finds out the sphere radius to use for the resize handles, based on
atom /chunk or glpane display (whichever decides the display of the end
atoms. The default value is 1.2.
@see: self.updateHandlePositions()
"""
self.handleSphereRadius1 = HANDLE_RADIUS_DEFAULT_VALUE
self.handleSphereRadius2 = HANDLE_RADIUS_DEFAULT_VALUE
return
def _update_resizeHandle_stopper_length(self):
"""
Update the limiting length at which the resize handle being dragged
should 'stop' without proceeding further in the drag direction.
The segment resize handle stops when you are dragging it towards the
other resizeend and the distance between the two ends reaches two
duplexes.
The self._resizeHandle_stopper_length computed in this method is
used as a lower limit of the 'range' option provided in declaration
of resize handle objects (see class definition for the details)
@see: self.updateHandlePositions()
"""
total_length = vlen(self.handlePoint1 - self.handlePoint2)
nanotubeRise = self.struct.nanotube.getRise()
self._resizeHandle_stopper_length = - total_length + nanotubeRise
return
def _gatherParameters(self):
"""
Return the parameters from the property manager UI.
@return: The endpoints of the nanotube.
@rtype: tuple (endPoint1, endPoint2).
"""
return self.propMgr.getParameters()
def _createStructure(self):
"""
Returns the current NanotubeSegment being edited with a new nanotube
chunk.
@return : Nanotube segment that include the new nanotube chunk.
@rtype: L{NanotubeSegment}
"""
try:
# Create a new nanotube chunk using new params.
n, m, type, endings, endPoint1, endPoint2 = self._gatherParameters()
from cnt.model.NanotubeParameters import NanotubeParameters
self.nanotube = NanotubeParameters()
nanotube = self.nanotube
nanotube.setChirality(n, m)
nanotube.setType(type)
nanotube.setEndings(endings)
nanotube.setEndPoints(endPoint1, endPoint2)
position = V(0.0, 0.0, 0.0)
ntChunk = nanotube.build(self.struct.name, self.win.assy, position)
nanotube.computeEndPointsFromChunk(ntChunk) # Needed.
self.struct.addchild(ntChunk)
#WARNING 2008-03-05:
#When we actually permit modifying a nanotube without recreating it,
#then the following properties must be set in self._modifyStructure
#as well. Needs more thought.
props =(nanotube.getChirality(),
nanotube.getType(),
nanotube.getEndings(),
nanotube.getEndPoints())
self.struct.setProps(props)
return self.struct
except (PluginBug, UserError):
self.struct.kill()
raise PluginBug("Internal error while trying to recreate a NanotubeSegment.")
return None
def _modifyStructure(self, params):
"""
Modify the structure based on the parameters specified.
Overrides EditCommand._modifystructure. This method removes the old
nanotube and replaces it with a new one using self._createStructure.
"""
if not pref_nt_segment_resize_by_recreating_nanotube():
self._modifyStructure_NEW_SEGMENT_RESIZE(params)
return
# To modify the structure, we need to:
# 1. Delete the current nanotube chunk inside the NanotubeSegment group.
# 2. Create a new new nanotube chunk using nanotube.build()
# 3. Add the newly generated nanotube to this NanotubeSegment.
# 4. Update all the nanotube parameters.
# Note: Steps 2-4 are done in self._createStructure()
assert self.struct
self.struct.members[0].kill() # Delete the current nanotube chunk.
self.previousParams = params
self.struct = self._createStructure()
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 _get_resizeEnd_final_position(self,
ladderEndAxisAtom,
numberOfBases,
nanotubeRise):
final_position = None
if self.grabbedHandle:
final_position = self.grabbedHandle.currentPosition
else:
other_axisEndAtom = self.struct.getOtherAxisEndAtom(ladderEndAxisAtom)
axis_vector = ladderEndAxisAtom.posn() - other_axisEndAtom.posn()
segment_length_to_add = 0 #@
final_position = ladderEndAxisAtom.posn() + norm(axis_vector)*segment_length_to_add
return final_position
def getStructureName(self):
"""
Returns the name string of self.struct if there is a valid structure.
Otherwise returns None. This information is used by the name edit field
of this command's PM when we call self.propMgr.show()
@see: EditNanotube_PropertyManager.show()
@see: self.setStructureName
"""
if self.hasValidStructure():
return self.struct.name
return None
def setStructureName(self, name):
"""
Sets the name of self.struct to param <name> (if there is a valid
structure.
The PM of this command callss this method while closing itself
@param name: name of the structure to be set.
@type name: string
@see: EditNanotube_PropertyManager.close()
@see: self.getStructureName()
"""
#@BUG: We call this method in self.propMgr.close(). But propMgr.close()
#is called even when the command is 'cancelled'. That means the
#structure will get changed even when user hits cancel button or
#exits the command by clicking on empty space.
#This should really be done in self._finalizeStructure but that
#method doesn't get called when you click on empty space to exit
#the command. See EditNanotube_GraphicsMode.leftUp for a detailed
#comment.
if self.hasValidStructure():
self.struct.name = name
return
def getCursorText(self):
"""
This is used as a callback method in NanotubeLine mode
@see: NanotubeLineMode.setParams, NanotubeLineMode_GM.Draw
"""
if self.grabbedHandle is None:
return
text = ''
textColor = env.prefs[cursorTextColor_prefs_key]
if not env.prefs[editNanotubeEditCommand_showCursorTextCheckBox_prefs_key]:
return text, textColor
currentPosition = self.grabbedHandle.currentPosition
fixedEndOfStructure = self.grabbedHandle.fixedEndOfStructure
nanotubeLength = vlen( currentPosition - fixedEndOfStructure )
nanotubeLengthString = self._getCursorText_length(nanotubeLength)
text = nanotubeLengthString
#@TODO: The following updates the PM as the cursor moves.
#Need to rename this method so that you that it also does more things
#than just to return a textString -- Ninad 2007-12-20
self.propMgr.ntLengthLineEdit.setText(nanotubeLengthString)
return text, textColor
def _getCursorText_length(self, nanotubeLength):
"""
Returns a string that gives the length of the Nanotube for the cursor
text
"""
nanotubeLengthString = ''
if env.prefs[editNanotubeEditCommand_cursorTextCheckBox_length_prefs_key]:
lengthUnitString = 'A'
#change the unit of length to nanometers if the length is > 10A
#fixes part of bug 2856
if nanotubeLength > 10.0:
lengthUnitString = 'nm'
nanotubeLength = nanotubeLength * 0.1
nanotubeLengthString = "%5.3f%s"%(nanotubeLength, lengthUnitString)
return nanotubeLengthString
def modifyStructure(self):
"""
Called when a resize handle is dragged to change the length of the
segment. (Called upon leftUp) . This method assigns the new parameters
for the segment after it is resized and calls
preview_or_finalize_structure which does the rest of the job.
Note that Client should call this public method and should never call
the private method self._modifyStructure. self._modifyStructure is
called only by self.preview_or_finalize_structure
@see: B{EditNanotube_ResizeHandle.on_release} (the caller)
@see: B{SelectChunks_GraphicsMode.leftUp} (which calls the
the relevent method in DragHandler API. )
@see: B{exprs.DraggableHandle_AlongLine}, B{exprs.DragBehavior}
@see: B{self.preview_or_finalize_structure }
@see: B{self._modifyStructure}
As of 2008-02-01 it recreates the structure
@see: a note in self._createStructure() about use of ntSegment.setProps
"""
if not pref_nt_segment_resize_by_recreating_nanotube():
self.modifyStructure_NEW_SEGMENT_RESIZE()
return
if self.grabbedHandle is None:
return
self.propMgr.endPoint1 = self.grabbedHandle.fixedEndOfStructure
self.propMgr.endPoint2 = self.grabbedHandle.currentPosition
#@length = vlen(self.propMgr.endPoint1 - self.propMgr.endPoint2 ) #@
self.preview_or_finalize_structure(previewing = True)
self.updateHandlePositions()
self.glpane.gl_update()
return
def modifyStructure_NEW_SEGMENT_RESIZE(self): #@ NOT FIXED
"""
Called when a resize handle is dragged to change the length of the
segment. (Called upon leftUp) . This method assigns the new parameters
for the segment after it is resized and calls
preview_or_finalize_structure which does the rest of the job.
Note that Client should call this public method and should never call
the private method self._modifyStructure. self._modifyStructure is
called only by self.preview_or_finalize_structure
@see: B{EditNanotube_ResizeHandle.on_release} (the caller)
@see: B{SelectChunks_GraphicsMode.leftUp} (which calls the
the relevent method in DragHandler API. )
@see: B{exprs.DraggableHandle_AlongLine}, B{exprs.DragBehavior}
@see: B{self.preview_or_finalize_structure }
@see: B{self._modifyStructure}
As of 2008-02-01 it recreates the structure
@see: a note in self._createStructure() about use of ntSegment.setProps
"""
#TODO: need to cleanup this and may be use use something like
#self.previousParams = params in the end -- 2008-03-24 (midnight)
#@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 duplex'
#see also self._modifyStructure_NEW_SEGMENT_RESIZE
if self.grabbedHandle is None:
return
self.propMgr.endPoint1 = self.grabbedHandle.fixedEndOfStructure
self.propMgr.endPoint2 = self.grabbedHandle.currentPosition
DEBUG_DO_EVERYTHING_INSIDE_MODIFYSTRUCTURE_METHOD = False
if DEBUG_DO_EVERYTHING_INSIDE_MODIFYSTRUCTURE_METHOD:
# TO DO: this entire block of code. --Mark 2008-04-03
print_compact_stack("modifyStructure_NEW_SEGMENT_RESIZE(): NOT FIXED")
length = vlen(self.grabbedHandle.fixedEndOfStructure - \
self.grabbedHandle.currentPosition )
endAtom1, endAtom2 = self.struct.getAxisEndAtoms() #@
for atm in (endAtom1, endAtom2):
if not same_vals(self.grabbedHandle.fixedEndOfStructure, atm.posn()):
ladderEndAxisAtom = atm
break
endPoint1, endPoint2 = self.struct.nanotube.getEndPoints()
old_dulex_length = vlen(endPoint1 - endPoint2)
nanotubeRise = self.struct.getProps() #@
params_to_set_in_propMgr = (
self.grabbedHandle.origin,
self.grabbedHandle.currentPosition,
)
##self._modifyStructure(params)
############################################
self.nanotube = NanotubeParameters() #@ Creates 5x5 CNT. Missing PM params.
length_diff = self._determine_how_to_change_length()
ladderEndAxisAtom = self.get_axisEndAtom_at_resize_end() #@
#@ Nanotube class needs modify() method.
self.nanotube.modify(self.struct,
length_diff,
ladderEndAxisAtom.posn(),
self.grabbedHandle.currentPosition)
#TODO: Important note: How does NE1 know that structure is modified?
#Because number of base pairs parameter in the PropMgr changes as you
#drag the handle . This is done in self.getCursorText() ... not the
#right place to do it. OR that method needs to be renamed to reflect
#this as suggested in that method -- Ninad 2008-03-25
self.preview_or_finalize_structure(previewing = True)
##self.previousParams = params_to_set_in_propMgr
self.glpane.gl_update()
return
def get_axisEndAtom_at_resize_end(self):
ladderEndAxisAtom = None
if self.grabbedHandle is not None:
ladderEndAxisAtom = self.struct.getAxisEndAtomAtPosition(self.grabbedHandle.origin)
else:
endAtom1, endAtom2 = self.struct.getAxisEndAtoms()
ladderEndAxisAtom = endAtom2
return ladderEndAxisAtom
def _determine_how_to_change_length(self): #@ NEEDS WORK
"""
Returns the difference in length between the original nanotube and the
modified nanotube, where:
0 = no change in length
> 0 = lengthen
< 0 = trim
"""
nanotubeRise = self.struct.nanotube.getRise()
endPoint1, endPoint2 = self.struct.nanotube.getEndPoints() #@
original_nanotube_length = vlen(endPoint1 - endPoint2)
new_nanotube_length = vlen(endPoint1 - endPoint2) #@
return new_nanotube_length - original_nanotube_length #@ ALWAYS RETURNS ZERO
def makeMenus(self):
"""
Create context menu for this command.
"""
if not hasattr(self, 'graphicsMode'):
return
selobj = self.glpane.selobj
if selobj is None:
return
self.Menu_spec = []
highlightedChunk = None
if isinstance(selobj, Chunk):
highlightedChunk = selobj
if isinstance(selobj, Atom):
highlightedChunk = selobj.molecule
elif isinstance(selobj, Bond):
chunk1 = selobj.atom1.molecule
chunk2 = selobj.atom2.molecule
if chunk1 is chunk2 and chunk1 is not None:
highlightedChunk = chunk1
if highlightedChunk is None:
return
highlightedChunk.make_glpane_cmenu_items(self.Menu_spec, self)
return
