class OrderDna_PropertyManager(Command_PropertyManager):
"""
The OrderDna_PropertyManager class provides a Property Manager
for the B{Order Dna} command on the flyout toolbar in the
Build > Dna mode.
@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 = "Order DNA"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildDna/OrderDna.png"
def __init__(self, command):
"""
Constructor for the property manager.
"""
_superclass.__init__(self, command)
self.assy = self.win.assy
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
self.update_includeStrands() # Updates the message box.
return
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.viewDnaOrderFileButton, SIGNAL("clicked()"),
self.viewDnaOrderFile)
change_connect(self.includeStrandsComboBox, SIGNAL("activated(int)"),
self.update_includeStrands)
return
def _addGroupBoxes(self):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Options")
self._loadGroupBox1(self._pmGroupBox1)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
includeStrandsChoices = [
"All strands in model", "Selected strands only"
]
self.includeStrandsComboBox = \
PM_ComboBox( pmGroupBox,
label = "Include strands:",
choices = includeStrandsChoices,
setAsDefault = True)
self.numberOfBasesLineEdit = \
PM_LineEdit( pmGroupBox,
label = "Total nucleotides:",
text = str(self.getNumberOfBases()))
self.numberOfBasesLineEdit.setEnabled(False)
self.numberOfXBasesLineEdit = \
PM_LineEdit( pmGroupBox,
label = "Unassigned:",
text = str(self.getNumberOfBases(unassignedOnly = True)))
self.numberOfXBasesLineEdit.setEnabled(False)
self.viewDnaOrderFileButton = \
PM_PushButton( pmGroupBox,
label = "",
text = "View DNA Order File...",
spanWidth = True)
return
def _addWhatsThisText(self):
"""
What's This text for widgets in this Property Manager.
"""
whatsThis_OrderDna_PropertyManager(self)
return
def _addToolTipText(self):
"""
Tool Tip text for widgets in the DNA Property Manager.
"""
pass
# Ask Bruce where this should live (i.e. class Part?) --Mark
def getAllDnaStrands(self, selectedOnly=False):
"""
Returns a list of all the DNA strands in the current part, or only
the selected strands if I{selectedOnly} is True.
@param selectedOnly: If True, return only the selected DNA strands.
@type selectedOnly: bool
"""
dnaStrandList = []
def func(node):
if isinstance(node, DnaStrand):
if selectedOnly:
if node.picked:
dnaStrandList.append(node)
else:
dnaStrandList.append(node)
self.win.assy.part.topnode.apply2all(func)
return dnaStrandList
def getNumberOfBases(self, selectedOnly=False, unassignedOnly=False):
"""
Returns the number of bases count for all the DNA strands in the
current part, or only the selected strand if I{selectedOnly} is True.
@param selectedOnly: If True, return only the number of bases in the
selected DNA strands.
@type selectedOnly: bool
@param unassignedOnly: If True, return only the number of unassigned
bases (i.e. base letters = X).
@type unassignedOnly: bool
"""
dnaSequenceString = ''
selectedOnly = self.includeStrandsComboBox.currentIndex()
strandList = self.getAllDnaStrands(selectedOnly)
for strand in strandList:
strandSequenceString = str(strand.getStrandSequence())
dnaSequenceString += strandSequenceString
if unassignedOnly:
return dnaSequenceString.count("X")
return len(dnaSequenceString)
def _update_UI_do_updates(self):
"""
Overrides superclass method.
"""
self.update_includeStrands()
return
def getDnaSequence(self, format='CSV'):
"""
Return the complete Dna sequence information string (i.e. all strand
sequences) in the specified format.
@return: The Dna sequence string
@rtype: string
"""
if format == 'CSV': #comma separated values.
separator = ','
dnaSequenceString = ''
selectedOnly = self.includeStrandsComboBox.currentIndex()
strandList = self.getAllDnaStrands(selectedOnly)
for strand in strandList:
dnaSequenceString = dnaSequenceString + strand.name + separator
strandSequenceString = str(strand.getStrandSequence())
if strandSequenceString:
strandSequenceString = strandSequenceString.upper()
strandLength = str(len(strandSequenceString)) + separator
dnaSequenceString = dnaSequenceString + strandLength + strandSequenceString
dnaSequenceString = dnaSequenceString + "\n"
return dnaSequenceString
def viewDnaOrderFile(self, openFileInEditor=True):
"""
Writes a DNA Order file in comma-separated values (CSV) format
and opens it in a text editor.
The user must save the file to a permanent location using the
text editor.
@see: Ui_DnaFlyout.orderDnaCommand
@see: writeDnaOrderFile()
@TODO: assy.getAllDnaObjects().
"""
dnaSequence = self.getDnaSequence(format='CSV')
if dnaSequence:
tmpdir = find_or_make_Nanorex_subdir('temp')
fileBaseName = 'DnaOrder'
temporaryFile = os.path.join(tmpdir, "%s.csv" % fileBaseName)
writeDnaOrderFile(temporaryFile, self.assy,
self.getNumberOfBases(),
self.getNumberOfBases(unassignedOnly=True),
dnaSequence)
if openFileInEditor:
open_file_in_editor(temporaryFile)
return
def update_includeStrands(self, ignoreVal=0):
"""
Slot method for "Include (strands)" combobox.
"""
idx = self.includeStrandsComboBox.currentIndex()
includeType = ["model", "selection"]
_numberOfBases = self.getNumberOfBases()
self.numberOfBasesLineEdit.setText(str(_numberOfBases) + " bases")
_numberOfXBases = self.getNumberOfBases(unassignedOnly=True)
self.numberOfXBasesLineEdit.setText(str(_numberOfXBases) + " bases")
# Make the background color red if there are any unassigned bases.
if _numberOfXBases:
self.numberOfXBasesLineEdit.setStyleSheet(\
"QLineEdit {"\
"background-color: rgb(255, 0, 0)"\
"}")
else:
self.numberOfXBasesLineEdit.setStyleSheet(\
"QLineEdit {"\
"background-color: rgb(255, 255, 255)"\
"}")
if _numberOfBases > 0:
self.viewDnaOrderFileButton.setEnabled(True)
msg = "Click on <b>View DNA Order File...</b> to preview a " \
"DNA order for all DNA strands in the current %s." \
% includeType[idx]
else:
self.viewDnaOrderFileButton.setEnabled(False)
msg = "<font color=red>" \
"There are no DNA strands in the current %s." \
% includeType[idx]
self.updateMessage(msg)
return
class Ui_BuildAtomsPropertyManager(Command_PropertyManager):
"""
The Ui_BuildAtomsPropertyManager class defines UI elements for the Property
Manager of the B{Build Atoms mode}.
@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
"""
# The title that appears in the Property Manager header
title = "Build Atoms"
# The name of this Property Manager. This will be set to
# the name of the PM_Dialog object via setObjectName().
pmName = title
# The relative path to the PNG file that appears in the header
iconPath = "ui/actions/Tools/Build Structures/BuildAtoms.png"
def __init__(self, command):
"""
Constructor for the B{Build Atoms} property manager class that defines
its UI.
@param command: The parent mode where this Property Manager is used
@type command: L{depositMode}
"""
self.previewGroupBox = None
self.regularElementChooser = None
self.PAM5Chooser = None
self.PAM3Chooser = None
self.elementChooser = None
self.advancedOptionsGroupBox = None
self.bondToolsGroupBox = None
self.selectionFilterCheckBox = None
self.filterlistLE = None
self.selectedAtomInfoLabel = None
#Initialize the following to None. (subclasses may not define this)
#Make sure you initialize it before adding groupboxes!
self.selectedAtomPosGroupBox = None
self.showSelectedAtomInfoCheckBox = None
_superclass.__init__(self, command)
self.showTopRowButtons(PM_DONE_BUTTON | PM_WHATS_THIS_BUTTON)
msg = ''
self.MessageGroupBox.insertHtmlMessage(msg, setAsDefault=False)
def _addGroupBoxes(self):
"""
Add various group boxes to the Build Atoms Property manager.
"""
self._addPreviewGroupBox()
self._addAtomChooserGroupBox()
self._addBondToolsGroupBox()
#@@@TODO HIDE the bonds tool groupbox initially as the
#by default, the atoms tool is active when BuildAtoms command is
#finist invoked.
self.bondToolsGroupBox.hide()
self._addSelectionOptionsGroupBox()
self._addAdvancedOptionsGroupBox()
def _addPreviewGroupBox(self):
"""
Adde the preview groupbox that shows the element selected in the
element chooser.
"""
self.previewGroupBox = PM_PreviewGroupBox(self, glpane=self.o)
def _addAtomChooserGroupBox(self):
"""
Add the Atom Chooser groupbox. This groupbox displays one of the
following three groupboxes depending on the choice selected in the
combobox:
a) Periodic Table Elements L{self.regularElementChooser}
b) PAM5 Atoms L{self.PAM5Chooser}
c) PAM3 Atoms L{self.PAM3Chooser}
@see: L{self.__updateAtomChooserGroupBoxes}
"""
self.atomChooserGroupBox = \
PM_GroupBox(self, title = "Atom Chooser")
self._loadAtomChooserGroupBox(self.atomChooserGroupBox)
self._updateAtomChooserGroupBoxes(currentIndex=0)
def _addElementChooserGroupBox(self, inPmGroupBox):
"""
Add the 'Element Chooser' groupbox. (present within the
Atom Chooser Groupbox)
"""
if not self.previewGroupBox:
return
elementViewer = self.previewGroupBox.elementViewer
self.regularElementChooser = \
PM_ElementChooser( inPmGroupBox,
parentPropMgr = self,
elementViewer = elementViewer)
def _add_PAM5_AtomChooserGroupBox(self, inPmGroupBox):
"""
Add the 'PAM5 Atom Chooser' groupbox (present within the
Atom Chooser Groupbox)
"""
if not self.previewGroupBox:
return
elementViewer = self.previewGroupBox.elementViewer
self.PAM5Chooser = \
PM_PAM5_AtomChooser( inPmGroupBox,
parentPropMgr = self,
elementViewer = elementViewer)
def _add_PAM3_AtomChooserGroupBox(self, inPmGroupBox):
"""
Add the 'PAM3 Atom Chooser' groupbox (present within the
Atom Chooser Groupbox)
"""
if not self.previewGroupBox:
return
elementViewer = self.previewGroupBox.elementViewer
self.PAM3Chooser = \
PM_PAM3_AtomChooser( inPmGroupBox,
parentPropMgr = self,
elementViewer = elementViewer)
def _hideAllAtomChooserGroupBoxes(self):
"""
Hides all Atom Chooser group boxes.
"""
if self.regularElementChooser:
self.regularElementChooser.hide()
if self.PAM5Chooser:
self.PAM5Chooser.hide()
if self.PAM3Chooser:
self.PAM3Chooser.hide()
def _addBondToolsGroupBox(self):
"""
Add the 'Bond Tools' groupbox.
"""
self.bondToolsGroupBox = \
PM_GroupBox( self, title = "Bond Tools")
self._loadBondToolsGroupBox(self.bondToolsGroupBox)
def _addSelectionOptionsGroupBox(self):
"""
Add 'Selection Options' groupbox
"""
self.selectionOptionsGroupBox = \
PM_GroupBox( self, title = "Selection Options" )
self._loadSelectionOptionsGroupBox(self.selectionOptionsGroupBox)
def _loadAtomChooserGroupBox(self, inPmGroupBox):
"""
Load the widgets inside the Atom Chooser groupbox.
@param inPmGroupBox: The Atom Chooser box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
atomChooserChoices = [
"Periodic Table Elements", "PAM5 Atoms", "PAM3 Atoms"
]
self.atomChooserComboBox = \
PM_ComboBox( inPmGroupBox,
label = '',
choices = atomChooserChoices,
index = 0,
setAsDefault = False,
spanWidth = True )
#Following fixes bug 2550
self.atomChooserComboBox.setFocusPolicy(Qt.NoFocus)
self._addElementChooserGroupBox(inPmGroupBox)
self._add_PAM5_AtomChooserGroupBox(inPmGroupBox)
self._add_PAM3_AtomChooserGroupBox(inPmGroupBox)
def _loadSelectionOptionsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Selection Options group box.
@param inPmGroupBox: The Selection Options box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
self.selectionFilterCheckBox = \
PM_CheckBox( inPmGroupBox,
text = "Enable atom selection filter",
widgetColumn = 0,
state = Qt.Unchecked )
self.selectionFilterCheckBox.setDefaultValue(False)
self.filterlistLE = PM_LineEdit(inPmGroupBox,
label="",
text="",
setAsDefault=False,
spanWidth=True)
self.filterlistLE.setReadOnly(True)
if self.selectionFilterCheckBox.isChecked():
self.filterlistLE.setEnabled(True)
else:
self.filterlistLE.setEnabled(False)
self.showSelectedAtomInfoCheckBox = \
PM_CheckBox(
inPmGroupBox,
text = "Show Selected Atom Info",
widgetColumn = 0,
state = Qt.Unchecked)
self.selectedAtomPosGroupBox = \
PM_GroupBox( inPmGroupBox, title = "")
self._loadSelectedAtomPosGroupBox(self.selectedAtomPosGroupBox)
self.toggle_selectedAtomPosGroupBox(show=0)
self.enable_or_disable_selectedAtomPosGroupBox(bool_enable=False)
self.reshapeSelectionCheckBox = \
PM_CheckBox( inPmGroupBox,
text = 'Dragging reshapes selection',
widgetColumn = 0,
state = Qt.Unchecked )
connect_checkbox_with_boolean_pref(self.reshapeSelectionCheckBox,
reshapeAtomsSelection_prefs_key)
env.prefs[reshapeAtomsSelection_prefs_key] = False
self.waterCheckBox = \
PM_CheckBox( inPmGroupBox,
text = "Z depth filter (water surface)",
widgetColumn = 0,
state = Qt.Unchecked )
def _loadSelectedAtomPosGroupBox(self, inPmGroupBox):
"""
Load the selected Atoms position groupbox It is a sub-gropbox of
L{self.selectionOptionsGroupBox)
@param inPmGroupBox: 'The Selected Atom Position Groupbox'
@type inPmGroupBox: L{PM_GroupBox}
"""
self.selectedAtomLineEdit = PM_LineEdit(inPmGroupBox,
label="Selected Atom:",
text="",
setAsDefault=False,
spanWidth=False)
self.selectedAtomLineEdit.setReadOnly(True)
self.selectedAtomLineEdit.setEnabled(False)
self.coordinateSpinboxes = PM_CoordinateSpinBoxes(inPmGroupBox)
# User input to specify x-coordinate
self.xCoordOfSelectedAtom = self.coordinateSpinboxes.xSpinBox
# User input to specify y-coordinate
self.yCoordOfSelectedAtom = self.coordinateSpinboxes.ySpinBox
# User input to specify z-coordinate
self.zCoordOfSelectedAtom = self.coordinateSpinboxes.zSpinBox
def _addAdvancedOptionsGroupBox(self):
"""
Add 'Advanced Options' groupbox
"""
self.advancedOptionsGroupBox = \
PM_GroupBox( self, title = "Advanced Options" )
self._loadAdvancedOptionsGroupBox(self.advancedOptionsGroupBox)
def _loadAdvancedOptionsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Advanced Options group box.
@param inPmGroupBox: The Advanced Options box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
self.autoBondCheckBox = \
PM_CheckBox( inPmGroupBox,
text = 'Auto bond',
widgetColumn = 0,
state = Qt.Checked )
self.highlightingCheckBox = \
PM_CheckBox( inPmGroupBox,
text = "Hover highlighting",
widgetColumn = 0,
state = Qt.Checked )
def _loadBondToolsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Bond Tools group box.
@param inPmGroupBox: The Bond Tools box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
# Button list to create a toolbutton row.
# Format:
# - buttonId,
# - buttonText ,
# - iconPath
# - tooltip
# - shortcut
# - column
BOND_TOOL_BUTTONS = \
[ ( "QToolButton", 0, "SINGLE", "", "", None, 0),
( "QToolButton", 1, "DOUBLE", "", "", None, 1),
( "QToolButton", 2, "TRIPLE", "", "", None, 2),
( "QToolButton", 3, "AROMATIC", "", "", None, 3),
( "QToolButton", 4, "GRAPHITIC", "", "", None, 4),
( "QToolButton", 5, "CUTBONDS", "", "", None, 5)
]
self.bondToolButtonRow = \
PM_ToolButtonRow(
inPmGroupBox,
title = "",
buttonList = BOND_TOOL_BUTTONS,
checkedId = None,
setAsDefault = True )
def _addWhatsThisText(self):
"""
"What's This" text for widgets in this Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_BuildAtomsPropertyManager
whatsThis_BuildAtomsPropertyManager(self)
def _addToolTipText(self):
"""
Tool Tip text for widgets in this Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_BuildAtomsPropertyManager
ToolTip_BuildAtomsPropertyManager(self)
def toggle_selectedAtomPosGroupBox(self, show=0):
"""
Show or hide L{self.selectedAtomPosGroupBox} depending on the state of
the checkbox (L{self.showSelectedAtomInfoCheckBox})
@param show: Flag that shows or hides the groupbox (can have values
0 or 1
@type show: int
"""
if show:
self.selectedAtomPosGroupBox.show()
else:
self.selectedAtomPosGroupBox.hide()
def enable_or_disable_selectedAtomPosGroupBox(self, bool_enable=False):
"""
Enable or disable Selected AtomPosGroupBox present within
'selection options' and also the checkbox that shows or hide this
groupbox. These two widgets are enabled when only a single atom is
selected from the 3D workspace.
@param bool_enable: Flag that enables or disables widgets
@type bool_enable: boolean
"""
if self.showSelectedAtomInfoCheckBox:
self.showSelectedAtomInfoCheckBox.setEnabled(bool_enable)
if self.selectedAtomPosGroupBox:
self.selectedAtomPosGroupBox.setEnabled(bool_enable)
def _updateAtomChooserGroupBoxes(self, currentIndex):
"""
Updates the Atom Chooser Groupbox. It displays one of the
following three groupboxes depending on the choice selected in the
combobox:
a) Periodic Table Elements L{self.regularElementChooser}
b) PAM5 Atoms L{self.PAM5Chooser}
c) PAM3 Atoms L{self.PAM3Chooser}
It also sets self.elementChooser to the current active Atom chooser
and updates the display accordingly in the Preview groupbox.
"""
self._hideAllAtomChooserGroupBoxes()
if currentIndex is 0:
self.elementChooser = self.regularElementChooser
self.regularElementChooser.show()
if currentIndex is 1:
self.elementChooser = self.PAM5Chooser
self.PAM5Chooser.show()
if currentIndex is 2:
self.elementChooser = self.PAM3Chooser
self.PAM3Chooser.show()
if self.elementChooser:
self.elementChooser.updateElementViewer()
self.updateMessage()
def updateMessage(self):
"""
Update the Message groupbox with informative message.
Subclasses should override this.
"""
pass
class Ui_MovePropertyManager(Command_PropertyManager):
# The title that appears in the Property Manager header
title = "Move"
# The name of this Property Manager. This will be set to
# the name of the PM_Dialog object via setObjectName().
pmName = title
# The relative path to the PNG file that appears in the header
iconPath = "ui/actions/Properties Manager/Translate_Components.png"
# The title(s) that appear in the property manager header.
# (these are changed depending on the active group box)
translateTitle = "Translate"
rotateTitle = "Rotate"
# The full path to PNG file(s) that appears in the header.
translateIconPath = "ui/actions/Properties Manager/Translate_Components.png"
rotateIconPath = "ui/actions/Properties Manager/Rotate_Components.png"
def __init__(self, command):
_superclass.__init__(self, command)
self.showTopRowButtons(PM_DONE_BUTTON | PM_WHATS_THIS_BUTTON)
def _addGroupBoxes(self):
"""
Add groupboxes to the Property Manager dialog.
"""
self.translateGroupBox = PM_GroupBox(self,
title="Translate",
connectTitleButton=False)
self.translateGroupBox.titleButton.setShortcut('T')
self._loadTranslateGroupBox(self.translateGroupBox)
self.rotateGroupBox = PM_GroupBox(self,
title="Rotate",
connectTitleButton=False)
self.rotateGroupBox.titleButton.setShortcut('R')
self._loadRotateGroupBox(self.rotateGroupBox)
self.translateGroupBox.collapse()
self.rotateGroupBox.collapse()
# == Begin Translate Group Box =====================
def _loadTranslateGroupBox(self, inPmGroupBox):
"""
Load widgets in the Translate group box.
@param inPmGroupBox: The Translate group box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
translateChoices = ["Free Drag", "By Delta XYZ", "To XYZ Position"]
self.translateComboBox = \
PM_ComboBox( inPmGroupBox,
label = '',
choices = translateChoices,
index = 0,
setAsDefault = False,
spanWidth = True )
self.freeDragTranslateGroupBox = PM_GroupBox(inPmGroupBox)
self._loadFreeDragTranslateGroupBox(self.freeDragTranslateGroupBox)
self.byDeltaGroupBox = PM_GroupBox(inPmGroupBox)
self._loadByDeltaGroupBox(self.byDeltaGroupBox)
self.toPositionGroupBox = PM_GroupBox(inPmGroupBox)
self._loadToPositionGroupBox(self.toPositionGroupBox)
self.updateTranslateGroupBoxes(0)
def _loadFreeDragTranslateGroupBox(self, inPmGroupBox):
"""
Load widgets in the Free Drag Translate group box, which is present
within the Translate groupbox.
@param inPmGroupBox: The Free Drag Translate group box in the Translate
group box.
@type inPmGroupBox: L{PM_GroupBox}
"""
# Button list to create a toolbutton row.
# Format:
# - buttonId,
# - buttonText ,
# - iconPath
# - tooltip
# - shortcut
# - column
BUTTON_LIST = [
( "QToolButton", 1, "MOVEDEFAULT",
"ui/actions/Properties Manager/Move_Free.png", "", "F", 0),
( "QToolButton", 2, "TRANSX",
"ui/actions/Properties Manager/TranslateX.png", "", "X", 1),
( "QToolButton", 3, "TRANSY",
"ui/actions/Properties Manager/TranslateY.png", "", "Y", 2),
( "QToolButton", 4, "TRANSZ",
"ui/actions/Properties Manager/TranslateZ.png", "", "Z", 3),
( "QToolButton", 5, "ROT_TRANS_ALONG_AXIS",
"ui/actions/Properties Manager/translate+rotate-A.png", "", \
"A", 4)
]
self.freeDragTranslateButtonGroup = \
PM_ToolButtonRow( inPmGroupBox,
title = "",
buttonList = BUTTON_LIST,
checkedId = 1,
setAsDefault = True,
)
self.transFreeButton = self.freeDragTranslateButtonGroup.getButtonById(
1)
self.transXButton = self.freeDragTranslateButtonGroup.getButtonById(2)
self.transYButton = self.freeDragTranslateButtonGroup.getButtonById(3)
self.transZButton = self.freeDragTranslateButtonGroup.getButtonById(4)
self.transAlongAxisButton = \
self.freeDragTranslateButtonGroup.getButtonById(5)
self.moveFromToButton = PM_ToolButton(
inPmGroupBox,
text = "Translate from/to",
iconPath = "ui/actions/Properties Manager"\
"/Translate_Components.png",
spanWidth = True
)
self.moveFromToButton.setCheckable(True)
self.moveFromToButton.setAutoRaise(True)
self.moveFromToButton.setToolButtonStyle(Qt.ToolButtonTextBesideIcon)
self.startCoordLineEdit = PM_LineEdit(
inPmGroupBox,
label = "ui/actions/Properties Manager"\
"/Move_Start_Point.png",
text = "Define 'from' and 'to' points",
setAsDefault = False,
)
self.startCoordLineEdit.setReadOnly(True)
self.startCoordLineEdit.setEnabled(False)
def _loadByDeltaGroupBox(self, inPmGroupBox):
"""
Load widgets in the translate By Delta group box, which is present
within the Translate groupbox.
@param inPmGroupBox: The Translate By Delta group box in the translate
group box.
@type inPmGroupBox: L{PM_GroupBox}
"""
self.moveDeltaXSpinBox = \
PM_DoubleSpinBox(
inPmGroupBox,
label = "ui/actions/Properties Manager/Delta_X.png",
value = 0.0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
singleStep = 1.0,
decimals = 3,
suffix = ' Angstroms',
spanWidth = False )
self.moveDeltaYSpinBox = \
PM_DoubleSpinBox(
inPmGroupBox,
label = "ui/actions/Properties Manager/Delta_Y.png",
value = 0.0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
singleStep = 1.0,
decimals = 3,
suffix = ' Angstroms',
spanWidth = False )
self.moveDeltaZSpinBox = \
PM_DoubleSpinBox(
inPmGroupBox,
label = "ui/actions/Properties Manager/Delta_Z.png",
value = 0.0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
singleStep = 1.0,
decimals = 3,
suffix = ' Angstroms',
spanWidth = False )
DELTA_BUTTONS = [
("QToolButton", 1, "Delta Plus",
"ui/actions/Properties Manager/Move_Delta_Plus.png", "", "+", 0),
("QToolButton", 2, "Delta Minus",
"ui/actions/Properties Manager/Move_Delta_Minus.png", "", "-", 1)
]
self.translateDeltaButtonRow = \
PM_ToolButtonRow( inPmGroupBox,
title = "",
buttonList = DELTA_BUTTONS,
label = 'Translate:',
isAutoRaise = True,
isCheckable = False
)
self.transDeltaPlusButton = \
self.translateDeltaButtonRow.getButtonById(1)
self.transDeltaMinusButton = \
self.translateDeltaButtonRow.getButtonById(2)
def _loadToPositionGroupBox(self, inPmGroupBox):
"""
Load widgets in the Translate To a given Position group box, which is
present within the Translate groupbox.
@param inPmGroupBox: Translate To Position group box in the Translate
group box.
@type inPmGroupBox: L{PM_GroupBox}
"""
self.toPositionspinboxes = PM_CoordinateSpinBoxes(inPmGroupBox)
self.moveXSpinBox = self.toPositionspinboxes.xSpinBox
self.moveYSpinBox = self.toPositionspinboxes.ySpinBox
self.moveZSpinBox = self.toPositionspinboxes.zSpinBox
self.moveAbsoluteButton = \
PM_PushButton( inPmGroupBox,
label = "",
text = "Move Selection",
spanWidth = True )
# == Begin Rotate Group Box =====================
def _loadRotateGroupBox(self, inPmGroupBox):
"""
Load widgets in the Rotate group box,
@param inPmGroupBox: The Rotate GroupBox in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
rotateChoices = ["Free Drag", "By Specified Angle"]
self.rotateComboBox = \
PM_ComboBox( inPmGroupBox,
label = '',
choices = rotateChoices,
index = 0,
setAsDefault = False,
spanWidth = True )
self.rotateAsUnitCB = \
PM_CheckBox( inPmGroupBox,
text = 'Rotate as a unit' ,
widgetColumn = 0,
state = Qt.Checked )
self.freeDragRotateGroupBox = PM_GroupBox(inPmGroupBox)
self._loadFreeDragRotateGroupBox(self.freeDragRotateGroupBox)
self.bySpecifiedAngleGroupBox = PM_GroupBox(inPmGroupBox)
self._loadBySpecifiedAngleGroupBox(self.bySpecifiedAngleGroupBox)
self.updateRotateGroupBoxes(0)
def _loadFreeDragRotateGroupBox(self, inPmGroupBox):
"""
Load widgets in the Free Drag Rotate group box, which is
present within the Rotate groupbox.
@param inPmGroupBox: The Free Drag Rotate group box in the Rotate
group box.
@type inPmGroupBox: L{PM_GroupBox}
"""
# Button list to create a toolbutton row.
# Format:
# - buttonId,
# - buttonText ,
# - iconPath
# - tooltip
# - shortcut
# - column
BUTTON_LIST = [
( "QToolButton", 1, "ROTATEDEFAULT",
"ui/actions/Properties Manager/Rotate_Free.png", "", "F", 0 ),
( "QToolButton", 2, "ROTATEX",
"ui/actions/Properties Manager/RotateX.png", "", "X", 1 ),
( "QToolButton", 3, "ROTATEY",
"ui/actions/Properties Manager/RotateY.png", "", "Y", 2 ),
( "QToolButton", 4, "ROTATEZ",
"ui/actions/Properties Manager/RotateZ.png", "", "Z", 3 ),
( "QToolButton", 5, "ROT_TRANS_ALONG_AXIS",
"ui/actions/Properties Manager/translate+rotate-A.png", "", \
"A", 4 )
]
self.freeDragRotateButtonGroup = \
PM_ToolButtonRow( inPmGroupBox,
title = "",
buttonList = BUTTON_LIST,
spanWidth = True,
checkedId = 1,
setAsDefault = True,
)
self.rotateFreeButton = self.freeDragRotateButtonGroup.getButtonById(1)
self.rotateXButton = self.freeDragRotateButtonGroup.getButtonById(2)
self.rotateYButton = self.freeDragRotateButtonGroup.getButtonById(3)
self.rotateZButton = self.freeDragRotateButtonGroup.getButtonById(4)
self.rotAlongAxisButton = \
self.freeDragRotateButtonGroup.getButtonById(5)
inPmGroupBox.setStyleSheet(
self.freeDragRotateButtonGroup._getStyleSheet())
X_ROW_LABELS = [("QLabel", "Delta Theta X:", 0), ("QLabel", "", 1),
("QLabel", "0.00", 2), ("QLabel", "Degrees", 3)]
Y_ROW_LABELS = [("QLabel", "Delta Theta Y:", 0), ("QLabel", "", 1),
("QLabel", "0.00", 2), ("QLabel", "Degrees", 3)]
Z_ROW_LABELS = [("QLabel", "Delta Theta Z:", 0), ("QLabel", "", 1),
("QLabel", "0.00", 2), ("QLabel", "Degrees", 3)]
self.rotateXLabelRow = PM_LabelRow(inPmGroupBox,
title="",
labelList=X_ROW_LABELS)
self.deltaThetaX_lbl = self.rotateXLabelRow.labels[2]
self.rotateYLabelRow = PM_LabelRow(inPmGroupBox,
title="",
labelList=Y_ROW_LABELS)
self.deltaThetaY_lbl = self.rotateYLabelRow.labels[2]
self.rotateZLabelRow = PM_LabelRow(inPmGroupBox,
title="",
labelList=Z_ROW_LABELS)
self.deltaThetaZ_lbl = self.rotateZLabelRow.labels[2]
self.rotateAboutPointButton = PM_ToolButton(
inPmGroupBox,
text = "Rotate selection about a point",
iconPath = "ui/actions/Properties Manager"\
"/Rotate_Components.png",
spanWidth = True
)
self.rotateAboutPointButton.setCheckable(True)
self.rotateAboutPointButton.setAutoRaise(True)
self.rotateAboutPointButton.setToolButtonStyle(
Qt.ToolButtonTextBesideIcon)
self.rotateStartCoordLineEdit = PM_LineEdit(
inPmGroupBox,
label = "ui/actions/Properties Manager"\
"/Move_Start_Point.png",
text = "Define 3 points",
setAsDefault = False,
)
self.rotateStartCoordLineEdit.setReadOnly(True)
self.rotateStartCoordLineEdit.setEnabled(False)
def _loadBySpecifiedAngleGroupBox(self, inPmGroupBox):
"""
Load widgets in the Rotate By Specified Angle group box, which is
present within the Rotate groupbox.
@param inPmGroupBox: Rotate By Specified Angle group box in the Rotate
group box.
@type inPmGroupBox: L{PM_GroupBox}
"""
# Button list to create a toolbutton row.
# Format:
# - buttonId,
# - buttonText ,
# - iconPath
# - tooltip
# - shortcut
# - column
BUTTON_LIST = [
("QToolButton", 1, "ROTATEX",
"ui/actions/Properties Manager/RotateX.png",
"Rotate about X axis", "X", 0),
("QToolButton", 2, "ROTATEY",
"ui/actions/Properties Manager/RotateY.png",
"Rotate about Y axis", "Y", 1),
("QToolButton", 3, "ROTATEZ",
"ui/actions/Properties Manager/RotateZ.png",
"Rotate about Z axis", "Z", 2),
]
self.rotateAroundAxisButtonRow = \
PM_ToolButtonRow( inPmGroupBox,
title = "",
buttonList = BUTTON_LIST,
alignment = 'Right',
label = 'Rotate Around:'
)
self.rotXaxisButton = \
self.rotateAroundAxisButtonRow.getButtonById(1)
self.rotYaxisButton = \
self.rotateAroundAxisButtonRow.getButtonById(2)
self.rotZaxisButton = \
self.rotateAroundAxisButtonRow.getButtonById(3)
self.rotateThetaSpinBox = \
PM_DoubleSpinBox(inPmGroupBox,
label = "Rotate By:",
value = 0.0,
setAsDefault = True,
minimum = 0,
maximum = 360.0,
singleStep = 1.0,
decimals = 2,
suffix = ' Degrees')
THETA_BUTTONS = [
("QToolButton", 1, "Theta Plus",
"ui/actions/Properties Manager/Move_Theta_Plus.png", "", "+", 0),
("QToolButton", 2, "Theta Minus",
"ui/actions/Properties Manager/Move_Theta_Minus.png", "", "-", 1)
]
self.rotateThetaButtonRow = \
PM_ToolButtonRow( inPmGroupBox,
title = "",
buttonList = THETA_BUTTONS,
label = 'Direction:',
isAutoRaise = True,
isCheckable = False
)
self.rotateThetaPlusButton = self.rotateThetaButtonRow.getButtonById(1)
self.rotateThetaMinusButton = self.rotateThetaButtonRow.getButtonById(
2)
# == End Rotate Group Box =====================
# == Slots for Translate group box
def _hideAllTranslateGroupBoxes(self):
"""
Hides all Translate group boxes.
"""
self.toPositionGroupBox.hide()
self.byDeltaGroupBox.hide()
self.freeDragTranslateGroupBox.hide()
def updateTranslateGroupBoxes(self, id):
"""
Update the translate group boxes displayed based on the translate
option selected.
@param id: Integer value corresponding to the combobox item in the
Translate group box.
@type id: int
"""
self._hideAllTranslateGroupBoxes()
if id is 0:
self.freeDragTranslateGroupBox.show()
if id is 1:
self.byDeltaGroupBox.show()
if id is 2:
self.toPositionGroupBox.show()
self.updateMessage()
def changeMoveOption(self, button):
"""
Subclasses should reimplement this method.
@param button: QToolButton that decides the type of translate operation
to be set.
@type button: QToolButton
L{http://doc.trolltech.com/4.2/qtoolbutton.html}
@see: B{MovePropertyManager.changeMoveOption} which overrides this
method
"""
pass
# == Slots for Rotate group box
def updateRotateGroupBoxes(self, id):
"""
Update the translate group boxes displayed based on the translate
option selected.
@param id: Integer value corresponding to the combobox item in the
Rotate group box.
@type id: int
"""
if id is 0:
self.bySpecifiedAngleGroupBox.hide()
self.freeDragRotateGroupBox.show()
if id is 1:
self.freeDragRotateGroupBox.hide()
self.bySpecifiedAngleGroupBox.show()
self.updateMessage()
def changeRotateOption(self, button):
"""
Subclasses should reimplement this method.
@param button: QToolButton that decides the type of rotate operation
to be set.
@type button: QToolButton
L{http://doc.trolltech.com/4.2/qtoolbutton.html}
@see: B{MovePropertyManage.changeRotateOption} which overrides this
method
"""
pass
def _addWhatsThisText(self):
"""
What's This text for some of the widgets in this Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_MovePropertyManager
whatsThis_MovePropertyManager(self)
def _addToolTipText(self):
"""
Tool Tip text for widgets in this Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_MovePropertyManager
ToolTip_MovePropertyManager(self)
class Ui_BuildAtomsPropertyManager(Command_PropertyManager):
"""
The Ui_BuildAtomsPropertyManager class defines UI elements for the Property
Manager of the B{Build Atoms mode}.
@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
"""
# The title that appears in the Property Manager header
title = "Build Atoms"
# The name of this Property Manager. This will be set to
# the name of the PM_Dialog object via setObjectName().
pmName = title
# The relative path to the PNG file that appears in the header
iconPath = "ui/actions/Tools/Build Structures/BuildAtoms.png"
def __init__(self, command):
"""
Constructor for the B{Build Atoms} property manager class that defines
its UI.
@param command: The parent mode where this Property Manager is used
@type command: L{depositMode}
"""
self.previewGroupBox = None
self.regularElementChooser = None
self.PAM5Chooser = None
self.PAM3Chooser = None
self.elementChooser = None
self.advancedOptionsGroupBox = None
self.bondToolsGroupBox = None
self.selectionFilterCheckBox = None
self.filterlistLE = None
self.selectedAtomInfoLabel = None
#Initialize the following to None. (subclasses may not define this)
#Make sure you initialize it before adding groupboxes!
self.selectedAtomPosGroupBox = None
self.showSelectedAtomInfoCheckBox = None
_superclass.__init__(self, command)
self.showTopRowButtons(PM_DONE_BUTTON | PM_WHATS_THIS_BUTTON)
msg = ''
self.MessageGroupBox.insertHtmlMessage(msg, setAsDefault=False)
def _addGroupBoxes(self):
"""
Add various group boxes to the Build Atoms Property manager.
"""
self._addPreviewGroupBox()
self._addAtomChooserGroupBox()
self._addBondToolsGroupBox()
#@@@TODO HIDE the bonds tool groupbox initially as the
#by default, the atoms tool is active when BuildAtoms command is
#finist invoked.
self.bondToolsGroupBox.hide()
self._addSelectionOptionsGroupBox()
self._addAdvancedOptionsGroupBox()
def _addPreviewGroupBox(self):
"""
Adde the preview groupbox that shows the element selected in the
element chooser.
"""
self.previewGroupBox = PM_PreviewGroupBox( self, glpane = self.o )
def _addAtomChooserGroupBox(self):
"""
Add the Atom Chooser groupbox. This groupbox displays one of the
following three groupboxes depending on the choice selected in the
combobox:
a) Periodic Table Elements L{self.regularElementChooser}
b) PAM5 Atoms L{self.PAM5Chooser}
c) PAM3 Atoms L{self.PAM3Chooser}
@see: L{self.__updateAtomChooserGroupBoxes}
"""
self.atomChooserGroupBox = \
PM_GroupBox(self, title = "Atom Chooser")
self._loadAtomChooserGroupBox(self.atomChooserGroupBox)
self._updateAtomChooserGroupBoxes(currentIndex = 0)
def _addElementChooserGroupBox(self, inPmGroupBox):
"""
Add the 'Element Chooser' groupbox. (present within the
Atom Chooser Groupbox)
"""
if not self.previewGroupBox:
return
elementViewer = self.previewGroupBox.elementViewer
self.regularElementChooser = \
PM_ElementChooser( inPmGroupBox,
parentPropMgr = self,
elementViewer = elementViewer)
def _add_PAM5_AtomChooserGroupBox(self, inPmGroupBox):
"""
Add the 'PAM5 Atom Chooser' groupbox (present within the
Atom Chooser Groupbox)
"""
if not self.previewGroupBox:
return
elementViewer = self.previewGroupBox.elementViewer
self.PAM5Chooser = \
PM_PAM5_AtomChooser( inPmGroupBox,
parentPropMgr = self,
elementViewer = elementViewer)
def _add_PAM3_AtomChooserGroupBox(self, inPmGroupBox):
"""
Add the 'PAM3 Atom Chooser' groupbox (present within the
Atom Chooser Groupbox)
"""
if not self.previewGroupBox:
return
elementViewer = self.previewGroupBox.elementViewer
self.PAM3Chooser = \
PM_PAM3_AtomChooser( inPmGroupBox,
parentPropMgr = self,
elementViewer = elementViewer)
def _hideAllAtomChooserGroupBoxes(self):
"""
Hides all Atom Chooser group boxes.
"""
if self.regularElementChooser:
self.regularElementChooser.hide()
if self.PAM5Chooser:
self.PAM5Chooser.hide()
if self.PAM3Chooser:
self.PAM3Chooser.hide()
def _addBondToolsGroupBox(self):
"""
Add the 'Bond Tools' groupbox.
"""
self.bondToolsGroupBox = \
PM_GroupBox( self, title = "Bond Tools")
self._loadBondToolsGroupBox(self.bondToolsGroupBox)
def _addSelectionOptionsGroupBox(self):
"""
Add 'Selection Options' groupbox
"""
self.selectionOptionsGroupBox = \
PM_GroupBox( self, title = "Selection Options" )
self._loadSelectionOptionsGroupBox(self.selectionOptionsGroupBox)
def _loadAtomChooserGroupBox(self, inPmGroupBox):
"""
Load the widgets inside the Atom Chooser groupbox.
@param inPmGroupBox: The Atom Chooser box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
atomChooserChoices = [ "Periodic Table Elements",
"PAM5 Atoms",
"PAM3 Atoms" ]
self.atomChooserComboBox = \
PM_ComboBox( inPmGroupBox,
label = '',
choices = atomChooserChoices,
index = 0,
setAsDefault = False,
spanWidth = True )
#Following fixes bug 2550
self.atomChooserComboBox.setFocusPolicy(Qt.NoFocus)
self._addElementChooserGroupBox(inPmGroupBox)
self._add_PAM5_AtomChooserGroupBox(inPmGroupBox)
self._add_PAM3_AtomChooserGroupBox(inPmGroupBox)
def _loadSelectionOptionsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Selection Options group box.
@param inPmGroupBox: The Selection Options box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
self.selectionFilterCheckBox = \
PM_CheckBox( inPmGroupBox,
text = "Enable atom selection filter",
widgetColumn = 0,
state = Qt.Unchecked )
self.selectionFilterCheckBox.setDefaultValue(False)
self.filterlistLE = PM_LineEdit( inPmGroupBox,
label = "",
text = "",
setAsDefault = False,
spanWidth = True )
self.filterlistLE.setReadOnly(True)
if self.selectionFilterCheckBox.isChecked():
self.filterlistLE.setEnabled(True)
else:
self.filterlistLE.setEnabled(False)
self.showSelectedAtomInfoCheckBox = \
PM_CheckBox(
inPmGroupBox,
text = "Show Selected Atom Info",
widgetColumn = 0,
state = Qt.Unchecked)
self.selectedAtomPosGroupBox = \
PM_GroupBox( inPmGroupBox, title = "")
self._loadSelectedAtomPosGroupBox(self.selectedAtomPosGroupBox)
self.toggle_selectedAtomPosGroupBox(show = 0)
self.enable_or_disable_selectedAtomPosGroupBox( bool_enable = False)
self.reshapeSelectionCheckBox = \
PM_CheckBox( inPmGroupBox,
text = 'Dragging reshapes selection',
widgetColumn = 0,
state = Qt.Unchecked )
connect_checkbox_with_boolean_pref( self.reshapeSelectionCheckBox,
reshapeAtomsSelection_prefs_key )
env.prefs[reshapeAtomsSelection_prefs_key] = False
self.waterCheckBox = \
PM_CheckBox( inPmGroupBox,
text = "Z depth filter (water surface)",
widgetColumn = 0,
state = Qt.Unchecked )
def _loadSelectedAtomPosGroupBox(self, inPmGroupBox):
"""
Load the selected Atoms position groupbox It is a sub-gropbox of
L{self.selectionOptionsGroupBox)
@param inPmGroupBox: 'The Selected Atom Position Groupbox'
@type inPmGroupBox: L{PM_GroupBox}
"""
self.selectedAtomLineEdit = PM_LineEdit( inPmGroupBox,
label = "Selected Atom:",
text = "",
setAsDefault = False,
spanWidth = False )
self.selectedAtomLineEdit.setReadOnly(True)
self.selectedAtomLineEdit.setEnabled(False)
self.coordinateSpinboxes = PM_CoordinateSpinBoxes(inPmGroupBox)
# User input to specify x-coordinate
self.xCoordOfSelectedAtom = self.coordinateSpinboxes.xSpinBox
# User input to specify y-coordinate
self.yCoordOfSelectedAtom = self.coordinateSpinboxes.ySpinBox
# User input to specify z-coordinate
self.zCoordOfSelectedAtom = self.coordinateSpinboxes.zSpinBox
def _addAdvancedOptionsGroupBox(self):
"""
Add 'Advanced Options' groupbox
"""
self.advancedOptionsGroupBox = \
PM_GroupBox( self, title = "Advanced Options" )
self._loadAdvancedOptionsGroupBox(self.advancedOptionsGroupBox)
def _loadAdvancedOptionsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Advanced Options group box.
@param inPmGroupBox: The Advanced Options box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
self.autoBondCheckBox = \
PM_CheckBox( inPmGroupBox,
text = 'Auto bond',
widgetColumn = 0,
state = Qt.Checked )
self.highlightingCheckBox = \
PM_CheckBox( inPmGroupBox,
text = "Hover highlighting",
widgetColumn = 0,
state = Qt.Checked )
def _loadBondToolsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Bond Tools group box.
@param inPmGroupBox: The Bond Tools box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
# Button list to create a toolbutton row.
# Format:
# - buttonId,
# - buttonText ,
# - iconPath
# - tooltip
# - shortcut
# - column
BOND_TOOL_BUTTONS = \
[ ( "QToolButton", 0, "SINGLE", "", "", None, 0),
( "QToolButton", 1, "DOUBLE", "", "", None, 1),
( "QToolButton", 2, "TRIPLE", "", "", None, 2),
( "QToolButton", 3, "AROMATIC", "", "", None, 3),
( "QToolButton", 4, "GRAPHITIC", "", "", None, 4),
( "QToolButton", 5, "CUTBONDS", "", "", None, 5)
]
self.bondToolButtonRow = \
PM_ToolButtonRow(
inPmGroupBox,
title = "",
buttonList = BOND_TOOL_BUTTONS,
checkedId = None,
setAsDefault = True )
def _addWhatsThisText(self):
"""
"What's This" text for widgets in this Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_BuildAtomsPropertyManager
whatsThis_BuildAtomsPropertyManager(self)
def _addToolTipText(self):
"""
Tool Tip text for widgets in this Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_BuildAtomsPropertyManager
ToolTip_BuildAtomsPropertyManager(self)
def toggle_selectedAtomPosGroupBox(self, show = 0):
"""
Show or hide L{self.selectedAtomPosGroupBox} depending on the state of
the checkbox (L{self.showSelectedAtomInfoCheckBox})
@param show: Flag that shows or hides the groupbox (can have values
0 or 1
@type show: int
"""
if show:
self.selectedAtomPosGroupBox.show()
else:
self.selectedAtomPosGroupBox.hide()
def enable_or_disable_selectedAtomPosGroupBox(self, bool_enable = False):
"""
Enable or disable Selected AtomPosGroupBox present within
'selection options' and also the checkbox that shows or hide this
groupbox. These two widgets are enabled when only a single atom is
selected from the 3D workspace.
@param bool_enable: Flag that enables or disables widgets
@type bool_enable: boolean
"""
if self.showSelectedAtomInfoCheckBox:
self.showSelectedAtomInfoCheckBox.setEnabled(bool_enable)
if self.selectedAtomPosGroupBox:
self.selectedAtomPosGroupBox.setEnabled(bool_enable)
def _updateAtomChooserGroupBoxes(self, currentIndex):
"""
Updates the Atom Chooser Groupbox. It displays one of the
following three groupboxes depending on the choice selected in the
combobox:
a) Periodic Table Elements L{self.regularElementChooser}
b) PAM5 Atoms L{self.PAM5Chooser}
c) PAM3 Atoms L{self.PAM3Chooser}
It also sets self.elementChooser to the current active Atom chooser
and updates the display accordingly in the Preview groupbox.
"""
self._hideAllAtomChooserGroupBoxes()
if currentIndex is 0:
self.elementChooser = self.regularElementChooser
self.regularElementChooser.show()
if currentIndex is 1:
self.elementChooser = self.PAM5Chooser
self.PAM5Chooser.show()
if currentIndex is 2:
self.elementChooser = self.PAM3Chooser
self.PAM3Chooser.show()
if self.elementChooser:
self.elementChooser.updateElementViewer()
self.updateMessage()
def updateMessage(self):
"""
Update the Message groupbox with informative message.
Subclasses should override this.
"""
pass
class Ui_MovePropertyManager(Command_PropertyManager):
# The title that appears in the Property Manager header
title = "Move"
# The name of this Property Manager. This will be set to
# the name of the PM_Dialog object via setObjectName().
pmName = title
# The relative path to the PNG file that appears in the header
iconPath = "ui/actions/Properties Manager/Translate_Components.png"
# The title(s) that appear in the property manager header.
# (these are changed depending on the active group box)
translateTitle = "Translate"
rotateTitle = "Rotate"
# The full path to PNG file(s) that appears in the header.
translateIconPath = "ui/actions/Properties Manager/Translate_Components.png"
rotateIconPath = "ui/actions/Properties Manager/Rotate_Components.png"
def __init__(self, command):
_superclass.__init__(self, command)
self.showTopRowButtons(PM_DONE_BUTTON | PM_WHATS_THIS_BUTTON)
def _addGroupBoxes(self):
"""
Add groupboxes to the Property Manager dialog.
"""
self.translateGroupBox = PM_GroupBox( self,
title = "Translate",
connectTitleButton = False)
self.translateGroupBox.titleButton.setShortcut('T')
self._loadTranslateGroupBox(self.translateGroupBox)
self.rotateGroupBox = PM_GroupBox( self,
title = "Rotate",
connectTitleButton = False)
self.rotateGroupBox.titleButton.setShortcut('R')
self._loadRotateGroupBox(self.rotateGroupBox)
self.translateGroupBox.collapse()
self.rotateGroupBox.collapse()
# == Begin Translate Group Box =====================
def _loadTranslateGroupBox(self, inPmGroupBox):
"""
Load widgets in the Translate group box.
@param inPmGroupBox: The Translate group box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
translateChoices = [ "Free Drag",
"By Delta XYZ",
"To XYZ Position" ]
self.translateComboBox = \
PM_ComboBox( inPmGroupBox,
label = '',
choices = translateChoices,
index = 0,
setAsDefault = False,
spanWidth = True )
self.freeDragTranslateGroupBox = PM_GroupBox( inPmGroupBox )
self._loadFreeDragTranslateGroupBox(self.freeDragTranslateGroupBox)
self.byDeltaGroupBox = PM_GroupBox( inPmGroupBox )
self._loadByDeltaGroupBox(self.byDeltaGroupBox)
self.toPositionGroupBox = PM_GroupBox( inPmGroupBox )
self._loadToPositionGroupBox(self.toPositionGroupBox)
self.updateTranslateGroupBoxes(0)
def _loadFreeDragTranslateGroupBox(self, inPmGroupBox):
"""
Load widgets in the Free Drag Translate group box, which is present
within the Translate groupbox.
@param inPmGroupBox: The Free Drag Translate group box in the Translate
group box.
@type inPmGroupBox: L{PM_GroupBox}
"""
# Button list to create a toolbutton row.
# Format:
# - buttonId,
# - buttonText ,
# - iconPath
# - tooltip
# - shortcut
# - column
BUTTON_LIST = [
( "QToolButton", 1, "MOVEDEFAULT",
"ui/actions/Properties Manager/Move_Free.png", "", "F", 0),
( "QToolButton", 2, "TRANSX",
"ui/actions/Properties Manager/TranslateX.png", "", "X", 1),
( "QToolButton", 3, "TRANSY",
"ui/actions/Properties Manager/TranslateY.png", "", "Y", 2),
( "QToolButton", 4, "TRANSZ",
"ui/actions/Properties Manager/TranslateZ.png", "", "Z", 3),
( "QToolButton", 5, "ROT_TRANS_ALONG_AXIS",
"ui/actions/Properties Manager/translate+rotate-A.png", "", \
"A", 4)
]
self.freeDragTranslateButtonGroup = \
PM_ToolButtonRow( inPmGroupBox,
title = "",
buttonList = BUTTON_LIST,
checkedId = 1,
setAsDefault = True,
)
self.transFreeButton =self.freeDragTranslateButtonGroup.getButtonById(1)
self.transXButton = self.freeDragTranslateButtonGroup.getButtonById(2)
self.transYButton = self.freeDragTranslateButtonGroup.getButtonById(3)
self.transZButton = self.freeDragTranslateButtonGroup.getButtonById(4)
self.transAlongAxisButton = \
self.freeDragTranslateButtonGroup.getButtonById(5)
self.moveFromToButton = PM_ToolButton(
inPmGroupBox,
text = "Translate from/to",
iconPath = "ui/actions/Properties Manager"\
"/Translate_Components.png",
spanWidth = True
)
self.moveFromToButton.setCheckable(True)
self.moveFromToButton.setAutoRaise(True)
self.moveFromToButton.setToolButtonStyle(
Qt.ToolButtonTextBesideIcon)
self.startCoordLineEdit = PM_LineEdit(
inPmGroupBox,
label = "ui/actions/Properties Manager"\
"/Move_Start_Point.png",
text = "Define 'from' and 'to' points",
setAsDefault = False,
)
self.startCoordLineEdit.setReadOnly(True)
self.startCoordLineEdit.setEnabled(False)
def _loadByDeltaGroupBox(self, inPmGroupBox):
"""
Load widgets in the translate By Delta group box, which is present
within the Translate groupbox.
@param inPmGroupBox: The Translate By Delta group box in the translate
group box.
@type inPmGroupBox: L{PM_GroupBox}
"""
self.moveDeltaXSpinBox = \
PM_DoubleSpinBox(
inPmGroupBox,
label = "ui/actions/Properties Manager/Delta_X.png",
value = 0.0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
singleStep = 1.0,
decimals = 3,
suffix = ' Angstroms',
spanWidth = False )
self.moveDeltaYSpinBox = \
PM_DoubleSpinBox(
inPmGroupBox,
label = "ui/actions/Properties Manager/Delta_Y.png",
value = 0.0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
singleStep = 1.0,
decimals = 3,
suffix = ' Angstroms',
spanWidth = False )
self.moveDeltaZSpinBox = \
PM_DoubleSpinBox(
inPmGroupBox,
label = "ui/actions/Properties Manager/Delta_Z.png",
value = 0.0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
singleStep = 1.0,
decimals = 3,
suffix = ' Angstroms',
spanWidth = False )
DELTA_BUTTONS = [
("QToolButton",1, "Delta Plus",
"ui/actions/Properties Manager/Move_Delta_Plus.png",
"", "+", 0 ),
( "QToolButton", 2, "Delta Minus",
"ui/actions/Properties Manager/Move_Delta_Minus.png",
"", "-", 1 )
]
self.translateDeltaButtonRow = \
PM_ToolButtonRow( inPmGroupBox,
title = "",
buttonList = DELTA_BUTTONS,
label = 'Translate:',
isAutoRaise = True,
isCheckable = False
)
self.transDeltaPlusButton = \
self.translateDeltaButtonRow.getButtonById(1)
self.transDeltaMinusButton = \
self.translateDeltaButtonRow.getButtonById(2)
def _loadToPositionGroupBox(self, inPmGroupBox):
"""
Load widgets in the Translate To a given Position group box, which is
present within the Translate groupbox.
@param inPmGroupBox: Translate To Position group box in the Translate
group box.
@type inPmGroupBox: L{PM_GroupBox}
"""
self.toPositionspinboxes = PM_CoordinateSpinBoxes(inPmGroupBox)
self.moveXSpinBox = self.toPositionspinboxes.xSpinBox
self.moveYSpinBox = self.toPositionspinboxes.ySpinBox
self.moveZSpinBox = self.toPositionspinboxes.zSpinBox
self.moveAbsoluteButton = \
PM_PushButton( inPmGroupBox,
label = "",
text = "Move Selection",
spanWidth = True )
# == Begin Rotate Group Box =====================
def _loadRotateGroupBox(self, inPmGroupBox):
"""
Load widgets in the Rotate group box,
@param inPmGroupBox: The Rotate GroupBox in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
rotateChoices = [ "Free Drag", "By Specified Angle"]
self.rotateComboBox = \
PM_ComboBox( inPmGroupBox,
label = '',
choices = rotateChoices,
index = 0,
setAsDefault = False,
spanWidth = True )
self.rotateAsUnitCB = \
PM_CheckBox( inPmGroupBox,
text = 'Rotate as a unit' ,
widgetColumn = 0,
state = Qt.Checked )
self.freeDragRotateGroupBox = PM_GroupBox( inPmGroupBox )
self._loadFreeDragRotateGroupBox(self.freeDragRotateGroupBox)
self.bySpecifiedAngleGroupBox = PM_GroupBox( inPmGroupBox )
self._loadBySpecifiedAngleGroupBox(self.bySpecifiedAngleGroupBox)
self.updateRotateGroupBoxes(0)
def _loadFreeDragRotateGroupBox(self, inPmGroupBox):
"""
Load widgets in the Free Drag Rotate group box, which is
present within the Rotate groupbox.
@param inPmGroupBox: The Free Drag Rotate group box in the Rotate
group box.
@type inPmGroupBox: L{PM_GroupBox}
"""
# Button list to create a toolbutton row.
# Format:
# - buttonId,
# - buttonText ,
# - iconPath
# - tooltip
# - shortcut
# - column
BUTTON_LIST = [
( "QToolButton", 1, "ROTATEDEFAULT",
"ui/actions/Properties Manager/Rotate_Free.png", "", "F", 0 ),
( "QToolButton", 2, "ROTATEX",
"ui/actions/Properties Manager/RotateX.png", "", "X", 1 ),
( "QToolButton", 3, "ROTATEY",
"ui/actions/Properties Manager/RotateY.png", "", "Y", 2 ),
( "QToolButton", 4, "ROTATEZ",
"ui/actions/Properties Manager/RotateZ.png", "", "Z", 3 ),
( "QToolButton", 5, "ROT_TRANS_ALONG_AXIS",
"ui/actions/Properties Manager/translate+rotate-A.png", "", \
"A", 4 )
]
self.freeDragRotateButtonGroup = \
PM_ToolButtonRow( inPmGroupBox,
title = "",
buttonList = BUTTON_LIST,
spanWidth = True,
checkedId = 1,
setAsDefault = True,
)
self.rotateFreeButton = self.freeDragRotateButtonGroup.getButtonById(1)
self.rotateXButton = self.freeDragRotateButtonGroup.getButtonById(2)
self.rotateYButton = self.freeDragRotateButtonGroup.getButtonById(3)
self.rotateZButton = self.freeDragRotateButtonGroup.getButtonById(4)
self.rotAlongAxisButton = \
self.freeDragRotateButtonGroup.getButtonById(5)
inPmGroupBox.setStyleSheet(
self.freeDragRotateButtonGroup._getStyleSheet())
X_ROW_LABELS = [("QLabel", "Delta Theta X:", 0),
("QLabel", "", 1),
("QLabel", "0.00", 2),
("QLabel", "Degrees", 3)]
Y_ROW_LABELS = [("QLabel", "Delta Theta Y:", 0),
("QLabel", "", 1),
("QLabel", "0.00", 2),
("QLabel", "Degrees", 3)]
Z_ROW_LABELS = [("QLabel", "Delta Theta Z:", 0),
("QLabel", "", 1),
("QLabel", "0.00", 2),
("QLabel", "Degrees", 3)]
self.rotateXLabelRow = PM_LabelRow( inPmGroupBox,
title = "",
labelList = X_ROW_LABELS )
self.deltaThetaX_lbl = self.rotateXLabelRow.labels[2]
self.rotateYLabelRow = PM_LabelRow( inPmGroupBox,
title = "",
labelList = Y_ROW_LABELS )
self.deltaThetaY_lbl = self.rotateYLabelRow.labels[2]
self.rotateZLabelRow = PM_LabelRow( inPmGroupBox,
title = "",
labelList = Z_ROW_LABELS )
self.deltaThetaZ_lbl = self.rotateZLabelRow.labels[2]
self.rotateAboutPointButton = PM_ToolButton(
inPmGroupBox,
text = "Rotate selection about a point",
iconPath = "ui/actions/Properties Manager"\
"/Rotate_Components.png",
spanWidth = True
)
self.rotateAboutPointButton.setCheckable(True)
self.rotateAboutPointButton.setAutoRaise(True)
self.rotateAboutPointButton.setToolButtonStyle(
Qt.ToolButtonTextBesideIcon)
self.rotateStartCoordLineEdit = PM_LineEdit(
inPmGroupBox,
label = "ui/actions/Properties Manager"\
"/Move_Start_Point.png",
text = "Define 3 points",
setAsDefault = False,
)
self.rotateStartCoordLineEdit.setReadOnly(True)
self.rotateStartCoordLineEdit.setEnabled(False)
def _loadBySpecifiedAngleGroupBox(self, inPmGroupBox):
"""
Load widgets in the Rotate By Specified Angle group box, which is
present within the Rotate groupbox.
@param inPmGroupBox: Rotate By Specified Angle group box in the Rotate
group box.
@type inPmGroupBox: L{PM_GroupBox}
"""
# Button list to create a toolbutton row.
# Format:
# - buttonId,
# - buttonText ,
# - iconPath
# - tooltip
# - shortcut
# - column
BUTTON_LIST = [
( "QToolButton", 1, "ROTATEX",
"ui/actions/Properties Manager/RotateX.png",
"Rotate about X axis", "X", 0 ),
( "QToolButton", 2, "ROTATEY",
"ui/actions/Properties Manager/RotateY.png",
"Rotate about Y axis", "Y", 1 ),
( "QToolButton", 3, "ROTATEZ",
"ui/actions/Properties Manager/RotateZ.png",
"Rotate about Z axis","Z", 2 ),
]
self.rotateAroundAxisButtonRow = \
PM_ToolButtonRow( inPmGroupBox,
title = "",
buttonList = BUTTON_LIST,
alignment = 'Right',
label = 'Rotate Around:'
)
self.rotXaxisButton = \
self.rotateAroundAxisButtonRow.getButtonById(1)
self.rotYaxisButton = \
self.rotateAroundAxisButtonRow.getButtonById(2)
self.rotZaxisButton = \
self.rotateAroundAxisButtonRow.getButtonById(3)
self.rotateThetaSpinBox = \
PM_DoubleSpinBox(inPmGroupBox,
label = "Rotate By:",
value = 0.0,
setAsDefault = True,
minimum = 0,
maximum = 360.0,
singleStep = 1.0,
decimals = 2,
suffix = ' Degrees')
THETA_BUTTONS = [
( "QToolButton", 1, "Theta Plus",
"ui/actions/Properties Manager/Move_Theta_Plus.png", "", "+", 0 ),
( "QToolButton", 2, "Theta Minus",
"ui/actions/Properties Manager/Move_Theta_Minus.png", "", "-", 1 )
]
self.rotateThetaButtonRow = \
PM_ToolButtonRow( inPmGroupBox,
title = "",
buttonList = THETA_BUTTONS,
label = 'Direction:',
isAutoRaise = True,
isCheckable = False
)
self.rotateThetaPlusButton = self.rotateThetaButtonRow.getButtonById(1)
self.rotateThetaMinusButton = self.rotateThetaButtonRow.getButtonById(2)
# == End Rotate Group Box =====================
# == Slots for Translate group box
def _hideAllTranslateGroupBoxes(self):
"""
Hides all Translate group boxes.
"""
self.toPositionGroupBox.hide()
self.byDeltaGroupBox.hide()
self.freeDragTranslateGroupBox.hide()
def updateTranslateGroupBoxes(self, id):
"""
Update the translate group boxes displayed based on the translate
option selected.
@param id: Integer value corresponding to the combobox item in the
Translate group box.
@type id: int
"""
self._hideAllTranslateGroupBoxes()
if id is 0:
self.freeDragTranslateGroupBox.show()
if id is 1:
self.byDeltaGroupBox.show()
if id is 2:
self.toPositionGroupBox.show()
self.updateMessage()
def changeMoveOption(self, button):
"""
Subclasses should reimplement this method.
@param button: QToolButton that decides the type of translate operation
to be set.
@type button: QToolButton
L{http://doc.trolltech.com/4.2/qtoolbutton.html}
@see: B{MovePropertyManager.changeMoveOption} which overrides this
method
"""
pass
# == Slots for Rotate group box
def updateRotateGroupBoxes(self, id):
"""
Update the translate group boxes displayed based on the translate
option selected.
@param id: Integer value corresponding to the combobox item in the
Rotate group box.
@type id: int
"""
if id is 0:
self.bySpecifiedAngleGroupBox.hide()
self.freeDragRotateGroupBox.show()
if id is 1:
self.freeDragRotateGroupBox.hide()
self.bySpecifiedAngleGroupBox.show()
self.updateMessage()
def changeRotateOption(self, button):
"""
Subclasses should reimplement this method.
@param button: QToolButton that decides the type of rotate operation
to be set.
@type button: QToolButton
L{http://doc.trolltech.com/4.2/qtoolbutton.html}
@see: B{MovePropertyManage.changeRotateOption} which overrides this
method
"""
pass
def _addWhatsThisText(self):
"""
What's This text for some of the widgets in this Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_MovePropertyManager
whatsThis_MovePropertyManager(self)
def _addToolTipText(self):
"""
Tool Tip text for widgets in this Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_MovePropertyManager
ToolTip_MovePropertyManager(self)
class CompareProteins_PropertyManager(Command_PropertyManager):
"""
The CompareProteins_PropertyManager class provides a Property Manager
for the B{Compare Proteins} command on the Build Protein flyout toolbar.
@ivar title: The title that appears in the property manager header.
@type title: str
@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
@ivar proteinChunk1: The first currently selected protein to be compared.
@type proteinChunk1: protein chunk
@ivar proteinChunk2: The second currently selected protein to be compared.
@type proteinChunk2: protein chunk
"""
title = "Compare Proteins"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildProtein/Compare.png"
proteinChunk1 = None
proteinChunk2 = None
def __init__(self, command):
"""
Constructor for the property manager.
"""
self.threshold = 10.0
_superclass.__init__(self, command)
self.showTopRowButtons(PM_DONE_BUTTON | PM_WHATS_THIS_BUTTON)
return
def connect_or_disconnect_signals(self, isConnect=True):
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.comparePushButton, SIGNAL("clicked()"), self._compareProteins)
change_connect(self.thresholdDoubleSpinBox, SIGNAL("valueChanged(double)"), self._thresholdChanged)
change_connect(self.hidePushButton, SIGNAL("clicked()"), self._hideDifferences)
return
def close(self):
"""
Closes the Property Manager. Overrides EditCommand_PM.close()
"""
env.history.statusbar_msg("")
self._resetAminoAcids()
_superclass.close(self)
# Restore the original global display style.
self.o.setGlobalDisplayStyle(self.originalDisplayStyle)
return
def show(self):
"""
Show the PM. Extends superclass method.
@note: _update_UI_do_updates() gets called immediately after this and
updates PM widgets with their correct values/settings.
"""
_superclass.show(self)
env.history.statusbar_msg("")
# Force the Global Display Style to "Protein" since this is the only way
# to see comparisons. The global display style will be restored when leaving
# this command (via self.close()).
self.originalDisplayStyle = self.o.displayMode
self.o.setGlobalDisplayStyle(diPROTEIN)
return
def _addGroupBoxes(self):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Compare")
self._loadGroupBox1(self._pmGroupBox1)
return
def _addWhatsThisText(self):
"""
What's This text for widgets in this Property Manager.
"""
pass
def _addToolTipText(self):
"""
Tool Tip text for widgets in this Property Manager.
"""
pass
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.structure1LineEdit = PM_LineEdit(pmGroupBox, label="First structure:", setAsDefault=False)
self.structure1LineEdit.setEnabled(False)
self.structure2LineEdit = PM_LineEdit(pmGroupBox, label="Second structure:", setAsDefault=False)
self.structure2LineEdit.setEnabled(False)
self.thresholdDoubleSpinBox = PM_DoubleSpinBox(
pmGroupBox,
label="Threshold:",
value=self.threshold,
setAsDefault=True,
minimum=0.0,
maximum=360.0,
decimals=1,
singleStep=30.0,
suffix=" deg",
spanWidth=False,
)
self.comparePushButton = PM_PushButton(pmGroupBox, text="Compare", setAsDefault=True)
self.hidePushButton = PM_PushButton(pmGroupBox, text="Hide differences", setAsDefault=True)
return
def _compareProteins(self):
"""
Slot for Compare button.
Compares two selected proteins of the same length.
Amino acids that differ greater than the "threshold"
value are displayed in two colors (red for the first protein
and yellow for the second protein) and are only visible when
the two proteins are displayed in the
reduced display style.
"""
from utilities.constants import red, orange, green, cyan
if not self.proteinChunk1 or not self.proteinChunk2:
return
protein_1 = self.proteinChunk1.protein
protein_2 = self.proteinChunk2.protein
if protein_1 and protein_2:
aa_list_1 = protein_1.get_amino_acids()
aa_list_2 = protein_2.get_amino_acids()
protein_1.collapse_all_rotamers()
protein_2.collapse_all_rotamers()
if len(aa_list_1) == len(aa_list_2):
for aa1, aa2 in zip(aa_list_1, aa_list_2):
aa1.color = None
aa2.color = None
# aa1.collapse()
# aa2.collapse()
if aa1.get_one_letter_code() != aa2.get_one_letter_code():
aa1.set_color(red)
aa1.expand()
aa2.set_color(yellow)
aa2.expand()
else:
max = 0.0
for chi in range(0, 3):
angle1 = aa1.get_chi_angle(chi)
angle2 = aa2.get_chi_angle(chi)
if angle1 and angle2:
if angle1 < 0.0:
angle1 += 360.0
if angle2 < 0.0:
angle2 += 360.0
diff = abs(angle1 - angle2)
if diff > max:
max = diff
if max >= self.threshold:
# This be a parameter.
aa1.set_color(green)
aa1.expand()
aa2.set_color(cyan)
aa2.expand()
self.win.glpane.gl_update()
else:
msg = "The lengths of compared proteins are not equal."
self.updateMessage(msg)
env.history.redmsg(msg)
return
def _hideDifferences(self):
"""
Slot for the "Hide differences" button.
Hides amino acids that differ greater than the "threshold" value.
@warning: Untested. Code looks suspicious.
"""
if not self.proteinChunk1 or not self.proteinChunk2:
return
protein_1 = self.proteinChunk1.protein
protein_2 = self.proteinChunk2.protein
if protein_1 and protein_2:
aa_list_1 = protein_1.get_amino_acids()
aa_list_2 = protein_2.get_amino_acids()
if len(aa_list_1) == len(aa_list_2):
protein_1.collapse_all_rotamers() # @@@
protein_2.collapse_all_rotamers() # @@@
for aa1, aa2 in zip(aa_list_1, aa_list_2):
aa1.color = None
aa2.color = None
aa1.collapse()
aa2.collapse()
self.win.glpane.gl_update()
return
def _thresholdChanged(self, value):
"""
Slot for Threshold spinbox.
"""
self.threshold = value
self._compareProteins()
return
def _resetAminoAcids(self):
"""
Resets the color and collapse all amino acids of all proteins.
"""
proteinChunkList = getAllProteinChunksInPart(self.win.assy)
for proteinChunk in proteinChunkList:
proteinChunk.protein.collapse_all_rotamers()
aa_list = proteinChunk.protein.get_amino_acids()
for aa in aa_list:
aa.color = None
aa.collapse()
self.win.glpane.gl_update()
return
def _update_UI_do_updates(self):
"""
Overrides superclass method.
@see: Command_PropertyManager._update_UI_do_updates()
"""
self.proteinChunk1 = None
self.proteinChunk2 = None
self.comparePushButton.setEnabled(False)
self.hidePushButton.setEnabled(False)
selectedProteinList = self.win.assy.getSelectedProteinChunks()
if len(selectedProteinList) == 0:
self.structure1LineEdit.setText("")
self.structure2LineEdit.setText("")
msg = (
"Select two structures of the same length in the graphics area, "
"then click the <b>Compare</b> button to compare them."
)
elif len(selectedProteinList) == 1:
self.proteinChunk1 = selectedProteinList[0]
aa1_count = " (%d)" % self.proteinChunk1.protein.count_amino_acids()
self.structure1LineEdit.setText(self.proteinChunk1.name + aa1_count)
self.structure2LineEdit.setText("")
msg = (
"Select one more structure in the graphics area that is the same "
"length as <b>" + self.proteinChunk1.name + "</b>. "
"Then click the <b>Compare</b> button to compare them."
)
elif len(selectedProteinList) == 2:
self.proteinChunk1 = selectedProteinList[0]
aa1_count = " (%d)" % self.proteinChunk1.protein.count_amino_acids()
self.structure1LineEdit.setText(self.proteinChunk1.name + aa1_count)
self.proteinChunk2 = selectedProteinList[1]
aa2_count = " (%d)" % self.proteinChunk2.protein.count_amino_acids()
self.structure2LineEdit.setText(self.proteinChunk2.name + aa2_count)
if aa1_count == aa2_count:
self.comparePushButton.setEnabled(True)
self.hidePushButton.setEnabled(True)
msg = "Click the <b>Compare</b> button to compare the two selected structures."
else:
msg = "<b>%s</b> and <b>%s</b> are not the same length." % (
self.proteinChunk1.name,
self.proteinChunk2.name,
)
msg = redmsg(msg)
else:
self.structure1LineEdit.setText("")
self.structure2LineEdit.setText("")
msg = redmsg("Too many proteins selected.")
self.updateMessage(msg)
env.history.redmsg(msg)
return
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 OrderDna_PropertyManager( PM_Dialog, DebugMenuMixin ):
"""
The OrderDna_PropertyManager class provides a Property Manager
for the B{Order Dna} command on the flyout toolbar in the
Build > Dna mode.
@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 = "Order Dna"
pmName = title
iconPath = "ui/actions/Command Toolbar/Order_DNA.png"
def __init__( self, parentCommand ):
"""
Constructor for the property manager.
"""
self.parentMode = parentCommand
self.w = self.parentMode.w
self.win = self.parentMode.w
self.pw = self.parentMode.pw
self.o = self.win.glpane
self.assy = self.win.assy
PM_Dialog.__init__(self, self.pmName, self.iconPath, self.title)
DebugMenuMixin._init1( self )
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
self.update_includeStrands() # Updates the message box.
"""
if self.getNumberOfBases():
msg = "Click on <b>View DNA Order File...</b> to preview a "\
"DNA order for all DNA strands in the current model."
else:
msg = "<font color=red>There is no DNA in the current model."
self.updateMessage(msg)
"""
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.viewDnaOrderFileButton,
SIGNAL("clicked()"),
self.viewDnaOrderFile)
change_connect( self.includeStrandsComboBox,
SIGNAL("activated(int)"),
self.update_includeStrands )
def ok_btn_clicked(self):
"""
Slot for the OK button
"""
self.win.toolsDone()
def show(self):
"""
Shows the Property Manager. Overrides PM_Dialog.show.
"""
PM_Dialog.show(self)
self.connect_or_disconnect_signals(isConnect = True)
def close(self):
"""
Closes the Property Manager. Overrides PM_Dialog.close.
"""
self.connect_or_disconnect_signals(False)
PM_Dialog.close(self)
def _addGroupBoxes( self ):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self, title = "Options" )
self._loadGroupBox1( self._pmGroupBox1 )
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
includeStrandsChoices = ["All strands in model",
"Selected strands only"]
self.includeStrandsComboBox = \
PM_ComboBox( pmGroupBox,
label = "Include strands:",
choices = includeStrandsChoices,
setAsDefault = True)
self.numberOfBasesLineEdit = \
PM_LineEdit( pmGroupBox,
label = "Number of bases:",
text = str(self.getNumberOfBases()))
self.numberOfBasesLineEdit.setEnabled(False)
self.viewDnaOrderFileButton = \
PM_PushButton( pmGroupBox,
label = "",
text = "View DNA Order File...",
spanWidth = True)
def _addWhatsThisText( self ):
"""
What's This text for widgets in the DNA Property Manager.
"""
pass
def _addToolTipText(self):
"""
Tool Tip text for widgets in the DNA Property Manager.
"""
pass
# Ask Bruce where this should live (i.e. class Part?) --Mark
def getAllDnaStrands(self, selectedOnly = False):
"""
Returns a list of all the DNA strands in the current part, or only
the selected strands if I{selectedOnly} is True.
@param selectedOnly: If True, return only the selected DNA strands.
@type selectedOnly: bool
"""
dnaStrandList = []
def func(node):
if isinstance(node, DnaStrand):
if selectedOnly:
if node.picked:
dnaStrandList.append(node)
else:
dnaStrandList.append(node)
self.win.assy.part.topnode.apply2all(func)
return dnaStrandList
def getNumberOfBases(self, selectedOnly = False):
"""
Returns the number of bases count for all the DNA strands in the
current part, or only the selected strand if I{selectedOnly} is True.
@param selectedOnly: If True, return only the selected DNA strands.
@type selectedOnly: bool
"""
dnaSequenceString = ''
selectedOnly = self.includeStrandsComboBox.currentIndex()
strandList = self.getAllDnaStrands(selectedOnly)
for strand in strandList:
strandSequenceString = str(strand.getStrandSequence())
dnaSequenceString += strandSequenceString
return len(dnaSequenceString)
def getDnaSequence(self, format = 'CSV'):
"""
Return the complete Dna sequence information string (i.e. all strand
sequences) in the specified format.
@return: The Dna sequence string
@rtype: string
"""
if format == 'CSV': #comma separated values.
separator = ','
dnaSequenceString = ''
selectedOnly = self.includeStrandsComboBox.currentIndex()
strandList = self.getAllDnaStrands(selectedOnly)
for strand in strandList:
dnaSequenceString = dnaSequenceString + strand.name + separator
strandSequenceString = str(strand.getStrandSequence())
if strandSequenceString:
strandSequenceString = strandSequenceString.upper()
dnaSequenceString = dnaSequenceString + strandSequenceString
dnaSequenceString = dnaSequenceString + "\n"
return dnaSequenceString
def viewDnaOrderFile(self, openFileInEditor = True):
"""
Opens a text editor and loads a temporary text file containing all the
DNA strand names and their sequences in the current DNA object. It will
look something like this:
Strand1,ATCAGCTACGCATCGCT
Strand2,TAGTCGATGCGTAGCGA
...
Strandn, ...
The user can then save the file to a permanent location using the
text editor the file is loaded (and displayed) in.
@see: Ui_DnaFlyout.orderDnaCommand
@see: writeDnaOrderFile()
@TODO: assy.getAllDnaObjects().
"""
dnaSequence = self.getDnaSequence(format = 'CSV')
if dnaSequence:
tmpdir = find_or_make_Nanorex_subdir('temp')
fileBaseName = 'DnaOrder'
temporaryFile = os.path.join(tmpdir, "%s.csv" % fileBaseName)
writeDnaOrderFile(temporaryFile,
self.assy,
dnaSequence)
if openFileInEditor:
open_file_in_editor(temporaryFile)
def update_includeStrands(self, ignoreVal = 0):
"""
Slot method for "Include (strands)" combobox.
"""
idx = self.includeStrandsComboBox.currentIndex()
includeType = ["model", "selection"]
_numberOfBases = self.getNumberOfBases()
self.numberOfBasesLineEdit.setText(str(_numberOfBases))
if _numberOfBases > 0:
self.viewDnaOrderFileButton.setEnabled(True)
msg = "Click on <b>View DNA Order File...</b> to preview a " \
"DNA order for all DNA strands in the current %s." \
% includeType[idx]
else:
self.viewDnaOrderFileButton.setEnabled(False)
msg = "<font color=red>" \
"There are no DNA strands in the current %s." \
% includeType[idx]
self.updateMessage(msg)
class EditProtein_PropertyManager(Command_PropertyManager):
"""
The ProteinDisplayStyle_PropertyManager class provides a Property Manager
for the B{Edit Protein} command on the Build Protein command toolbar.
The selected peptide/protein is displayed in the protein reduced display
style. The user can select individual rotamers and edit their chi angles.
This is useful for certain types of protein design protocols using a
3rd party program like Rosetta.
@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 = "Protein Properties"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildProtein/EditProtein.png"
current_protein = None # The currently selected peptide.
previous_protein = None # The last peptide selected.
current_aa = None # The current amino acid.
def __init__( self, command ):
"""
Constructor for the property manager.
"""
self.currentWorkingDirectory = env.prefs[workingDirectory_prefs_key]
_superclass.__init__(self, command)
self.sequenceEditor = self.win.createProteinSequenceEditorIfNeeded()
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
return
def connect_or_disconnect_signals(self, isConnect = True):
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.nameLineEdit,
SIGNAL("editingFinished()"),
self._nameChanged)
change_connect(self.currentResidueComboBox,
SIGNAL("activated(int)"),
self.setCurrentAminoAcid)
change_connect(self.prevButton,
SIGNAL("clicked()"),
self._expandPreviousRotamer)
change_connect(self.nextButton,
SIGNAL("clicked()"),
self._expandNextRotamer)
change_connect(self.recenterViewCheckBox,
SIGNAL("toggled(bool)"),
self._centerViewToggled)
change_connect(self.showAllResiduesCheckBox,
SIGNAL("toggled(bool)"),
self._showAllResidues)
# Rotamer control widgets.
change_connect(self.chi1Dial,
SIGNAL("valueChanged(int)"),
self._rotateChi1)
change_connect(self.chi2Dial,
SIGNAL("valueChanged(int)"),
self._rotateChi2)
change_connect(self.chi3Dial,
SIGNAL("valueChanged(int)"),
self._rotateChi3)
# Chi4 dial is hidden.
change_connect(self.chi4Dial,
SIGNAL("valueChanged(double)"),
self._rotateChi4)
return
#==
def _nameChanged(self):
"""
Slot for "Name" field.
@TODO: Include a validator for the name field.
"""
if not self.current_protein:
return
_name = str(self.nameLineEdit.text())
if not _name: # Minimal test. Need to implement a validator.
if self.current_protein:
self.nameLineEdit.setText(self.current_protein.name)
return
self.current_protein.name = _name
msg = "Editing structure <b>%s</b>." % _name
self.updateMessage(msg)
return
def update_name_field(self):
"""
Update the name field showing the name of the currently selected protein.
clear the combobox list.
"""
if not self.current_protein:
self.nameLineEdit.setText("")
else:
self.nameLineEdit.setText(self.current_protein.name)
return
def update_length_field(self):
"""
Update the name field showing the name of the currently selected protein.
clear the combobox list.
"""
if not self.current_protein:
self.lengthLineEdit.setText("")
else:
length_str = "%d residues" % self.current_protein.protein.count_amino_acids()
self.lengthLineEdit.setText(length_str)
return
def update_residue_combobox(self):
"""
Update the residue combobox with the amino acid sequence of the
currently selected protein. If there is no currently selected protein,
clear the combobox list.
"""
self.currentResidueComboBox.clear()
if not self.current_protein:
return
aa_list = self.current_protein.protein.get_amino_acid_id_list()
for j in range(len(aa_list)):
aa_id, residue_id = aa_list[j].strip().split(":")
self.currentResidueComboBox.addItem(residue_id)
pass
self.setCurrentAminoAcid()
return
def close(self):
"""
Closes the Property Manager. Overrides EditCommand_PM.close()
"""
self.sequenceEditor.hide()
env.history.statusbar_msg("")
if self.current_protein:
self.current_protein.setDisplayStyle(self.previous_protein_display_style)
self.previous_protein = None
# Update name in case the it was changed by the user.
self.current_protein.name = str(self.nameLineEdit.text())
_superclass.close(self)
return
def show(self):
"""
Show the PM. Extends superclass method.
@note: _update_UI_do_updates() gets called immediately after this and
updates PM widgets with their correct values/settings.
"""
_superclass.show(self)
env.history.statusbar_msg("")
return
def _addGroupBoxes( self ):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self,
title = "Parameters")
self._loadGroupBox1( self._pmGroupBox1 )
self._pmGroupBox2 = PM_GroupBox( self,
title = "Rotamer Controls")
self._loadGroupBox2( self._pmGroupBox2 )
return
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.nameLineEdit = PM_LineEdit( pmGroupBox,
label = "Name:")
self.lengthLineEdit = PM_LineEdit( pmGroupBox,
label = "Length:")
self.lengthLineEdit.setEnabled(False)
self.currentResidueComboBox = PM_ComboBox( pmGroupBox,
label = "Current residue:",
setAsDefault = False)
BUTTON_LIST = [
("QToolButton", 1, "Previous residue",
"ui/actions/Properties Manager/Previous.png",
"", "Previous residue", 0 ),
( "QToolButton", 2, "Next residue",
"ui/actions/Properties Manager/Next.png",
"", "Next residue", 1 )
]
self.prevNextButtonRow = \
PM_ToolButtonRow( pmGroupBox,
title = "",
buttonList = BUTTON_LIST,
label = 'Previous / Next:',
isAutoRaise = True,
isCheckable = False
)
self.prevButton = self.prevNextButtonRow.getButtonById(1)
self.nextButton = self.prevNextButtonRow.getButtonById(2)
self.recenterViewCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Center view on current residue",
setAsDefault = True,
state = Qt.Unchecked,
widgetColumn = 0,
spanWidth = True)
self.lockEditedCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Lock edited rotamers",
setAsDefault = True,
state = Qt.Checked,
widgetColumn = 0,
spanWidth = True)
self.showAllResiduesCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Show all residues",
setAsDefault = False,
state = Qt.Unchecked,
widgetColumn = 0,
spanWidth = True)
return
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.discreteStepsCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Use discrete steps",
setAsDefault = True,
state = Qt.Unchecked)
self.chi1Dial = \
PM_Dial( pmGroupBox,
label = "Chi1:",
value = 0.000,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
wrapping = True,
suffix = "deg",
spanWidth = False)
self.chi1Dial.setEnabled(False)
self.chi2Dial = \
PM_Dial( pmGroupBox,
label = "Chi2:",
value = 0.000,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
suffix = "deg",
spanWidth = False)
self.chi2Dial.setEnabled(False)
self.chi3Dial = \
PM_Dial( pmGroupBox,
label = "Chi3:",
value = 0.000,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
suffix = "deg",
spanWidth = False)
self.chi3Dial.setEnabled(False)
self.chi4Dial = \
PM_Dial( pmGroupBox,
label = "Chi4:",
value = 0.000,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
suffix = "deg",
spanWidth = False)
self.chi4Dial.setEnabled(False)
self.chi4Dial.hide()
return
def _addWhatsThisText( self ):
pass
def _addToolTipText(self):
pass
def _expandNextRotamer(self):
"""
Displays the next rotamer in the chain.
@attention: this only works when the GDS is a reduced display style.
"""
if not self.current_protein:
return
self.current_protein.protein.traverse_forward()
self.setCurrentAminoAcid()
return
def _expandPreviousRotamer(self):
"""
Displays the previous rotamer in the chain.
@attention: this only works when the GDS is a reduced display style.
"""
if not self.current_protein:
return
self.current_protein.protein.traverse_backward()
self.setCurrentAminoAcid()
return
def _centerViewToggled(self, checked):
"""
Slot for "Center view on current residue" checkbox.
"""
if checked:
self.display_and_recenter()
return
def _showAllResidues(self, show):
"""
Slot for "Show all residues" checkbox.
"""
if not self.current_protein:
return
print "Show =",show
if show:
self._expandAllRotamers()
else:
self._collapseAllRotamers()
return
def _collapseAllRotamers(self):
"""
Hides all the rotamers (except the current rotamer).
"""
self.display_and_recenter()
return
def _expandAllRotamers(self):
"""
Displays all the rotamers.
"""
if not self.current_protein:
return
self.current_protein.protein.expand_all_rotamers()
self.win.glpane.gl_update()
return
def display_and_recenter(self):
"""
Recenter the view on the current amino acid selected in the
residue combobox (or the sequence editor). All rotamers
except the current rotamer are collapsed (hidden).
"""
if not self.current_protein:
return
# Uncheck the "Show all residues" checkbox since they are being collapsed.
# Disconnect signals so that showAllResiduesCheckBox won't general a signal.
self.connect_or_disconnect_signals(isConnect = False)
self.showAllResiduesCheckBox.setChecked(False)
self.connect_or_disconnect_signals(isConnect = True)
self.current_protein.protein.collapse_all_rotamers()
# Display the current amino acid and center it in the view if the
# "Center view on current residue" is checked.
if self.current_aa:
self.current_protein.protein.expand_rotamer(self.current_aa)
self._update_chi_angles(self.current_aa)
if self.recenterViewCheckBox.isChecked():
ca_atom = self.current_aa.get_c_alpha_atom()
if ca_atom:
self.win.glpane.pov = -ca_atom.posn()
self.win.glpane.gl_update()
return
def _update_chi_angles(self, aa):
"""
"""
angle = aa.get_chi_angle(0)
if angle:
self.chi1Dial.setEnabled(True)
self.chi1Dial.setValue(angle)
else:
self.chi1Dial.setEnabled(False)
self.chi1Dial.setValue(0.0)
angle = aa.get_chi_angle(1)
if angle:
self.chi2Dial.setEnabled(True)
self.chi2Dial.setValue(angle)
else:
self.chi2Dial.setEnabled(False)
self.chi2Dial.setValue(0.0)
angle = aa.get_chi_angle(2)
if angle:
self.chi3Dial.setEnabled(True)
self.chi3Dial.setValue(angle)
else:
self.chi3Dial.setEnabled(False)
self.chi3Dial.setValue(0.0)
angle = aa.get_chi_angle(3)
if angle:
self.chi4Dial.setEnabled(True)
self.chi4Dial.setValue(angle)
else:
self.chi4Dial.setEnabled(False)
self.chi4Dial.setValue(0.0)
return
def setCurrentAminoAcid(self, aa_index = -1):
"""
Set the current amino acid to I{aa_index} and update the
"Current residue" combobox and the sequence editor.
@param aa_index: the amino acid index. If negative, update the PM and
sequence editor based on the current aa_index.
@type aa_index: int
@note: This is the slot for the "Current residue" combobox.
"""
if not self.current_protein:
return
if aa_index < 0:
aa_index = self.current_protein.protein.get_current_amino_acid_index()
if 0: # Debugging statement
print"setCurrentAminoAcid(): aa_index=", aa_index
self.currentResidueComboBox.setCurrentIndex(aa_index)
self.current_protein.protein.set_current_amino_acid_index(aa_index)
self.current_aa = self.current_protein.protein.get_current_amino_acid()
self.display_and_recenter()
self.sequenceEditor.setCursorPosition(aa_index)
return
def _rotateChiAngle(self, chi, angle):
"""
Rotate around chi1 angle.
"""
if not self.current_protein:
return
if self.current_aa:
self.current_protein.protein.expand_rotamer(self.current_aa)
self.current_aa.set_chi_angle(chi, angle)
self.win.glpane.gl_update()
return
def _rotateChi1(self, angle):
"""
Slot for Chi1 dial.
"""
self._rotateChiAngle(0, angle)
self.chi1Dial.updateValueLabel()
return
def _rotateChi2(self, angle):
"""
Slot for Chi2 dial.
"""
self._rotateChiAngle(1, angle)
self.chi2Dial.updateValueLabel()
return
def _rotateChi3(self, angle):
"""
Slot for Chi3 dial.
"""
self._rotateChiAngle(2, angle)
self.chi3Dial.updateValueLabel()
return
def _rotateChi4(self, angle):
"""
Slot for Chi4 dial.
@note: this dial is currently hidden and unused.
"""
self._rotateChiAngle(3, angle)
return
def _update_UI_do_updates(self):
"""
Overrides superclass method.
@see: Command_PropertyManager._update_UI_do_updates()
"""
self.current_protein = self.win.assy.getSelectedProteinChunk()
if self.current_protein is self.previous_protein:
if 0:
print "Edit Protein: _update_UI_do_updates() - DO NOTHING."
return
# It is common that the user will unselect the current protein.
# If so, set current_protein to previous_protein so that it
# (the previously selected protein) remains the current protein
# in the PM and sequence editor.
if not self.current_protein:
self.current_protein = self.previous_protein
return
# Update all PM widgets that need to be since something has changed.
if 0:
print "Edit Protein: _update_UI_do_updates() - UPDATING THE PMGR."
self.update_name_field()
self.update_length_field()
self.sequenceEditor.updateSequence(proteinChunk = self.current_protein)
self.update_residue_combobox()
# NOTE: Changing the display style of the protein chunks can take some
# time. We should put up the wait (hourglass) cursor and restore
# before returning.
if self.previous_protein:
self.previous_protein.setDisplayStyle(self.previous_protein_display_style)
self.previous_protein = self.current_protein
if self.current_protein:
self.previous_protein_display_style = self.current_protein.getDisplayStyle()
self.current_protein.setDisplayStyle(diPROTEIN)
if self.current_protein:
msg = "Editing structure <b>%s</b>." % self.current_protein.name
else:
msg = "Select a single structure to edit."
self.updateMessage(msg)
return
class CompareProteins_PropertyManager(Command_PropertyManager):
"""
The CompareProteins_PropertyManager class provides a Property Manager
for the B{Compare Proteins} command on the Build Protein flyout toolbar.
@ivar title: The title that appears in the property manager header.
@type title: str
@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
@ivar proteinChunk1: The first currently selected protein to be compared.
@type proteinChunk1: protein chunk
@ivar proteinChunk2: The second currently selected protein to be compared.
@type proteinChunk2: protein chunk
"""
title = "Compare Proteins"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildProtein/Compare.png"
proteinChunk1 = None
proteinChunk2 = None
def __init__(self, command):
"""
Constructor for the property manager.
"""
self.threshold = 10.0
_superclass.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
return
def connect_or_disconnect_signals(self, isConnect=True):
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.comparePushButton, SIGNAL("clicked()"),
self._compareProteins)
change_connect(self.thresholdDoubleSpinBox,
SIGNAL("valueChanged(double)"), self._thresholdChanged)
change_connect(self.hidePushButton, SIGNAL("clicked()"),
self._hideDifferences)
return
def close(self):
"""
Closes the Property Manager. Overrides EditCommand_PM.close()
"""
env.history.statusbar_msg("")
self._resetAminoAcids()
_superclass.close(self)
# Restore the original global display style.
self.o.setGlobalDisplayStyle(self.originalDisplayStyle)
return
def show(self):
"""
Show the PM. Extends superclass method.
@note: _update_UI_do_updates() gets called immediately after this and
updates PM widgets with their correct values/settings.
"""
_superclass.show(self)
env.history.statusbar_msg("")
# Force the Global Display Style to "Protein" since this is the only way
# to see comparisons. The global display style will be restored when leaving
# this command (via self.close()).
self.originalDisplayStyle = self.o.displayMode
self.o.setGlobalDisplayStyle(diPROTEIN)
return
def _addGroupBoxes(self):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Compare")
self._loadGroupBox1(self._pmGroupBox1)
return
def _addWhatsThisText(self):
"""
What's This text for widgets in this Property Manager.
"""
pass
def _addToolTipText(self):
"""
Tool Tip text for widgets in this Property Manager.
"""
pass
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.structure1LineEdit = \
PM_LineEdit( pmGroupBox,
label = "First structure:",
setAsDefault = False)
self.structure1LineEdit.setEnabled(False)
self.structure2LineEdit = \
PM_LineEdit( pmGroupBox,
label = "Second structure:",
setAsDefault = False)
self.structure2LineEdit.setEnabled(False)
self.thresholdDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Threshold:",
value = self.threshold,
setAsDefault = True,
minimum = 0.0,
maximum = 360.0,
decimals = 1,
singleStep = 30.0,
suffix = " deg",
spanWidth = False)
self.comparePushButton = \
PM_PushButton( pmGroupBox,
text = "Compare",
setAsDefault = True)
self.hidePushButton = \
PM_PushButton( pmGroupBox,
text = "Hide differences",
setAsDefault = True)
return
def _compareProteins(self):
"""
Slot for Compare button.
Compares two selected proteins of the same length.
Amino acids that differ greater than the "threshold"
value are displayed in two colors (red for the first protein
and yellow for the second protein) and are only visible when
the two proteins are displayed in the
reduced display style.
"""
from utilities.constants import red, orange, green, cyan
if not self.proteinChunk1 or \
not self.proteinChunk2:
return
protein_1 = self.proteinChunk1.protein
protein_2 = self.proteinChunk2.protein
if protein_1 and \
protein_2:
aa_list_1 = protein_1.get_amino_acids()
aa_list_2 = protein_2.get_amino_acids()
protein_1.collapse_all_rotamers()
protein_2.collapse_all_rotamers()
if len(aa_list_1) == len(aa_list_2):
for aa1, aa2 in zip(aa_list_1, aa_list_2):
aa1.color = None
aa2.color = None
#aa1.collapse()
#aa2.collapse()
if aa1.get_one_letter_code() != aa2.get_one_letter_code():
aa1.set_color(red)
aa1.expand()
aa2.set_color(yellow)
aa2.expand()
else:
max = 0.0
for chi in range(0, 3):
angle1 = aa1.get_chi_angle(chi)
angle2 = aa2.get_chi_angle(chi)
if angle1 and \
angle2:
if angle1 < 0.0:
angle1 += 360.0
if angle2 < 0.0:
angle2 += 360.0
diff = abs(angle1 - angle2)
if diff > max:
max = diff
if max >= self.threshold:
# This be a parameter.
aa1.set_color(green)
aa1.expand()
aa2.set_color(cyan)
aa2.expand()
self.win.glpane.gl_update()
else:
msg = "The lengths of compared proteins are not equal."
self.updateMessage(msg)
env.history.redmsg(msg)
return
def _hideDifferences(self):
"""
Slot for the "Hide differences" button.
Hides amino acids that differ greater than the "threshold" value.
@warning: Untested. Code looks suspicious.
"""
if not self.proteinChunk1 or \
not self.proteinChunk2:
return
protein_1 = self.proteinChunk1.protein
protein_2 = self.proteinChunk2.protein
if protein_1 and \
protein_2:
aa_list_1 = protein_1.get_amino_acids()
aa_list_2 = protein_2.get_amino_acids()
if len(aa_list_1) == len(aa_list_2):
protein_1.collapse_all_rotamers() #@@@
protein_2.collapse_all_rotamers() #@@@
for aa1, aa2 in zip(aa_list_1, aa_list_2):
aa1.color = None
aa2.color = None
aa1.collapse()
aa2.collapse()
self.win.glpane.gl_update()
return
def _thresholdChanged(self, value):
"""
Slot for Threshold spinbox.
"""
self.threshold = value
self._compareProteins()
return
def _resetAminoAcids(self):
"""
Resets the color and collapse all amino acids of all proteins.
"""
proteinChunkList = getAllProteinChunksInPart(self.win.assy)
for proteinChunk in proteinChunkList:
proteinChunk.protein.collapse_all_rotamers()
aa_list = proteinChunk.protein.get_amino_acids()
for aa in aa_list:
aa.color = None
aa.collapse()
self.win.glpane.gl_update()
return
def _update_UI_do_updates(self):
"""
Overrides superclass method.
@see: Command_PropertyManager._update_UI_do_updates()
"""
self.proteinChunk1 = None
self.proteinChunk2 = None
self.comparePushButton.setEnabled(False)
self.hidePushButton.setEnabled(False)
selectedProteinList = self.win.assy.getSelectedProteinChunks()
if len(selectedProteinList) == 0:
self.structure1LineEdit.setText("")
self.structure2LineEdit.setText("")
msg = "Select two structures of the same length in the graphics area, "\
"then click the <b>Compare</b> button to compare them."
elif len(selectedProteinList) == 1:
self.proteinChunk1 = selectedProteinList[0]
aa1_count = " (%d)" % self.proteinChunk1.protein.count_amino_acids(
)
self.structure1LineEdit.setText(self.proteinChunk1.name +
aa1_count)
self.structure2LineEdit.setText("")
msg = "Select one more structure in the graphics area that is the same "\
"length as <b>" + self.proteinChunk1.name + "</b>. "\
"Then click the <b>Compare</b> button to compare them."
elif len(selectedProteinList) == 2:
self.proteinChunk1 = selectedProteinList[0]
aa1_count = " (%d)" % self.proteinChunk1.protein.count_amino_acids(
)
self.structure1LineEdit.setText(self.proteinChunk1.name +
aa1_count)
self.proteinChunk2 = selectedProteinList[1]
aa2_count = " (%d)" % self.proteinChunk2.protein.count_amino_acids(
)
self.structure2LineEdit.setText(self.proteinChunk2.name +
aa2_count)
if aa1_count == aa2_count:
self.comparePushButton.setEnabled(True)
self.hidePushButton.setEnabled(True)
msg = "Click the <b>Compare</b> button to compare the two selected structures."
else:
msg = "<b>%s</b> and <b>%s</b> are not the same length." % \
(self.proteinChunk1.name, self.proteinChunk2.name)
msg = redmsg(msg)
else:
self.structure1LineEdit.setText("")
self.structure2LineEdit.setText("")
msg = redmsg("Too many proteins selected.")
self.updateMessage(msg)
env.history.redmsg(msg)
return
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 OrderDna_PropertyManager(Command_PropertyManager):
"""
The OrderDna_PropertyManager class provides a Property Manager
for the B{Order Dna} command on the flyout toolbar in the
Build > Dna mode.
@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 = "Order DNA"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildDna/OrderDna.png"
def __init__( self, command ):
"""
Constructor for the property manager.
"""
_superclass.__init__(self, command)
self.assy = self.win.assy
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
self.update_includeStrands() # Updates the message box.
return
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.viewDnaOrderFileButton,
SIGNAL("clicked()"),
self.viewDnaOrderFile)
change_connect( self.includeStrandsComboBox,
SIGNAL("activated(int)"),
self.update_includeStrands )
return
def _addGroupBoxes( self ):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self, title = "Options" )
self._loadGroupBox1( self._pmGroupBox1 )
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
includeStrandsChoices = ["All strands in model",
"Selected strands only"]
self.includeStrandsComboBox = \
PM_ComboBox( pmGroupBox,
label = "Include strands:",
choices = includeStrandsChoices,
setAsDefault = True)
self.numberOfBasesLineEdit = \
PM_LineEdit( pmGroupBox,
label = "Total nucleotides:",
text = str(self.getNumberOfBases()))
self.numberOfBasesLineEdit.setEnabled(False)
self.numberOfXBasesLineEdit = \
PM_LineEdit( pmGroupBox,
label = "Unassigned:",
text = str(self.getNumberOfBases(unassignedOnly = True)))
self.numberOfXBasesLineEdit.setEnabled(False)
self.viewDnaOrderFileButton = \
PM_PushButton( pmGroupBox,
label = "",
text = "View DNA Order File...",
spanWidth = True)
return
def _addWhatsThisText(self):
"""
What's This text for widgets in this Property Manager.
"""
whatsThis_OrderDna_PropertyManager(self)
return
def _addToolTipText(self):
"""
Tool Tip text for widgets in the DNA Property Manager.
"""
pass
# Ask Bruce where this should live (i.e. class Part?) --Mark
def getAllDnaStrands(self, selectedOnly = False):
"""
Returns a list of all the DNA strands in the current part, or only
the selected strands if I{selectedOnly} is True.
@param selectedOnly: If True, return only the selected DNA strands.
@type selectedOnly: bool
"""
dnaStrandList = []
def func(node):
if isinstance(node, DnaStrand):
if selectedOnly:
if node.picked:
dnaStrandList.append(node)
else:
dnaStrandList.append(node)
self.win.assy.part.topnode.apply2all(func)
return dnaStrandList
def getNumberOfBases(self, selectedOnly = False, unassignedOnly = False):
"""
Returns the number of bases count for all the DNA strands in the
current part, or only the selected strand if I{selectedOnly} is True.
@param selectedOnly: If True, return only the number of bases in the
selected DNA strands.
@type selectedOnly: bool
@param unassignedOnly: If True, return only the number of unassigned
bases (i.e. base letters = X).
@type unassignedOnly: bool
"""
dnaSequenceString = ''
selectedOnly = self.includeStrandsComboBox.currentIndex()
strandList = self.getAllDnaStrands(selectedOnly)
for strand in strandList:
strandSequenceString = str(strand.getStrandSequence())
dnaSequenceString += strandSequenceString
if unassignedOnly:
return dnaSequenceString.count("X")
return len(dnaSequenceString)
def _update_UI_do_updates(self):
"""
Overrides superclass method.
"""
self.update_includeStrands()
return
def getDnaSequence(self, format = 'CSV'):
"""
Return the complete Dna sequence information string (i.e. all strand
sequences) in the specified format.
@return: The Dna sequence string
@rtype: string
"""
if format == 'CSV': #comma separated values.
separator = ','
dnaSequenceString = ''
selectedOnly = self.includeStrandsComboBox.currentIndex()
strandList = self.getAllDnaStrands(selectedOnly)
for strand in strandList:
dnaSequenceString = dnaSequenceString + strand.name + separator
strandSequenceString = str(strand.getStrandSequence())
if strandSequenceString:
strandSequenceString = strandSequenceString.upper()
strandLength = str(len(strandSequenceString)) + separator
dnaSequenceString = dnaSequenceString + strandLength + strandSequenceString
dnaSequenceString = dnaSequenceString + "\n"
return dnaSequenceString
def viewDnaOrderFile(self, openFileInEditor = True):
"""
Writes a DNA Order file in comma-separated values (CSV) format
and opens it in a text editor.
The user must save the file to a permanent location using the
text editor.
@see: Ui_DnaFlyout.orderDnaCommand
@see: writeDnaOrderFile()
@TODO: assy.getAllDnaObjects().
"""
dnaSequence = self.getDnaSequence(format = 'CSV')
if dnaSequence:
tmpdir = find_or_make_Nanorex_subdir('temp')
fileBaseName = 'DnaOrder'
temporaryFile = os.path.join(tmpdir, "%s.csv" % fileBaseName)
writeDnaOrderFile(temporaryFile,
self.assy,
self.getNumberOfBases(),
self.getNumberOfBases(unassignedOnly = True),
dnaSequence)
if openFileInEditor:
open_file_in_editor(temporaryFile)
return
def update_includeStrands(self, ignoreVal = 0):
"""
Slot method for "Include (strands)" combobox.
"""
idx = self.includeStrandsComboBox.currentIndex()
includeType = ["model", "selection"]
_numberOfBases = self.getNumberOfBases()
self.numberOfBasesLineEdit.setText(str(_numberOfBases) + " bases")
_numberOfXBases = self.getNumberOfBases(unassignedOnly = True)
self.numberOfXBasesLineEdit.setText(str(_numberOfXBases) + " bases")
# Make the background color red if there are any unassigned bases.
if _numberOfXBases:
self.numberOfXBasesLineEdit.setStyleSheet(\
"QLineEdit {"\
"background-color: rgb(255, 0, 0)"\
"}")
else:
self.numberOfXBasesLineEdit.setStyleSheet(\
"QLineEdit {"\
"background-color: rgb(255, 255, 255)"\
"}")
if _numberOfBases > 0:
self.viewDnaOrderFileButton.setEnabled(True)
msg = "Click on <b>View DNA Order File...</b> to preview a " \
"DNA order for all DNA strands in the current %s." \
% includeType[idx]
else:
self.viewDnaOrderFileButton.setEnabled(False)
msg = "<font color=red>" \
"There are no DNA strands in the current %s." \
% includeType[idx]
self.updateMessage(msg)
return
