class InsertDna_PropertyManager(DnaOrCnt_PropertyManager):
"""
The InsertDna_PropertyManager class provides a Property Manager
for the B{Insert Dna} command.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@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
"""
title = "Insert DNA"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildDna/InsertDna.png"
def __init__(self, command):
"""
Constructor for the DNA Duplex property manager.
"""
self.endPoint1 = None
self.endPoint2 = None
self._conformation = "B-DNA"
self._numberOfBases = 0
self._basesPerTurn = getDuplexBasesPerTurn(self._conformation)
self._duplexRise = getDuplexRise(self._conformation)
self._duplexLength = getDuplexLength(self._conformation,
self._numberOfBases)
_superclass.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_CANCEL_BUTTON | \
PM_WHATS_THIS_BUTTON)
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
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self._placementOptions.buttonGroup,
SIGNAL("buttonClicked(int)"),
self.activateSpecifyReferencePlaneTool)
change_connect(self.conformationComboBox,
SIGNAL("currentIndexChanged(int)"),
self.conformationComboBoxChanged)
change_connect(self.numberOfBasePairsSpinBox,
SIGNAL("valueChanged(int)"), self.numberOfBasesChanged)
change_connect(self.basesPerTurnDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.basesPerTurnChanged)
change_connect(self.duplexRiseDoubleSpinBox,
SIGNAL("valueChanged(double)"), self.duplexRiseChanged)
change_connect(self.showCursorTextCheckBox,
SIGNAL('stateChanged(int)'),
self._update_state_of_cursorTextGroupBox)
self.duplexRiseDoubleSpinBox.connectWithState(
Preferences_StateRef_double(bdnaRise_prefs_key,
env.prefs[bdnaRise_prefs_key]))
self.basesPerTurnDoubleSpinBox.connectWithState(
Preferences_StateRef_double(bdnaBasesPerTurn_prefs_key,
env.prefs[bdnaBasesPerTurn_prefs_key]))
def show(self):
_superclass.show(self)
self.updateMessage("Specify the DNA parameters below, then click "\
"two endpoints in the graphics area to insert a DNA duplex.")
def _addGroupBoxes(self):
"""
Add the DNA Property Manager group boxes.
"""
self._pmReferencePlaneGroupBox = PM_GroupBox(self,
title="Placement Options")
self._loadReferencePlaneGroupBox(self._pmReferencePlaneGroupBox)
self._pmGroupBox1 = PM_GroupBox(self, title="Endpoints")
self._loadGroupBox1(self._pmGroupBox1)
self._pmGroupBox1.hide()
self._pmGroupBox2 = PM_GroupBox(self, title="Parameters")
self._loadGroupBox2(self._pmGroupBox2)
self._displayOptionsGroupBox = PM_GroupBox(self,
title="Display Options")
self._loadDisplayOptionsGroupBox(self._displayOptionsGroupBox)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 3.
"""
#Folllowing toolbutton facilitates entering a temporary DnaLineMode
#to create a DNA using endpoints of the specified line.
self.specifyDnaLineButton = PM_ToolButton(
pmGroupBox,
text="Specify Endpoints",
iconPath="ui/actions/Properties Manager/Pencil.png",
spanWidth=True)
self.specifyDnaLineButton.setCheckable(True)
self.specifyDnaLineButton.setAutoRaise(True)
self.specifyDnaLineButton.setToolButtonStyle(
Qt.ToolButtonTextBesideIcon)
#EndPoint1 and endPoint2 coordinates. These widgets are hidden
# as of 2007- 12 - 05
self._endPoint1SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
label="End Point 1")
self.x1SpinBox = self._endPoint1SpinBoxes.xSpinBox
self.y1SpinBox = self._endPoint1SpinBoxes.ySpinBox
self.z1SpinBox = self._endPoint1SpinBoxes.zSpinBox
self._endPoint2SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
label="End Point 2")
self.x2SpinBox = self._endPoint2SpinBoxes.xSpinBox
self.y2SpinBox = self._endPoint2SpinBoxes.ySpinBox
self.z2SpinBox = self._endPoint2SpinBoxes.zSpinBox
self._endPoint1SpinBoxes.hide()
self._endPoint2SpinBoxes.hide()
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box 4.
"""
self.conformationComboBox = \
PM_ComboBox( pmGroupBox,
label = "Conformation:",
choices = ["B-DNA"],
setAsDefault = True)
dnaModelChoices = ['PAM3', 'PAM5']
self.dnaModelComboBox = \
PM_ComboBox( pmGroupBox,
label = "Model:",
choices = dnaModelChoices,
setAsDefault = True)
self.basesPerTurnDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Bases per turn:",
value = env.prefs[bdnaBasesPerTurn_prefs_key],
setAsDefault = True,
minimum = 8.0,
maximum = 20.0,
decimals = 2,
singleStep = 0.1 )
self.duplexRiseDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Rise:",
value = env.prefs[bdnaRise_prefs_key],
setAsDefault = True,
minimum = 2.0,
maximum = 4.0,
decimals = 3,
singleStep = 0.01 )
# Strand Length (i.e. the number of bases)
self.numberOfBasePairsSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Base pairs:",
value = self._numberOfBases,
setAsDefault = False,
minimum = 0,
maximum = 10000 )
self.numberOfBasePairsSpinBox.setDisabled(True)
# Duplex Length
self.duplexLengthLineEdit = \
PM_LineEdit( pmGroupBox,
label = "Duplex length: ",
text = "0.0 Angstroms",
setAsDefault = False)
self.duplexLengthLineEdit.setDisabled(True)
def _loadDisplayOptionsGroupBox(self, pmGroupBox):
"""
Load widgets in the Display Options GroupBox
@see: DnaOrCnt_PropertyManager. _loadDisplayOptionsGroupBox
"""
#Call the superclass method that loads the cursor text checkboxes.
#Note, as of 2008-05-19, the superclass, DnaOrCnt_PropertyManager
#only loads the cursor text groupboxes. Subclasses like this can
#call custom methods like self._loadCursorTextCheckBoxes etc if they
#don't need all groupboxes that the superclass loads.
_superclass._loadDisplayOptionsGroupBox(self, pmGroupBox)
self._rubberbandLineGroupBox = PM_GroupBox(pmGroupBox,
title='Rubber band line:')
dnaLineChoices = ['Ribbons', 'Ladder']
self.dnaRubberBandLineDisplayComboBox = \
PM_ComboBox( self._rubberbandLineGroupBox ,
label = " Display as:",
choices = dnaLineChoices,
setAsDefault = True)
self.lineSnapCheckBox = \
PM_CheckBox(self._rubberbandLineGroupBox ,
text = 'Enable line snap' ,
widgetColumn = 1,
state = Qt.Checked
)
def _connect_showCursorTextCheckBox(self):
"""
Connect the show cursor text checkbox with user prefs_key.
Overrides
DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox
"""
connect_checkbox_with_boolean_pref(
self.showCursorTextCheckBox,
dnaDuplexEditCommand_showCursorTextCheckBox_prefs_key)
def _params_for_creating_cursorTextCheckBoxes(self):
"""
Returns params needed to create various cursor text checkboxes connected
to prefs_keys that allow custom cursor texts.
@return: A list containing tuples in the following format:
('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes
uses this data to create checkboxes with the the given names and
connects them to the provided preference keys. (Note that
PM_PrefsCheckBoxes puts thes within a GroupBox)
@rtype: list
@see: PM_PrefsCheckBoxes
@see: self._loadDisplayOptionsGroupBox where this list is used.
@see: Superclass method which is overridden here --
DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes()
"""
params = \
[ #Format: (" checkbox text", prefs_key)
("Number of base pairs",
dnaDuplexEditCommand_cursorTextCheckBox_numberOfBasePairs_prefs_key),
("Number of turns",
dnaDuplexEditCommand_cursorTextCheckBox_numberOfTurns_prefs_key),
("Duplex length",
dnaDuplexEditCommand_cursorTextCheckBox_length_prefs_key),
("Angle",
dnaDuplexEditCommand_cursorTextCheckBox_angle_prefs_key) ]
return params
def _addToolTipText(self):
"""
Tool Tip text for widgets in the DNA Property Manager.
"""
pass
def conformationComboBoxChanged(self, inIndex):
"""
Slot for the Conformation combobox. It is called whenever the
Conformation choice is changed.
@param inIndex: The new index.
@type inIndex: int
"""
conformation = self.conformationComboBox.currentText()
if conformation == "B-DNA":
self.basesPerTurnDoubleSpinBox.setValue("10.0")
elif conformation == "Z-DNA":
self.basesPerTurnDoubleSpinBox.setValue("12.0")
else:
msg = redmsg("conformationComboBoxChanged(): \
Error - unknown DNA conformation. Index = " + inIndex)
env.history.message(msg)
self.duplexLengthSpinBox.setSingleStep(getDuplexRise(conformation))
def numberOfBasesChanged(self, numberOfBases):
"""
Slot for the B{Number of Bases} spinbox.
"""
# Update the Duplex Length lineEdit widget.
text = str(getDuplexLength(self._conformation,
numberOfBases,
self._duplexRise)) \
+ " Angstroms"
self.duplexLengthLineEdit.setText(text)
return
def basesPerTurnChanged(self, basesPerTurn):
"""
Slot for the B{Bases per turn} spinbox.
"""
self.command.basesPerTurn = basesPerTurn
self._basesPerTurn = basesPerTurn
return
def duplexRiseChanged(self, rise):
"""
Slot for the B{Rise} spinbox.
"""
self.command.duplexRise = rise
self._duplexRise = rise
return
def getParameters(self):
"""
Return the parameters from this property manager
to be used to create the DNA duplex.
@return: A tuple containing the parameters
@rtype: tuple
@see: L{InsertDna_EditCommand._gatherParameters} where this is used
"""
numberOfBases = self.numberOfBasePairsSpinBox.value()
dnaForm = str(self.conformationComboBox.currentText())
basesPerTurn = self.basesPerTurnDoubleSpinBox.value()
duplexRise = self.duplexRiseDoubleSpinBox.value()
dnaModel = str(self.dnaModelComboBox.currentText())
# First endpoint (origin) of DNA duplex
x1 = self.x1SpinBox.value()
y1 = self.y1SpinBox.value()
z1 = self.z1SpinBox.value()
# Second endpoint (direction vector/axis) of DNA duplex.
x2 = self.x2SpinBox.value()
y2 = self.y2SpinBox.value()
z2 = self.z2SpinBox.value()
if not self.endPoint1:
self.endPoint1 = V(x1, y1, z1)
if not self.endPoint2:
self.endPoint2 = V(x2, y2, z2)
return (numberOfBases, dnaForm, dnaModel, basesPerTurn, duplexRise,
self.endPoint1, self.endPoint2)
def _addWhatsThisText(self):
"""
What's This text for widgets in this Property Manager.
"""
whatsThis_InsertDna_PropertyManager(self)
class EditNanotube_PropertyManager(DnaOrCnt_PropertyManager):
"""
The NanotubeSegmenta_PropertyManager class provides a Property Manager
for the EditNanotube_EditCommand.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@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
"""
title = "Nanotube Properties"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildNanotube/EditNanotube.png"
def __init__(self, command):
"""
Constructor for the Cnt Segment Properties property manager.
"""
#For model changed signal
self.previousSelectionParams = None
#see self.connect_or_disconnect_signals for comment about this flag
self.isAlreadyConnected = False
self.isAlreadyDisconnected = False
# Initialized here. Their values will be set in
# _update_widgets_in_PM_before_show()
self.endPoint1 = V(0, 0, 0)
self.endPoint2 = V(0, 0, 0)
_superclass.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_CANCEL_BUTTON | \
PM_WHATS_THIS_BUTTON)
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
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.nameLineEdit, SIGNAL("editingFinished()"),
self._nameChanged)
change_connect(self.showCursorTextCheckBox,
SIGNAL('stateChanged(int)'),
self._update_state_of_cursorTextGroupBox)
return
def show(self):
"""
Show this property manager. Overrides EditCommand_PM.show()
This method also retrives the name information from the
command's structure for its name line edit field.
@see: EditNanotube_EditCommand.getStructureName()
@see: self.close()
"""
_superclass.show(self)
#if self.command is not None:
#name = self.command.getStructureName()
#if name is not None:
#self.nameLineEdit.setText(name)
def close(self):
"""
Close this property manager.
Also sets the name of the self.command's structure to the one
displayed in the line edit field.
@see self.show()
@see: EditNanotube_EditCommand.setStructureName
"""
if self.command is not None:
name = str(self.nameLineEdit.text())
self.command.setStructureName(name)
_superclass.close(self)
def _connect_showCursorTextCheckBox(self):
"""
Connect the show cursor text checkbox with user prefs_key.
Overrides
DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox
"""
connect_checkbox_with_boolean_pref(
self.showCursorTextCheckBox,
editNanotubeEditCommand_showCursorTextCheckBox_prefs_key)
def _params_for_creating_cursorTextCheckBoxes(self):
"""
Returns params needed to create various cursor text checkboxes connected
to prefs_keys that allow custom cursor texts.
@return: A list containing tuples in the following format:
('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes
uses this data to create checkboxes with the the given names and
connects them to the provided preference keys. (Note that
PM_PrefsCheckBoxes puts thes within a GroupBox)
@rtype: list
@see: PM_PrefsCheckBoxes
@see: self._loadDisplayOptionsGroupBox where this list is used.
@see: Superclass method which is overridden here --
DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes()
"""
params = \
[ #Format: (" checkbox text", prefs_key)
("Nanotube length",
editNanotubeEditCommand_cursorTextCheckBox_length_prefs_key)
]
return params
def setParameters(self, params):
"""
This is called when entering "Nanotube Segment Properties
(i.e. "Edit properties...") to retrieve and set parameters of the
nanotube segment that might be modified during this command and
are needed to regenerate the nanotube segment.
@param params: The parameters of the nanotube segment.
These parameters are retreived via
L{NanotubeSegment.getProps()}, called from
L{EditNanotube_EditCommand.editStructure()}.
Parameters:
- n, m (chirality)
- type (i.e. carbon or boron nitride)
- endings (none, hydrogen, nitrogen)
- endpoints (endPoint1, endPoint2)
@type params: list (n, m), type, endings, (endPoint1, endPoint2)
@note: Any widgets in the property manager that display these
parameters should be updated here.
@see: L{NanotubeSegment.getProps()}
TODO:
- Make this a EditCommand_PM API method?
- See also the routines GraphicsMode.setParams or object.setProps
..better to name them all in one style?
"""
(self.n, self.m), self.type, self.endings,\
(self.endPoint1, self.endPoint2) = params
# This is needed to update the endpoints since the Nanotube segment
# may have been moved (i.e. translated or rotated). In that case,
# the endpoints are not updated, so we recompute them here.
nanotubeChunk = self.command.struct.members[0]
self.endPoint1, self.endPoint2, radius = \
self.command.struct.nanotube.computeEndPointsFromChunk(nanotubeChunk)
if 0:
print "\n--------------"
print "setParameters():"
print "Struct=", self.command.struct
print "N, M:", self.n, self.m
print "type:", self.type
print "endings:", self.endings
print "pt1, pt2:", self.endPoint1, self.endPoint2
def getParameters(self):
"""
Get the parameters that the edit command will use to determine if
any have changed. If any have, then the nanotube will be modified.
"""
if 0:
print "\n--------------"
print "getParameters():"
print "Struct=", self.command.struct
print "N, M:", self.n, self.m
print "type:", self.type
print "endings:", self.endings
print "pt1, pt2:", self.endPoint1, self.endPoint2
return (self.n, self.m, self.type, self.endings, self.endPoint1,
self.endPoint2)
def _update_widgets_in_PM_before_show(self):
"""
This is called only when user is editing an existing structure.
Its different than self.update_widgets_in_pm_before_show. (that method
is called just before showing the property manager)
@see: EditNanotube_EditCommand.editStructure()
"""
if self.command and self.command.hasValidStructure():
self.nanotube = self.command.struct.nanotube
self.n, self.m = self.nanotube.getChirality()
self.type = self.nanotube.getType()
self.endings = self.nanotube.getEndings()
self.endPoint1, self.endPoint2 = self.nanotube.getEndPoints()
pass
# Note that _update_widgets_in_PM_before_show() is called in
# self.show, before you connect the signals. So, for the
# 'first show' we will need to manually set the value of any
# widgets that need updated. But later, when a different
# NanotubeSegment is clicked, (while still in
# EditNanotube_EditCommand, the propMgr will already be connected
# so any calls in that case is redundant.
self.updateNameField()
self.updateLength()
self.updateNanotubeDiameter()
self.updateChirality()
return
def _update_UI_do_updates(self):
"""
Overrides superclass method.
@see: Command_PropertyManager._update_UI_do_updates()
"""
self._update_widgets_in_PM_before_show()
if self.command.struct:
msg = "Editing structure <b>%s</b>." % \
self.command.getStructureName()
else:
msg = "Select a nanotube to edit."
self.updateMessage(msg)
return
def _addGroupBoxes(self):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Parameters")
self._loadGroupBox1(self._pmGroupBox1)
self._displayOptionsGroupBox = PM_GroupBox(self,
title="Display Options")
self._loadDisplayOptionsGroupBox(self._displayOptionsGroupBox)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 4.
"""
self.nameLineEdit = PM_LineEdit(pmGroupBox,
label="Name:",
text="",
setAsDefault=False)
# Nanotube Length
self.ntLengthLineEdit = \
PM_LineEdit( pmGroupBox,
label = "Length: ",
text = "0.0 Angstroms",
setAsDefault = False)
self.ntLengthLineEdit.setDisabled(True)
# Nanotube Radius
self.ntDiameterLineEdit = \
PM_LineEdit( pmGroupBox,
label = "Nanotube Diameter: ",
setAsDefault = False)
self.ntDiameterLineEdit.setDisabled(True)
# Nanotube chirality. These are disabled (read-only) for now. --Mark
self.chiralityNSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Chirality (n) :",
minimum = 2,
maximum = 100,
setAsDefault = True )
self.chiralityNSpinBox.setDisabled(True)
self.chiralityMSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Chirality (m) :",
minimum = 0,
maximum = 100,
setAsDefault = True )
self.chiralityMSpinBox.setDisabled(True)
def _addWhatsThisText(self):
"""
Add what's this text.
"""
pass
def _addToolTipText(self):
"""
Add Tooltip text
"""
pass
def _nameChanged(self):
"""
Slot for "Name" field.
@TODO: Include a validator for the name field.
"""
_name = str(self.nameLineEdit.text())
if not _name: # Minimal test. Need to implement a validator.
self.updateNameField()
return
self.command.setStructureName(_name)
msg = "Editing structure <b>%s</b>." % _name
self.updateMessage(msg)
return
def updateNameField(self):
"""
Update the name field showing the name of the currently selected protein.
clear the combobox list.
"""
if self.command.hasValidStructure():
self.nameLineEdit.setEnabled(True)
self.nameLineEdit.setText(self.command.getStructureName())
else:
self.nameLineEdit.setDisabled(True)
self.nameLineEdit.setText("")
return
def updateLength(self):
"""
Update the nanotube Length lineEdit widget.
"""
if self.command.hasValidStructure():
_nanotubeLength = vlen(self.endPoint1 - self.endPoint2)
_lengthText = "%-7.4f Angstroms" % (_nanotubeLength)
else:
_lengthText = ""
self.ntLengthLineEdit.setText(_lengthText)
return
def updateNanotubeDiameter(self):
"""
Update the nanotube Diameter lineEdit widget.
"""
if self.command.hasValidStructure():
_diameterText = "%-7.4f Angstroms" % (self.nanotube.getDiameter())
else:
_diameterText = ""
self.ntDiameterLineEdit.setText(_diameterText)
return
def updateChirality(self):
"""
Update the nanotube chirality spinboxes (read-only).
"""
if self.command.hasValidStructure():
n, m = self.nanotube.getChirality()
else:
n = 0
m = 0
self.chiralityNSpinBox.setValue(n)
self.chiralityMSpinBox.setValue(m)
return
pass # End of EditNanotube_PropertyManager class
class EditNanotube_PropertyManager( DnaOrCnt_PropertyManager ):
"""
The NanotubeSegmenta_PropertyManager class provides a Property Manager
for the EditNanotube_EditCommand.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@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
"""
title = "Nanotube Properties"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildNanotube/EditNanotube.png"
def __init__( self, command ):
"""
Constructor for the Cnt Segment Properties property manager.
"""
#For model changed signal
self.previousSelectionParams = None
#see self.connect_or_disconnect_signals for comment about this flag
self.isAlreadyConnected = False
self.isAlreadyDisconnected = False
# Initialized here. Their values will be set in
# _update_widgets_in_PM_before_show()
self.endPoint1 = V(0, 0, 0)
self.endPoint2 = V(0, 0, 0)
_superclass.__init__( self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_CANCEL_BUTTON | \
PM_WHATS_THIS_BUTTON)
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
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.nameLineEdit,
SIGNAL("editingFinished()"),
self._nameChanged)
change_connect(self.showCursorTextCheckBox,
SIGNAL('stateChanged(int)'),
self._update_state_of_cursorTextGroupBox)
return
def show(self):
"""
Show this property manager. Overrides EditCommand_PM.show()
This method also retrives the name information from the
command's structure for its name line edit field.
@see: EditNanotube_EditCommand.getStructureName()
@see: self.close()
"""
_superclass.show(self)
#if self.command is not None:
#name = self.command.getStructureName()
#if name is not None:
#self.nameLineEdit.setText(name)
def close(self):
"""
Close this property manager.
Also sets the name of the self.command's structure to the one
displayed in the line edit field.
@see self.show()
@see: EditNanotube_EditCommand.setStructureName
"""
if self.command is not None:
name = str(self.nameLineEdit.text())
self.command.setStructureName(name)
_superclass.close(self)
def _connect_showCursorTextCheckBox(self):
"""
Connect the show cursor text checkbox with user prefs_key.
Overrides
DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox
"""
connect_checkbox_with_boolean_pref(
self.showCursorTextCheckBox ,
editNanotubeEditCommand_showCursorTextCheckBox_prefs_key)
def _params_for_creating_cursorTextCheckBoxes(self):
"""
Returns params needed to create various cursor text checkboxes connected
to prefs_keys that allow custom cursor texts.
@return: A list containing tuples in the following format:
('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes
uses this data to create checkboxes with the the given names and
connects them to the provided preference keys. (Note that
PM_PrefsCheckBoxes puts thes within a GroupBox)
@rtype: list
@see: PM_PrefsCheckBoxes
@see: self._loadDisplayOptionsGroupBox where this list is used.
@see: Superclass method which is overridden here --
DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes()
"""
params = \
[ #Format: (" checkbox text", prefs_key)
("Nanotube length",
editNanotubeEditCommand_cursorTextCheckBox_length_prefs_key)
]
return params
def setParameters(self, params):
"""
This is called when entering "Nanotube Segment Properties
(i.e. "Edit properties...") to retrieve and set parameters of the
nanotube segment that might be modified during this command and
are needed to regenerate the nanotube segment.
@param params: The parameters of the nanotube segment.
These parameters are retreived via
L{NanotubeSegment.getProps()}, called from
L{EditNanotube_EditCommand.editStructure()}.
Parameters:
- n, m (chirality)
- type (i.e. carbon or boron nitride)
- endings (none, hydrogen, nitrogen)
- endpoints (endPoint1, endPoint2)
@type params: list (n, m), type, endings, (endPoint1, endPoint2)
@note: Any widgets in the property manager that display these
parameters should be updated here.
@see: L{NanotubeSegment.getProps()}
TODO:
- Make this a EditCommand_PM API method?
- See also the routines GraphicsMode.setParams or object.setProps
..better to name them all in one style?
"""
(self.n, self.m), self.type, self.endings,\
(self.endPoint1, self.endPoint2) = params
# This is needed to update the endpoints since the Nanotube segment
# may have been moved (i.e. translated or rotated). In that case,
# the endpoints are not updated, so we recompute them here.
nanotubeChunk = self.command.struct.members[0]
self.endPoint1, self.endPoint2, radius = \
self.command.struct.nanotube.computeEndPointsFromChunk(nanotubeChunk)
if 0:
print "\n--------------"
print "setParameters():"
print "Struct=", self.command.struct
print "N, M:", self.n, self.m
print "type:", self.type
print "endings:", self.endings
print "pt1, pt2:", self.endPoint1, self.endPoint2
def getParameters(self):
"""
Get the parameters that the edit command will use to determine if
any have changed. If any have, then the nanotube will be modified.
"""
if 0:
print "\n--------------"
print "getParameters():"
print "Struct=", self.command.struct
print "N, M:", self.n, self.m
print "type:", self.type
print "endings:", self.endings
print "pt1, pt2:", self.endPoint1, self.endPoint2
return (self.n, self.m,
self.type,
self.endings,
self.endPoint1, self.endPoint2)
def _update_widgets_in_PM_before_show(self):
"""
This is called only when user is editing an existing structure.
Its different than self.update_widgets_in_pm_before_show. (that method
is called just before showing the property manager)
@see: EditNanotube_EditCommand.editStructure()
"""
if self.command and self.command.hasValidStructure():
self.nanotube = self.command.struct.nanotube
self.n, self.m = self.nanotube.getChirality()
self.type = self.nanotube.getType()
self.endings = self.nanotube.getEndings()
self.endPoint1, self.endPoint2 = self.nanotube.getEndPoints()
pass
# Note that _update_widgets_in_PM_before_show() is called in
# self.show, before you connect the signals. So, for the
# 'first show' we will need to manually set the value of any
# widgets that need updated. But later, when a different
# NanotubeSegment is clicked, (while still in
# EditNanotube_EditCommand, the propMgr will already be connected
# so any calls in that case is redundant.
self.updateNameField()
self.updateLength()
self.updateNanotubeDiameter()
self.updateChirality()
return
def _update_UI_do_updates(self):
"""
Overrides superclass method.
@see: Command_PropertyManager._update_UI_do_updates()
"""
self._update_widgets_in_PM_before_show()
if self.command.struct:
msg = "Editing structure <b>%s</b>." % \
self.command.getStructureName()
else:
msg = "Select a nanotube to edit."
self.updateMessage(msg)
return
def _addGroupBoxes( self ):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self, title = "Parameters" )
self._loadGroupBox1( self._pmGroupBox1 )
self._displayOptionsGroupBox = PM_GroupBox( self,
title = "Display Options" )
self._loadDisplayOptionsGroupBox( self._displayOptionsGroupBox )
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 4.
"""
self.nameLineEdit = PM_LineEdit( pmGroupBox,
label = "Name:",
text = "",
setAsDefault = False)
# Nanotube Length
self.ntLengthLineEdit = \
PM_LineEdit( pmGroupBox,
label = "Length: ",
text = "0.0 Angstroms",
setAsDefault = False)
self.ntLengthLineEdit.setDisabled(True)
# Nanotube Radius
self.ntDiameterLineEdit = \
PM_LineEdit( pmGroupBox,
label = "Nanotube Diameter: ",
setAsDefault = False)
self.ntDiameterLineEdit.setDisabled(True)
# Nanotube chirality. These are disabled (read-only) for now. --Mark
self.chiralityNSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Chirality (n) :",
minimum = 2,
maximum = 100,
setAsDefault = True )
self.chiralityNSpinBox.setDisabled(True)
self.chiralityMSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Chirality (m) :",
minimum = 0,
maximum = 100,
setAsDefault = True )
self.chiralityMSpinBox.setDisabled(True)
def _addWhatsThisText(self):
"""
Add what's this text.
"""
pass
def _addToolTipText(self):
"""
Add Tooltip text
"""
pass
def _nameChanged(self):
"""
Slot for "Name" field.
@TODO: Include a validator for the name field.
"""
_name = str(self.nameLineEdit.text())
if not _name: # Minimal test. Need to implement a validator.
self.updateNameField()
return
self.command.setStructureName(_name)
msg = "Editing structure <b>%s</b>." % _name
self.updateMessage(msg)
return
def updateNameField(self):
"""
Update the name field showing the name of the currently selected protein.
clear the combobox list.
"""
if self.command.hasValidStructure():
self.nameLineEdit.setEnabled(True)
self.nameLineEdit.setText(self.command.getStructureName())
else:
self.nameLineEdit.setDisabled(True)
self.nameLineEdit.setText("")
return
def updateLength( self ):
"""
Update the nanotube Length lineEdit widget.
"""
if self.command.hasValidStructure():
_nanotubeLength = vlen(self.endPoint1 - self.endPoint2)
_lengthText = "%-7.4f Angstroms" % (_nanotubeLength)
else:
_lengthText = ""
self.ntLengthLineEdit.setText(_lengthText)
return
def updateNanotubeDiameter(self):
"""
Update the nanotube Diameter lineEdit widget.
"""
if self.command.hasValidStructure():
_diameterText = "%-7.4f Angstroms" % (self.nanotube.getDiameter())
else:
_diameterText = ""
self.ntDiameterLineEdit.setText(_diameterText)
return
def updateChirality( self ):
"""
Update the nanotube chirality spinboxes (read-only).
"""
if self.command.hasValidStructure():
n, m = self.nanotube.getChirality()
else:
n = 0
m = 0
self.chiralityNSpinBox.setValue(n)
self.chiralityMSpinBox.setValue(m)
return
pass # End of EditNanotube_PropertyManager class
class DnaDuplexPropertyManager( DnaOrCnt_PropertyManager ):
"""
The DnaDuplexPropertyManager class provides a Property Manager
for the B{Build > DNA > Duplex} command.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@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
"""
title = "Insert DNA"
pmName = title
iconPath = "ui/actions/Tools/Build Structures/InsertDsDna.png"
def __init__( self, win, editCommand ):
"""
Constructor for the DNA Duplex property manager.
"""
self.endPoint1 = None
self.endPoint2 = None
self._conformation = "B-DNA"
self._numberOfBases = 0
self._basesPerTurn = getDuplexBasesPerTurn(self._conformation)
self._duplexRise = getDuplexRise(self._conformation)
self._duplexLength = getDuplexLength(self._conformation,
self._numberOfBases)
_superclass.__init__( self,
win,
editCommand)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_CANCEL_BUTTON | \
PM_WHATS_THIS_BUTTON)
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
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self._placementOptions.buttonGroup,
SIGNAL("buttonClicked(int)"),
self.activateSpecifyReferencePlaneTool)
change_connect( self.conformationComboBox,
SIGNAL("currentIndexChanged(int)"),
self.conformationComboBoxChanged )
change_connect( self.numberOfBasePairsSpinBox,
SIGNAL("valueChanged(int)"),
self.numberOfBasesChanged )
change_connect( self.basesPerTurnDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.basesPerTurnChanged )
change_connect( self.duplexRiseDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.duplexRiseChanged )
change_connect(self.showCursorTextCheckBox,
SIGNAL('stateChanged(int)'),
self._update_state_of_cursorTextGroupBox)
self.duplexRiseDoubleSpinBox.connectWithState(
Preferences_StateRef_double( bdnaRise_prefs_key,
env.prefs[bdnaRise_prefs_key] )
)
self.basesPerTurnDoubleSpinBox.connectWithState(
Preferences_StateRef_double( bdnaBasesPerTurn_prefs_key,
env.prefs[bdnaBasesPerTurn_prefs_key] )
)
def ok_btn_clicked(self):
"""
Slot for the OK button
"""
if self.editCommand:
self.editCommand.preview_or_finalize_structure(previewing = False)
##env.history.message(self.editCommand.logMessage)
self.win.toolsDone()
def cancel_btn_clicked(self):
"""
Slot for the Cancel button.
"""
if self.editCommand:
self.editCommand.cancelStructure()
self.win.toolsCancel()
def _update_widgets_in_PM_before_show(self):
"""
Update various widgets in this Property manager.
Overrides superclass method
@see: MotorPropertyManager._update_widgets_in_PM_before_show
@see: self.show where it is called.
"""
pass
def getFlyoutActionList(self):
""" returns custom actionlist that will be used in a specific mode
or editing a feature etc Example: while in movie mode,
the _createFlyoutToolBar method calls
this """
#'allActionsList' returns all actions in the flyout toolbar
#including the subcontrolArea actions
allActionsList = []
#Action List for subcontrol Area buttons.
#In this mode there is really no subcontrol area.
#We will treat subcontrol area same as 'command area'
#(subcontrol area buttons will have an empty list as their command area
#list). We will set the Comamnd Area palette background color to the
#subcontrol area.
subControlAreaActionList =[]
self.exitEditCommandAction.setChecked(True)
subControlAreaActionList.append(self.exitEditCommandAction)
separator = QAction(self.w)
separator.setSeparator(True)
subControlAreaActionList.append(separator)
allActionsList.extend(subControlAreaActionList)
#Empty actionlist for the 'Command Area'
commandActionLists = []
#Append empty 'lists' in 'commandActionLists equal to the
#number of actions in subControlArea
for i in range(len(subControlAreaActionList)):
lst = []
commandActionLists.append(lst)
params = (subControlAreaActionList, commandActionLists, allActionsList)
return params
def _addGroupBoxes( self ):
"""
Add the DNA Property Manager group boxes.
"""
self._pmReferencePlaneGroupBox = PM_GroupBox( self,
title = "Placement Options" )
self._loadReferencePlaneGroupBox( self._pmReferencePlaneGroupBox )
self._pmGroupBox1 = PM_GroupBox( self, title = "Endpoints" )
self._loadGroupBox1( self._pmGroupBox1 )
self._pmGroupBox1.hide()
self._pmGroupBox2 = PM_GroupBox( self, title = "Parameters" )
self._loadGroupBox2( self._pmGroupBox2 )
self._displayOptionsGroupBox = PM_GroupBox( self,
title = "Display Options" )
self._loadDisplayOptionsGroupBox( self._displayOptionsGroupBox )
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 3.
"""
#Folllowing toolbutton facilitates entering a temporary DnaLineMode
#to create a DNA using endpoints of the specified line.
self.specifyDnaLineButton = PM_ToolButton(
pmGroupBox,
text = "Specify Endpoints",
iconPath = "ui/actions/Properties Manager/Pencil.png",
spanWidth = True
)
self.specifyDnaLineButton.setCheckable(True)
self.specifyDnaLineButton.setAutoRaise(True)
self.specifyDnaLineButton.setToolButtonStyle(
Qt.ToolButtonTextBesideIcon)
#EndPoint1 and endPoint2 coordinates. These widgets are hidden
# as of 2007- 12 - 05
self._endPoint1SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
label = "End Point 1")
self.x1SpinBox = self._endPoint1SpinBoxes.xSpinBox
self.y1SpinBox = self._endPoint1SpinBoxes.ySpinBox
self.z1SpinBox = self._endPoint1SpinBoxes.zSpinBox
self._endPoint2SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
label = "End Point 2")
self.x2SpinBox = self._endPoint2SpinBoxes.xSpinBox
self.y2SpinBox = self._endPoint2SpinBoxes.ySpinBox
self.z2SpinBox = self._endPoint2SpinBoxes.zSpinBox
self._endPoint1SpinBoxes.hide()
self._endPoint2SpinBoxes.hide()
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box 4.
"""
self.conformationComboBox = \
PM_ComboBox( pmGroupBox,
label = "Conformation:",
choices = ["B-DNA"],
setAsDefault = True)
dnaModelChoices = ['PAM3', 'PAM5']
self.dnaModelComboBox = \
PM_ComboBox( pmGroupBox,
label = "Model:",
choices = dnaModelChoices,
setAsDefault = True)
self.basesPerTurnDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Bases per turn:",
value = env.prefs[bdnaBasesPerTurn_prefs_key],
setAsDefault = True,
minimum = 8.0,
maximum = 20.0,
decimals = 2,
singleStep = 0.1 )
self.duplexRiseDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Rise:",
value = env.prefs[bdnaRise_prefs_key],
setAsDefault = True,
minimum = 2.0,
maximum = 4.0,
decimals = 3,
singleStep = 0.01 )
# Strand Length (i.e. the number of bases)
self.numberOfBasePairsSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Base pairs:",
value = self._numberOfBases,
setAsDefault = False,
minimum = 0,
maximum = 10000 )
self.numberOfBasePairsSpinBox.setDisabled(True)
# Duplex Length
self.duplexLengthLineEdit = \
PM_LineEdit( pmGroupBox,
label = "Duplex length: ",
text = "0.0 Angstroms",
setAsDefault = False)
self.duplexLengthLineEdit.setDisabled(True)
def _loadDisplayOptionsGroupBox(self, pmGroupBox):
"""
Load widgets in the Display Options GroupBox
@see: DnaOrCnt_PropertyManager. _loadDisplayOptionsGroupBox
"""
#Call the superclass method that loads the cursor text checkboxes.
#Note, as of 2008-05-19, the superclass, DnaOrCnt_PropertyManager
#only loads the cursor text groupboxes. Subclasses like this can
#call custom methods like self._loadCursorTextCheckBoxes etc if they
#don't need all groupboxes that the superclass loads.
_superclass._loadDisplayOptionsGroupBox(self, pmGroupBox)
self._rubberbandLineGroupBox = PM_GroupBox(
pmGroupBox,
title = 'Rubber band line:')
dnaLineChoices = ['Ribbons', 'Ladder']
self.dnaRubberBandLineDisplayComboBox = \
PM_ComboBox( self._rubberbandLineGroupBox ,
label = " Display as:",
choices = dnaLineChoices,
setAsDefault = True)
self.lineSnapCheckBox = \
PM_CheckBox(self._rubberbandLineGroupBox ,
text = 'Enable line snap' ,
widgetColumn = 1,
state = Qt.Checked
)
def _connect_showCursorTextCheckBox(self):
"""
Connect the show cursor text checkbox with user prefs_key.
Overrides
DnaOrCnt_PropertyManager._connect_showCursorTextCheckBox
"""
connect_checkbox_with_boolean_pref(
self.showCursorTextCheckBox ,
dnaDuplexEditCommand_showCursorTextCheckBox_prefs_key)
def _params_for_creating_cursorTextCheckBoxes(self):
"""
Returns params needed to create various cursor text checkboxes connected
to prefs_keys that allow custom cursor texts.
@return: A list containing tuples in the following format:
('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes
uses this data to create checkboxes with the the given names and
connects them to the provided preference keys. (Note that
PM_PrefsCheckBoxes puts thes within a GroupBox)
@rtype: list
@see: PM_PrefsCheckBoxes
@see: self._loadDisplayOptionsGroupBox where this list is used.
@see: Superclass method which is overridden here --
DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes()
"""
params = \
[ #Format: (" checkbox text", prefs_key)
("Number of base pairs",
dnaDuplexEditCommand_cursorTextCheckBox_numberOfBasePairs_prefs_key),
("Number of turns",
dnaDuplexEditCommand_cursorTextCheckBox_numberOfTurns_prefs_key),
("Duplex length",
dnaDuplexEditCommand_cursorTextCheckBox_length_prefs_key),
("Angle",
dnaDuplexEditCommand_cursorTextCheckBox_angle_prefs_key) ]
return params
def _addToolTipText(self):
"""
Tool Tip text for widgets in the DNA Property Manager.
"""
pass
def conformationComboBoxChanged( self, inIndex ):
"""
Slot for the Conformation combobox. It is called whenever the
Conformation choice is changed.
@param inIndex: The new index.
@type inIndex: int
"""
conformation = self.conformationComboBox.currentText()
if conformation == "B-DNA":
self.basesPerTurnDoubleSpinBox.setValue("10.0")
elif conformation == "Z-DNA":
self.basesPerTurnDoubleSpinBox.setValue("12.0")
else:
msg = redmsg("conformationComboBoxChanged(): \
Error - unknown DNA conformation. Index = "+ inIndex)
env.history.message(msg)
self.duplexLengthSpinBox.setSingleStep(getDuplexRise(conformation))
def numberOfBasesChanged( self, numberOfBases ):
"""
Slot for the B{Number of Bases} spinbox.
"""
# Update the Duplex Length lineEdit widget.
text = str(getDuplexLength(self._conformation,
numberOfBases,
self._duplexRise)) \
+ " Angstroms"
self.duplexLengthLineEdit.setText(text)
return
def basesPerTurnChanged( self, basesPerTurn ):
"""
Slot for the B{Bases per turn} spinbox.
"""
self.editCommand.basesPerTurn = basesPerTurn
self._basesPerTurn = basesPerTurn
return
def duplexRiseChanged( self, rise ):
"""
Slot for the B{Rise} spinbox.
"""
self.editCommand.duplexRise = rise
self._duplexRise = rise
return
def getParameters(self):
"""
Return the parameters from this property manager
to be used to create the DNA duplex.
@return: A tuple containing the parameters
@rtype: tuple
@see: L{DnaDuplex_EditCommand._gatherParameters} where this is used
"""
numberOfBases = self.numberOfBasePairsSpinBox.value()
dnaForm = str(self.conformationComboBox.currentText())
basesPerTurn = self.basesPerTurnDoubleSpinBox.value()
duplexRise = self.duplexRiseDoubleSpinBox.value()
dnaModel = str(self.dnaModelComboBox.currentText())
# First endpoint (origin) of DNA duplex
x1 = self.x1SpinBox.value()
y1 = self.y1SpinBox.value()
z1 = self.z1SpinBox.value()
# Second endpoint (direction vector/axis) of DNA duplex.
x2 = self.x2SpinBox.value()
y2 = self.y2SpinBox.value()
z2 = self.z2SpinBox.value()
if not self.endPoint1:
self.endPoint1 = V(x1, y1, z1)
if not self.endPoint2:
self.endPoint2 = V(x2, y2, z2)
return (numberOfBases,
dnaForm,
dnaModel,
basesPerTurn,
duplexRise,
self.endPoint1,
self.endPoint2)
def _addWhatsThisText(self):
"""
What's This text for widgets in this Property Manager.
"""
whatsThis_DnaDuplexPropertyManager(self)
