def _loadWidgets(self):
"""
Load the widgets in the Groupbox
"""
baseNumberChoices = ('None (default)',
'Strands and segments',
'Strands only',
'Segments only')
self._baseNumberComboBox = \
PM_ComboBox( self,
label = "Base numbers:",
choices = baseNumberChoices,
setAsDefault = True)
numberingOrderChoices = ('5\' to 3\' (default)',
'3\' to 5\'' )
self._baseNumberingOrderComboBox = \
PM_ComboBox( self,
label = "Base numbers:",
choices = numberingOrderChoices,
setAsDefault = True)
prefs_key = dnaBaseNumberLabelColor_prefs_key
self._baseNumberLabelColorChooser = \
PM_ColorComboBox(self,
color = env.prefs[prefs_key])
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box 4.
"""
self.conformationComboBox = \
PM_ComboBox( pmGroupBox,
label = "Conformation:",
choices = ["B-DNA"],
setAsDefault = True)
dnaModelChoices = ['PAM3', 'PAM5']
self.dnaModelComboBox = \
PM_ComboBox( pmGroupBox,
label = "Model:",
choices = dnaModelChoices,
setAsDefault = True)
self.basesPerTurnDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Bases per turn:",
value = env.prefs[bdnaBasesPerTurn_prefs_key],
setAsDefault = True,
minimum = 8.0,
maximum = 20.0,
decimals = 2,
singleStep = 0.1 )
self.duplexRiseDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Rise:",
value = env.prefs[bdnaRise_prefs_key],
setAsDefault = True,
minimum = 2.0,
maximum = 4.0,
decimals = 3,
singleStep = 0.01 )
# Strand Length (i.e. the number of bases)
self.numberOfBasePairsSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Base pairs:",
value = self._numberOfBases,
setAsDefault = False,
minimum = 0,
maximum = 10000 )
self.numberOfBasePairsSpinBox.setDisabled(True)
# Duplex Length
self.duplexLengthLineEdit = \
PM_LineEdit( pmGroupBox,
label = "Duplex length: ",
text = "0.0 Angstroms",
setAsDefault = False)
self.duplexLengthLineEdit.setDisabled(True)
def _loadPM_ComboBox(self, inPmGroupBox):
"""
PM_ComboBox widgets.
"""
choices = [ "First", "Second", "Third (Default)", "Forth" ]
self.comboBox1= \
PM_ComboBox( inPmGroupBox,
label = 'Choices: ',
choices = choices,
index = 2,
setAsDefault = True,
spanWidth = False )
self.comboBox2= \
PM_ComboBox( inPmGroupBox,
label = ' :Choices',
labelColumn = 1,
choices = choices,
index = 2,
setAsDefault = True,
spanWidth = False )
self.comboBox3= \
PM_ComboBox( inPmGroupBox,
label = ' Choices (SpanWidth = True):',
labelColumn = 1,
choices = choices,
index = 2,
setAsDefault = True,
spanWidth = True )
self.nestedGroupBox1 = \
PM_GroupBox( inPmGroupBox,
title = "Group Box Title" )
self.comboBox4= \
PM_ComboBox( self.nestedGroupBox1,
label = "Choices:",
choices = choices,
index = 2,
setAsDefault = True,
spanWidth = False )
self.nestedGroupBox2 = \
PM_GroupBox( inPmGroupBox,
title = "Group Box Title" )
self.comboBox6= \
PM_ComboBox( self.nestedGroupBox2,
label = "Choices:",
choices = choices,
index = 2,
setAsDefault = True,
spanWidth = True )
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box.
"""
dnaRenditionChoices = ['3D (default)',
'2D with base letters',
'2D ball and stick',
'2D ladder']
self.dnaRenditionComboBox = \
PM_ComboBox( pmGroupBox,
label = "Rendition:",
choices = dnaRenditionChoices,
setAsDefault = True)
dnaComponentChoices = ['Axis',
'Strands',
'Struts',
'Nucleotides']
self.dnaComponentComboBox = \
PM_ComboBox( pmGroupBox,
label = "Component:",
choices = dnaComponentChoices,
setAsDefault = True)
self._loadAxisGroupBox()
self._loadStrandsGroupBox()
self._loadStrutsGroupBox()
self._loadNucleotidesGroupBox()
widgetList = [self.axisGroupBox,
self.strandsGroupBox,
self.strutsGroupBox,
self.nucleotidesGroupBox]
self.dnaComponentStackedWidget = \
PM_StackedWidget( pmGroupBox,
self.dnaComponentComboBox,
widgetList )
standLabelColorChoices = ['Hide',
'Show (in strand color)',
'Black',
'White',
'Custom color...']
self.standLabelColorComboBox = \
PM_ComboBox( pmGroupBox,
label = "Strand labels:",
choices = standLabelColorChoices,
setAsDefault = True)
# This disables "Component" widgets if rendition style is 2D.
self.change_dnaRendition(env.prefs[dnaRendition_prefs_key])
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box.
@param pmGroupBox: group box that contains protein display choices
@see: L{PM_GroupBox}
"""
proteinStyleChoices = [
'CA trace (wire)', 'CA trace (cylinders)',
'CA trace (ball and stick)', 'Tube', 'Ladder', 'Zigzag',
'Flat ribbon', 'Solid ribbon', 'Cartoons', 'Fancy cartoons',
'Peptide tiles'
]
self.proteinStyleComboBox = \
PM_ComboBox( pmGroupBox,
label = "Style:",
choices = proteinStyleChoices,
setAsDefault = True)
scaleChoices = ['Constant', 'Secondary structure', 'B-factor']
self.scaleComboBox = \
PM_ComboBox( pmGroupBox,
label = "Scaling:",
choices = scaleChoices,
setAsDefault = True)
self.scaleFactorDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Scaling factor:",
value = 1.00,
setAsDefault = True,
minimum = 0.1,
maximum = 3.0,
decimals = 1,
singleStep = 0.1 )
self.splineDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Resolution:",
value = 3,
setAsDefault = True,
minimum = 2,
maximum = 8,
decimals = 0,
singleStep = 1 )
self.smoothingCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Smoothing",
setAsDefault = True)
def _loadGroupBox3(self, pmGroupBox):
"""
Load widgets in group box.
"""
# hover highlighting style and color
self.hoverHighlightingStyleComboBox = \
PM_ComboBox( pmGroupBox,
label = "Highlighting:",
)
self._loadHoverHighlightingStyleItems()
hhColorList = [
yellow, orange, red, magenta, cyan, blue, white, black, gray
]
hhColorNames = [
"Yellow (default)", "Orange", "Red", "Magenta", "Cyan", "Blue",
"White", "Black", "Other color..."
]
self.hoverHighlightingColorComboBox = \
PM_ColorComboBox(pmGroupBox,
colorList = hhColorList,
colorNames = hhColorNames,
color = env.prefs[hoverHighlightingColor_prefs_key]
)
# selection style and color
self.selectionStyleComboBox = \
PM_ComboBox( pmGroupBox,
label = "Selection:",
)
self._loadSelectionStyleItems()
selColorList = [
darkgreen, green, orange, red, magenta, cyan, blue, white, black,
gray
]
selColorNames = [
"Dark green (default)", "Green", "Orange", "Red", "Magenta",
"Cyan", "Blue", "White", "Black", "Other color..."
]
self.selectionColorComboBox = \
PM_ColorComboBox(pmGroupBox,
colorList = selColorList,
colorNames = selColorNames,
color = env.prefs[selectionColor_prefs_key]
)
return
def _loadAxisGroupBox(self):
"""
Load the Axis group box.
"""
axisGroupBox = PM_GroupBox( None )
self.axisGroupBox = axisGroupBox
axisShapeChoices = ['None', 'Wide tube', 'Narrow tube']
self.axisShapeComboBox = \
PM_ComboBox( axisGroupBox ,
label = "Shape:",
choices = axisShapeChoices,
setAsDefault = True)
self.axisScaleDoubleSpinBox = \
PM_DoubleSpinBox( axisGroupBox,
label = "Scale:",
value = 1.00,
setAsDefault = True,
minimum = 0.1,
maximum = 2.0,
decimals = 2,
singleStep = 0.1 )
axisColorChoices = ['Same as chunk',
'Base order',
'Base order (discrete)',
'Base type',
'Strand order']
self.axisColorComboBox = \
PM_ComboBox( axisGroupBox ,
label = "Color:",
choices = axisColorChoices,
setAsDefault = True)
endingTypeChoices = ['Flat',
'Taper start',
'Taper end',
'Taper both',
'Spherical']
self.axisEndingStyleComboBox = \
PM_ComboBox( axisGroupBox ,
label = "Ending style:",
choices = endingTypeChoices,
setAsDefault = True)
def _loadGroupBox1(self, inPmGroupBox):
"""
Load widgets into group box 1.
"""
# User input to specify what type of element/atom to generate
elementComboBoxItems = self._sElementSymbolList
self.elementComboBox = \
PM_ComboBox( inPmGroupBox,
label = "Elements :",
choices = elementComboBoxItems,
index = 0,
setAsDefault = True,
spanWidth = False )
# User input to specify x-coordinate
# of the generated atom's position.
self.xCoordinateField = \
PM_DoubleSpinBox( inPmGroupBox,
label = "x :",
value = 0.0,
setAsDefault = True,
minimum = self._sMinCoordinateValue,
maximum = self._sMaxCoordinateValue,
singleStep = self._sStepCoordinateValue,
decimals = self._sCoordinateDecimals,
suffix = ' ' + self._sCoordinateUnits )
return
def _loadProductSpecsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Product specifications group box.
@param inPmGroupBox: The roduct specifications box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
productChoices = ['Rod', 'Ring']
self.extrude_productTypeComboBox = \
PM_ComboBox( inPmGroupBox,
label = 'Final product:',
labelColumn = 0,
choices = productChoices,
index = 0,
setAsDefault = True,
spanWidth = False )
# names used in the code, same order
#if you comment out items from combobox, you also have to remove them
# from this list unless they are at the end!!!
self.extrude_productTypeComboBox_ptypes = ["straight rod", \
"closed ring", \
"corkscrew"]
self.extrudeSpinBox_n = \
PM_SpinBox( inPmGroupBox,
label = "Number of copies:",
labelColumn = 0,
value = 3,
minimum = 1,
maximum = 99
)
#@WARNING: This method initializes some instance varaiables for various
#checkboxes. (Example: self.mergeCopiesCheckBox.default = False).
#These values are needed in extrudemode.py. This
#won't be needed once extrudeMode.py is cleaned up. -- ninad 2007-09-10
self.extrudeBondCriterionSlider = \
PM_Slider( inPmGroupBox,
currentValue = 100,
minimum = 0,
maximum = 300,
label = 'Tolerence'
)
self.extrudeBondCriterionLabel = \
self.extrudeBondCriterionSlider.labelWidget
self.extrudeBondCriterionSlider_dflt = 100
self.extrudeBondCriterionSlider.setPageStep(5)
self.makeBondsCheckBox = \
PM_CheckBox(inPmGroupBox,
text = 'Make bonds' ,
widgetColumn = 0,
state = Qt.Checked
)
self.makeBondsCheckBox.default = True
self.makeBondsCheckBox.attr = 'whendone_make_bonds'
self.makeBondsCheckBox.repaintQ = False
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 _loadDisplayOptionsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Display Options groupbox.
@param inPmGroupBox: The Display Options groupbox
@type inPmGroupBox: L{PM_GroupBox}
"""
displayChoices = ['Tubes', 'Spheres']
self.dispModeComboBox = \
PM_ComboBox( inPmGroupBox,
label = 'Display style:',
choices = displayChoices,
index = 0,
setAsDefault = False,
spanWidth = False )
self.gridLineCheckBox = PM_CheckBox(inPmGroupBox,
text="Show grid lines",
widgetColumn=0,
state=Qt.Checked)
self.fullModelCheckBox = PM_CheckBox(inPmGroupBox,
text="Show model",
widgetColumn=0,
state=Qt.Unchecked)
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 _loadDisplayOptionsGroupBox(self, pmGroupBox):
"""
Load widgets in the Display Options GroupBox
@see: DnaOrCnt_PropertyManager. _loadDisplayOptionsGroupBox
"""
#Call the superclass method that loads the cursor text checkboxes.
#Note, as of 2008-05-19, the superclass, DnaOrCnt_PropertyManager
#only loads the cursor text groupboxes. Subclasses like this can
#call custom methods like self._loadCursorTextCheckBoxes etc if they
#don't need all groupboxes that the superclass loads.
_superclass._loadDisplayOptionsGroupBox(self, pmGroupBox)
self._rubberbandLineGroupBox = PM_GroupBox(pmGroupBox,
title='Rubber band line:')
dnaLineChoices = ['Ribbons', 'Ladder']
self.dnaRubberBandLineDisplayComboBox = \
PM_ComboBox( self._rubberbandLineGroupBox ,
label = " Display as:",
choices = dnaLineChoices,
setAsDefault = True)
self.lineSnapCheckBox = \
PM_CheckBox(self._rubberbandLineGroupBox ,
text = 'Enable line snap' ,
widgetColumn = 1,
state = Qt.Checked
)
def _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 _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 1.
@param pmGroupBox: group box that contains protein name combo box and
number of amino acids spin box
@see: L{PM_GroupBox}
"""
self._updateProteinList()
if len(self.protein_name_list) >= 1:
self.set_current_protein_chunk_name(self.protein_name_list[0])
self.structureComboBox = PM_ComboBox(pmGroupBox,
label="Name:",
choices=self.protein_name_list,
setAsDefault=False)
#Urmi 20080713: May be useful to set the minimum value to not zero
#Now it does not matter, since its disabled. But zero as the minimum
#value in a spinbox does not work otherwise.
self.numberOfAASpinBox = \
PM_SpinBox( pmGroupBox,
label = "Amino Acids:",
value = 0,
setAsDefault = False,
minimum = 0,
maximum = 10000 )
#for now we do not allow changing number of residues
self.numberOfAASpinBox.setEnabled(False)
self.editPropertiesPushButton = PM_PushButton(pmGroupBox,
text="Edit Sequence",
setAsDefault=True)
def _loadStrandsGroupBox(self):
"""
Load the Strands group box.
"""
strandsGroupBox = PM_GroupBox( None )
self.strandsGroupBox = strandsGroupBox
strandsShapeChoices = ['None', 'Cylinders', 'Tube']
self.strandsShapeComboBox = \
PM_ComboBox( strandsGroupBox ,
label = "Shape:",
choices = strandsShapeChoices,
setAsDefault = True)
self.strandsScaleDoubleSpinBox = \
PM_DoubleSpinBox( strandsGroupBox,
label = "Scale:",
value = 1.00,
setAsDefault = True,
minimum = 0.1,
maximum = 5.0,
decimals = 2,
singleStep = 0.1 )
strandsColorChoices = ['Same as chunk',
'Base order',
'Strand order']
self.strandsColorComboBox = \
PM_ComboBox( strandsGroupBox ,
label = "Color:",
choices = strandsColorChoices,
setAsDefault = True)
strandsArrowsChoices = ['None',
'5\'',
'3\'',
'5\' and 3\'']
self.strandsArrowsComboBox = \
PM_ComboBox( strandsGroupBox ,
label = "Arrows:",
choices = strandsArrowsChoices,
setAsDefault = True)
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 _loadNucleotidesGroupBox(self):
"""
Load the Nucleotides group box.
"""
nucleotidesGroupBox = PM_GroupBox( None )
self.nucleotidesGroupBox = nucleotidesGroupBox
nucleotidesShapeChoices = ['None',
'Sugar spheres',
'Base cartoons']
self.nucleotidesShapeComboBox = \
PM_ComboBox( nucleotidesGroupBox ,
label = "Shape:",
choices = nucleotidesShapeChoices,
setAsDefault = True)
self.nucleotidesScaleDoubleSpinBox = \
PM_DoubleSpinBox( nucleotidesGroupBox,
label = "Scale:",
value = 1.00,
setAsDefault = True,
minimum = 0.1,
maximum = 3.0,
decimals = 2,
singleStep = 0.1 )
nucleotidesColorChoices = ['Same as strand',
'Base order',
'Strand order',
'Base type']
self.nucleotidesColorComboBox = \
PM_ComboBox( nucleotidesGroupBox ,
label = "Color:",
choices = nucleotidesColorChoices,
setAsDefault = True)
self.dnaStyleBasesDisplayLettersCheckBox = \
PM_CheckBox(nucleotidesGroupBox ,
text = 'Display base letters',
widgetColumn = 1
)
def _loadLayerPropertiesGroupBox(self, inPmGroupBox):
"""
Load widgets in the Layer Properties group box.
@param inPmGroupBox: The Layer Properties groupbox in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
self.currentLayerComboBox = \
PM_ComboBox( inPmGroupBox,
index = 0,
spanWidth = True
)
self.addLayerButton = PM_PushButton(inPmGroupBox)
self.addLayerButton.setIcon(
geticon('ui/actions/Properties Manager/addlayer.png'))
self.addLayerButton.setFixedSize(QSize(26, 26))
self.addLayerButton.setIconSize(QSize(22, 22))
# A widget list to create a widget row.
# Format:
# - Widget type,
# - widget object,
# - column
firstRowWidgetList = [('PM_ComboBox', self.currentLayerComboBox, 1),
('PM_PushButton', self.addLayerButton, 2)]
widgetRow = PM_WidgetRow(
inPmGroupBox,
title='',
widgetList=firstRowWidgetList,
label="Layer:",
labelColumn=0,
)
self.layerCellsSpinBox = \
PM_SpinBox( inPmGroupBox,
label = "Lattice cells:",
labelColumn = 0,
value = 2,
minimum = 1,
maximum = 25
)
self.layerThicknessLineEdit = PM_LineEdit(inPmGroupBox,
label="Thickness:",
text="",
setAsDefault=False,
spanWidth=False)
#self.layerThicknessLineEdit.setReadOnly(True)
self.layerThicknessLineEdit.setDisabled(True)
tooltip = "Thickness of layer in Angstroms"
self.layerThicknessLineEdit.setToolTip(tooltip)
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box 2.
"""
self.modelComboBox = \
PM_ComboBox( pmGroupBox,
label = "Model :",
choices = self._modelChoices,
setAsDefault = True)
self.conformationComboBox = \
PM_ComboBox( pmGroupBox,
label = "Conformation :",
choices = ["B-DNA"],
setAsDefault = True)
self.connect(self.conformationComboBox,
SIGNAL("currentIndexChanged(int)"),
self.conformationComboBoxChanged)
self.basesPerTurnComboBox= \
PM_ComboBox( pmGroupBox,
label = "Bases Per Turn :",
choices = ["10.0", "10.5", "10.67"],
setAsDefault = True)
# I may decide to reintroduce "base-pair chunks" at a later time.
# Please talk to me if you have a strong feeling about including
# this. Mark 2007-08-19.
createChoices = ["Strand chunks", \
"Single chunk" ]
#@ "Base-pair chunks"]
self.createComboBox = \
PM_ComboBox( pmGroupBox,
label = "Create :",
choices = createChoices,
index = 0,
setAsDefault = True,
spanWidth = False )
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in 1st group box.
@param pmGroupBox: The 1st group box in the PM.
@type pmGroupBox: L{PM_GroupBox}
"""
self.axesCombobox = PM_ComboBox(pmGroupBox,
label='Axes: ',
choices=self._axes_display_choices,
index=0,
setAsDefault=True,
spanWidth=False)
self.basesCombobox = PM_ComboBox(pmGroupBox,
label='Bases: ',
choices=self._bases_display_choices,
index=0,
setAsDefault=True,
spanWidth=False)
def _loadStrutsGroupBox(self):
"""
Load the Struts group box.
"""
strutsGroupBox = PM_GroupBox( None )
self.strutsGroupBox = strutsGroupBox
strutsShapeChoices = ['None',
'Base-axis-base cylinders',
'Straight cylinders']
self.strutsShapeComboBox = \
PM_ComboBox( strutsGroupBox ,
label = "Shape:",
choices = strutsShapeChoices,
setAsDefault = True)
self.strutsScaleDoubleSpinBox = \
PM_DoubleSpinBox( strutsGroupBox,
label = "Scale:",
value = 1.00,
setAsDefault = True,
minimum = 0.1,
maximum = 3.0,
decimals = 2,
singleStep = 0.1 )
strutsColorChoices = ['Same as strand',
'Base order',
'Strand order',
'Base type']
self.strutsColorComboBox = \
PM_ComboBox( strutsGroupBox ,
label = "Color:",
choices = strutsColorChoices,
setAsDefault = True)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
#stereoSettingsGroupBox = PM_GroupBox( None )
self.stereoEnabledCheckBox = \
PM_CheckBox(pmGroupBox,
text = 'Enable Stereo View',
widgetColumn = 1
)
stereoModeChoices = [
'Relaxed view', 'Cross-eyed view', 'Red/blue anaglyphs',
'Red/cyan anaglyphs', 'Red/green anaglyphs'
]
self.stereoModeComboBox = \
PM_ComboBox( pmGroupBox,
label = "Stereo Mode:",
choices = stereoModeChoices,
setAsDefault = True)
self.stereoModeComboBox.setCurrentIndex(
env.prefs[stereoViewMode_prefs_key] - 1)
self.stereoSeparationSlider = \
PM_Slider( pmGroupBox,
currentValue = 50,
minimum = 0,
maximum = 300,
label = 'Separation'
)
self.stereoSeparationSlider.setValue(
env.prefs[stereoViewSeparation_prefs_key])
self.stereoAngleSlider = \
PM_Slider( pmGroupBox,
currentValue = 50,
minimum = 0,
maximum = 100,
label = 'Angle'
)
self.stereoAngleSlider.setValue(env.prefs[stereoViewAngle_prefs_key])
self._updateWidgets()
def _loadFuseOptionsGroupBox(self, inPmGroupBox):
"""
Load the widgets inside the Fuse Options groupbox.
"""
#@ Warning: If you change fuseChoices, you must also change the
# constants MAKEBONDS and FUSEATOMS in FuseChunks_Command.py.
# This implementation is fragile and should be fixed. Mark 2008-07-16
fuseChoices = ['Make bonds between chunks',
'Fuse overlapping atoms']
self.fuseComboBox = \
PM_ComboBox( inPmGroupBox,
label = '',
choices = fuseChoices,
index = 0,
setAsDefault = False,
spanWidth = True)
self.connect(self.fuseComboBox,
SIGNAL("activated(const QString&)"),
self.parentMode.change_fuse_mode)
self.fusePushButton = PM_PushButton( inPmGroupBox,
label = "",
text = "Make Bonds",
spanWidth = True )
self.connect( self.fusePushButton,
SIGNAL("clicked()"),
self.parentMode.fuse_something)
self.toleranceSlider = PM_Slider( inPmGroupBox,
currentValue = 100,
minimum = 0,
maximum = 300,
label = \
'Tolerance:100% => 0 bondable pairs'
)
self.connect(self.toleranceSlider,
SIGNAL("valueChanged(int)"),
self.parentMode.tolerance_changed)
self.mergeChunksCheckBox = PM_CheckBox( inPmGroupBox,
text = 'Merge chunks',
widgetColumn = 0,
state = Qt.Checked )
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in groubox 1.
"""
self.heightField = \
PM_DoubleSpinBox( pmGroupBox,
label = "Height :",
value = 20.0,
setAsDefault = True,
minimum = 1.0,
maximum = 100.0,
singleStep = 1.0,
decimals = 3,
suffix = ' Angstroms')
self.widthField = \
PM_DoubleSpinBox( pmGroupBox,
label = "Width :",
value = 20.0,
setAsDefault = True,
minimum = 1.0,
maximum = 100.0,
singleStep = 1.0,
decimals = 3,
suffix = ' Angstroms')
self.bondLengthField = \
PM_DoubleSpinBox( pmGroupBox,
label = "Bond Length :",
value = CC_GRAPHITIC_BONDLENGTH,
setAsDefault = True,
minimum = 1.0,
maximum = 3.0,
singleStep = 0.1,
decimals = 3,
suffix = ' Angstroms')
endingChoices = ["None", "Hydrogen", "Nitrogen"]
self.endingsComboBox= \
PM_ComboBox( pmGroupBox,
label = "Endings :",
choices = endingChoices,
index = 0,
setAsDefault = True,
spanWidth = False )
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box.
"""
#background color combo box
self.backgroundColorComboBox = \
PM_ComboBox( pmGroupBox,
label = "Color:",
spanWidth = False)
self._loadBackgroundColorItems()
self.enableFogCheckBox = \
PM_CheckBox( pmGroupBox, text = "Enable fog" )
connect_checkbox_with_boolean_pref( self.enableFogCheckBox, fogEnabled_prefs_key )
return
def _loadWidgetSelectorGroupBox(self, inPmGroupBox):
"""
Widget selector group box.
"""
# The widget choices are set via self._getGroupBoxTitles() later.
widgetTypeChoices = [ "PM_CheckBox" ]
self.widgetSelectorComboBox = \
PM_ComboBox( inPmGroupBox,
label = "Select a PM widget:",
choices = widgetTypeChoices,
index = 0,
setAsDefault = False,
spanWidth = True )
self.connect(self.widgetSelectorComboBox,
SIGNAL("currentIndexChanged(int)"),
self._updateGroupBoxes)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
aa_list = []
for mol in self.win.assy.molecules:
if mol.isProteinChunk():
aa_list = mol.protein.get_amino_acid_id_list()
break
self.aminoAcidsComboBox = PM_ComboBox(pmGroupBox,
label="Residue:",
choices=aa_list,
setAsDefault=False)
self.previousAAPushButton = \
PM_PushButton( pmGroupBox,
text = "Previous AA",
setAsDefault = True)
self.nextAAPushButton = \
PM_PushButton( pmGroupBox,
text = "Next AA",
setAsDefault = True)
self.recenterViewCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Re-center view",
setAsDefault = True,
state = Qt.Checked)
self.expandAllPushButton = \
PM_PushButton( pmGroupBox,
text = "Expand All",
setAsDefault = True)
self.collapseAllPushButton = \
PM_PushButton( pmGroupBox,
text = "Collapse All",
setAsDefault = True)
def _loadGroupBox5(self, pmGroupBox):
"""
Load widgets in group box 5.
"""
self._rubberbandLineGroupBox = PM_GroupBox(pmGroupBox,
title='Rubber band Line:')
ntLineChoices = ['Ladder']
self.ntRubberBandLineDisplayComboBox = \
PM_ComboBox( self._rubberbandLineGroupBox ,
label = " Display as:",
choices = ntLineChoices,
setAsDefault = True)
self.lineSnapCheckBox = \
PM_CheckBox(self._rubberbandLineGroupBox ,
text = 'Enable line snap' ,
widgetColumn = 1,
state = Qt.Checked
)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
convertChoices = [
"Convert from PAM3 to PAM5", "Convert from PAM5 to PAM3"
]
self._convertChoiceComboBox = \
PM_ComboBox( pmGroupBox,
label = "",
choices = convertChoices,
index = 0,
setAsDefault = True,
spanWidth = True)
self._convertButton = \
PM_PushButton( pmGroupBox,
label = "",
text = "Convert Selection Now",
spanWidth = True)
return