def _loadGroupBox3(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.enableMaterialPropertiesComboBox = \
PM_CheckBox( pmGroupBox, text = "On")
self.finishDoubleSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
maximum = 1.0,
minimum = 0.0,
decimals = 2,
singleStep = .1,
label = "Finish:")
self.shininessDoubleSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
maximum = 60,
minimum = 15,
decimals = 2,
label = "Shininess:")
self.brightnessDoubleSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
maximum = 1.0,
minimum = 0.0,
decimals = 2,
singleStep = .1,
label = "Brightness:")
return
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 _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in 1st group box.
@param pmGroupBox: The 1st group box in the PM.
@type pmGroupBox: L{PM_GroupBox}
"""
self.widthDblSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
label = "Width:",
value = 16.0,
setAsDefault = True,
minimum = 1.0,
maximum = 10000.0, # 1000 nm
singleStep = 1.0,
decimals = 1,
suffix = ' Angstroms')
self.heightDblSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
label =" Height:",
value = 16.0,
setAsDefault = True,
minimum = 1.0,
maximum = 10000.0, # 1000 nm
singleStep = 1.0,
decimals = 1,
suffix = ' Angstroms')
self.aspectRatioCheckBox = \
PM_CheckBox(pmGroupBox,
text = 'Maintain Aspect Ratio of:' ,
widgetColumn = 1,
state = Qt.Unchecked
)
self.aspectRatioSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "",
value = 1.0,
setAsDefault = True,
minimum = 0.1,
maximum = 10.0,
singleStep = 0.1,
decimals = 2,
suffix = " to 1.00")
if self.aspectRatioCheckBox.isChecked():
self.aspectRatioSpinBox.setEnabled(True)
else:
self.aspectRatioSpinBox.setEnabled(False)
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in groubox 2.
"""
if self.editCommand and self.editCommand.struct:
length = self.editCommand.struct.length
width = self.editCommand.struct.width
spoke_radius = self.editCommand.struct.sradius
normcolor = self.editCommand.struct.normcolor
else:
length = 10
width = 1
spoke_radius = 0.2
normcolor = gray
self.motorLengthDblSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
label = "Motor length :",
value = length,
setAsDefault = True,
minimum = 0.5,
maximum = 500.0,
singleStep = 0.5,
decimals = 1,
suffix = ' Angstroms')
self.motorWidthDblSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
label="Motor width :",
value = width,
setAsDefault = True,
minimum = 0.1,
maximum = 50.0,
singleStep = 0.1,
decimals = 1,
suffix = ' Angstroms')
self.spokeRadiusDblSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
label = "Spoke radius :",
value = spoke_radius,
setAsDefault = True,
minimum = 0.1,
maximum = 50.0,
singleStep = 0.1,
decimals = 1,
suffix = ' Angstroms')
self.motorColorComboBox = \
PM_ColorComboBox(pmGroupBox,
color = normcolor)
return
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 4.
"""
self.nameLineEdit = PM_LineEdit(pmGroupBox,
label="Strand name:",
text="",
setAsDefault=False)
self.numberOfBasesSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Number of bases:",
value = self._numberOfBases,
setAsDefault = False,
minimum = 2,
maximum = 10000 )
self.basesPerTurnDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Bases per turn:",
value = self.basesPerTurn,
setAsDefault = True,
minimum = 8.0,
maximum = 20.0,
decimals = 2,
singleStep = 0.1 )
self.duplexRiseDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Rise:",
value = self.duplexRise,
setAsDefault = True,
minimum = 2.0,
maximum = 4.0,
decimals = 3,
singleStep = 0.01 )
self.disableStructHighlightingCheckbox = \
PM_CheckBox( pmGroupBox,
text = "Don't highlight while editing DNA",
widgetColumn = 0,
state = Qt.Unchecked,
setAsDefault = True,
spanWidth = True
)
#As of 2008-03-31, the properties such as number of bases will be
#editable only by using the resize handles. post FNANO we will support
#the
self.numberOfBasesSpinBox.setEnabled(False)
self.basesPerTurnDoubleSpinBox.setEnabled(False)
self.duplexRiseDoubleSpinBox.setEnabled(False)
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 _loadOffsetSpecsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Offset specs groupbox (which is a groupbox within
the B{Advanced Options group box}).
@param inPmGroupBox: The Offset Specs gropbox box
@type inPmGroupBox: L{PM_GroupBox}
"""
self.extrudeSpinBox_length = \
PM_DoubleSpinBox( inPmGroupBox,
label = "Total offset",
value = 7.0,
setAsDefault = True,
minimum = 0.1,
maximum = 2000.0,
singleStep = 1,
decimals = 3,
suffix = ' Angstroms'
)
self.extrudeSpinBox_x = \
PM_DoubleSpinBox( inPmGroupBox,
label = "X offset",
value = 0,
minimum = -1000.0,
maximum = 1000.0,
singleStep = 1,
decimals = 3,
suffix = ' Angstroms'
)
self.extrudeSpinBox_y = \
PM_DoubleSpinBox( inPmGroupBox,
label = "Y offset",
value = 0,
minimum = -1000.0,
maximum = 1000.0,
singleStep = 1,
decimals = 3,
suffix = ' Angstroms'
)
self.extrudeSpinBox_z = \
PM_DoubleSpinBox( inPmGroupBox,
label = "Z offset",
value = 0,
minimum = -1000.0,
maximum = 1000.0,
singleStep = 1,
decimals = 3,
suffix = ' Angstroms'
)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 4.
"""
self.nameLineEdit = PM_LineEdit(pmGroupBox,
label="Segment name:",
text="",
setAsDefault=False)
# Strand Length (i.e. the number of bases)
self.numberOfBasePairsSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Base pairs:",
value = self._numberOfBases,
setAsDefault = False,
minimum = 2,
maximum = 10000 )
self.basesPerTurnDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Bases per turn:",
value = self.basesPerTurn,
setAsDefault = True,
minimum = 8.0,
maximum = 20.0,
decimals = 2,
singleStep = 0.1 )
self.basesPerTurnDoubleSpinBox.setDisabled(True)
self.duplexRiseDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Rise:",
value = self.duplexRise,
setAsDefault = True,
minimum = 2.0,
maximum = 4.0,
decimals = 3,
singleStep = 0.01 )
self.duplexRiseDoubleSpinBox.setDisabled(True)
# Duplex Length
self.duplexLengthLineEdit = \
PM_LineEdit( pmGroupBox,
label = "Duplex length: ",
text = "0.0 Angstroms",
setAsDefault = False)
self.duplexLengthLineEdit.setDisabled(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 _loadGroupBox4(self, inPmGroupBox):
"""
Load widgets in group box 4.
"""
# "Number of Nanotubes" SpinBox
self.mwntCountSpinBox = \
PM_SpinBox( inPmGroupBox,
label = "Number:",
value = 1,
setAsDefault = True,
minimum = 1,
maximum = 10,
suffix = " nanotubes" )
self.mwntCountSpinBox.setSpecialValueText("SWNT")
# "Spacing" lineedit.
self.mwntSpacingDoubleSpinBox = \
PM_DoubleSpinBox( inPmGroupBox,
label = "Spacing:",
value = 2.46,
setAsDefault = True,
minimum = 1.0,
maximum = 10.0,
singleStep = 0.1,
decimals = 3,
suffix = " Angstroms" )
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in MotorParamsGroupBox.
"""
if self.editCommand and self.editCommand.struct:
force = self.editCommand.struct.force
stiffness = self.editCommand.struct.stiffness
enable_minimize = self.editCommand.struct.enable_minimize
else:
force = 0.0
stiffness = 0.0
enable_minimize = False
self.forceDblSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
label = "Force:",
value = force,
setAsDefault = True,
minimum = 0.0,
maximum = 5000.0,
singleStep = 1.0,
decimals = 1,
suffix =' pN')
self.stiffnessDblSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
label = "Stiffness:",
value = stiffness,
setAsDefault = True,
minimum = 0.0,
maximum = 1000.0,
singleStep = 1.0,
decimals = 1,
suffix =' N/m')
self.enableMinimizeCheckBox = \
PM_CheckBox(pmGroupBox,
text ="Enable in minimize",
widgetColumn = 1
)
self.enableMinimizeCheckBox.setChecked(enable_minimize)
self.directionPushButton = \
PM_PushButton(pmGroupBox,
label = "Direction :",
text = "Reverse",
spanWidth = False)
return
def loadGroupBox1(self, inPmGroupBox):
"""
Load widgets into groupbox 1.
"""
# User input to specify x-coordinate
# of the generated atom's position.
self.xCoordinateField = \
PM_DoubleSpinBox( inPmGroupBox,
label = \
"ui/actions/Properties Manager/X_Coordinate.png",
value = 0.0,
setAsDefault = True,
minimum = self._sMinCoordinateValue,
maximum = self._sMaxCoordinateValue,
singleStep = self._sStepCoordinateValue,
decimals = self._sCoordinateDecimals,
suffix = ' ' + self._sCoordinateUnits )
# User input to specify y-coordinate
# of the generated atom's position.
self.yCoordinateField = \
PM_DoubleSpinBox( inPmGroupBox,
label = \
"ui/actions/Properties Manager/Y_Coordinate.png",
value = 0.0,
setAsDefault = True,
minimum = self._sMinCoordinateValue,
maximum = self._sMaxCoordinateValue,
singleStep = self._sStepCoordinateValue,
decimals = self._sCoordinateDecimals,
suffix = ' ' + self._sCoordinateUnits )
# User input to specify z-coordinate
# of the generated atom's position.
self.zCoordinateField = \
PM_DoubleSpinBox( inPmGroupBox,
label = \
"ui/actions/Properties Manager/Z_Coordinate.png",
value = 0.0,
setAsDefault = True,
minimum = self._sMinCoordinateValue,
maximum = self._sMaxCoordinateValue,
singleStep = self._sStepCoordinateValue,
decimals = self._sCoordinateDecimals,
suffix = ' ' + self._sCoordinateUnits )
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, inPmGroupBox):
"""
Load widgets in group box 2.
"""
self.zDistortionField = \
PM_DoubleSpinBox( inPmGroupBox,
label = "Z-distortion :",
value = 0.0,
setAsDefault = True,
minimum = 0.0,
maximum = 10.0,
singleStep = 0.1,
decimals = 3,
suffix = " Angstroms" )
self.xyDistortionField = \
PM_DoubleSpinBox( inPmGroupBox,
label = "XY-distortion :",
value = 0.0,
setAsDefault = True,
minimum = 0.0,
maximum = 2.0,
singleStep = 0.1,
decimals = 3,
suffix = " Angstroms" )
self.twistSpinBox = \
PM_SpinBox( inPmGroupBox,
label = "Twist :",
value = 0,
setAsDefault = True,
minimum = 0,
maximum = 100, # What should maximum be?
suffix = " deg/A" )
self.bendSpinBox = \
PM_SpinBox( inPmGroupBox,
label = "Bend :",
value = 0,
setAsDefault = True,
minimum = 0,
maximum = 360,
suffix = " deg" )
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.discreteStepsCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Use discrete steps",
setAsDefault = True,
state = Qt.Unchecked)
self.chi1SpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Chi1 angle:",
value = 0.000,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
decimals = 1,
singleStep = 1.0,
spanWidth = False)
self.chi2SpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Chi2 angle:",
value = 0.000,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
decimals = 1,
singleStep = 1.0,
spanWidth = False)
self.chi3SpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Chi3 angle:",
value = 0.000,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
decimals = 1,
singleStep = 1.0,
spanWidth = False)
def _loadCoordinateSpinBoxes(self):
"""
Load the coordinateSpinboxes groupbox with the x, y, z spinboxes
"""
# User input to specify x-coordinate
self.xSpinBox = \
PM_DoubleSpinBox( self,
label = \
"ui/actions/Properties Manager/X_Coordinate.png",
value = 0.0,
setAsDefault = True,
minimum = - 9999999,
maximum = 9999999,
singleStep = 1,
decimals = 3,
suffix = " A")
# User input to specify y-coordinate
self.ySpinBox = \
PM_DoubleSpinBox( self,
label = \
"ui/actions/Properties Manager/Y_Coordinate.png",
value = 0.0,
setAsDefault = True,
minimum = - 9999999,
maximum = 9999999,
singleStep = 1,
decimals = 3,
suffix = " A")
# User input to specify z-coordinate
self.zSpinBox = \
PM_DoubleSpinBox( self,
label = \
"ui/actions/Properties Manager/Z_Coordinate.png",
value = 0.0,
setAsDefault = True,
minimum = - 9999999,
maximum = 9999999,
singleStep = 1,
decimals = 3,
suffix = " A")
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 _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 _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 _loadPM_DoubleSpinBox(self, inPmGroupBox):
"""
PM_DoubleSpinBox widgets.
"""
self.doubleSpinBox = \
PM_DoubleSpinBox( inPmGroupBox,
#label="Spanning DoubleSpinBox :",
label = "", # No label
value = 5.0,
setAsDefault = True,
minimum = 1.0,
maximum = 10.0,
singleStep = 1.0,
decimals = 1,
suffix = ' Suffix',
spanWidth = True )
# Add a prefix example.
self.doubleSpinBox.setPrefix("Prefix ")
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.
"""
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 _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 loadTestWidgets1(self, inPmGroupBox):
"""
Adds widgets to <inPmGroupBox>.
Used for testing purposes. Mark 2007-05-24
"""
# I intend to create a special PropMgr to display all widget types
# for testing purposes. For now, I just add them to the end of the
# Graphene Sheet property manager. Mark 2007-05-22
self.spinBox = \
PM_SpinBox( inPmGroupBox,
label = "Spinbox:",
value = 5,
setAsDefault = True,
minimum = 2,
maximum = 10,
suffix = ' things',
spanWidth = True )
self.doubleSpinBox = \
PM_DoubleSpinBox( inPmGroupBox,
#label="Spanning DoubleSpinBox :",
label = "", # No label
value = 5.0,
setAsDefault = True,
minimum = 1.0,
maximum = 10.0,
singleStep = 1.0,
decimals = 1,
suffix = ' Suffix',
spanWidth = True )
# Add a prefix example.
self.doubleSpinBox.setPrefix("Prefix ")
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.textEdit = \
PM_TextEdit( inPmGroupBox,
label = "TextEdit:",
spanWidth = False )
self.spanTextEdit = \
PM_TextEdit( inPmGroupBox,
label = "",
spanWidth = True )
self.groupBox = \
PM_GroupBox( inPmGroupBox,
title = "Group Box Title" )
self.comboBox2= \
PM_ComboBox( self.groupBox,
label = "Choices:",
choices = choices,
index = 2,
setAsDefault = True,
spanWidth = False )
self.groupBox2 = \
PM_GroupBox( inPmGroupBox,
title = "Group Box Title" )
self.comboBox3= \
PM_ComboBox( self.groupBox2,
label = "Choices:",
choices = choices,
index = 2,
setAsDefault = True,
spanWidth = True )
self.pushButton1 = \
PM_PushButton( inPmGroupBox,
label = "",
text = "PushButton1" )
self.pushButton2 = \
PM_PushButton( inPmGroupBox,
label = "",
text = "PushButton2",
spanWidth = True )
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)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 1.
"""
# Duplex Length
self.duplexLengthSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Duplex Length: ",
value = 0,
setAsDefault = False,
minimum = 0,
maximum = 34000,
singleStep = self.getDuplexRise("B-DNA"),
decimals = 3,
suffix = ' Angstroms')
self.connect(self.duplexLengthSpinBox, SIGNAL("valueChanged(double)"),
self.duplexLengthChanged)
# Strand Length
self.strandLengthSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Strand Length :",
value = 0,
setAsDefault = False,
minimum = 0,
maximum = 10000,
suffix = ' bases' )
self.connect(self.strandLengthSpinBox, SIGNAL("valueChanged(int)"),
self.strandLengthChanged)
# New Base choices
newBaseChoices = []
for theBase in basesDict.keys():
newBaseChoices = newBaseChoices \
+ [ theBase + ' (' \
+ basesDict[theBase]['Name'] + ')' ]
try:
defaultBaseChoice = basesDict.keys().index('N')
except:
defaultBaseChoice = 0
# Strand Sequence
self.sequenceTextEdit = \
PM_TextEdit( pmGroupBox,
label = "",
spanWidth = True )
self.sequenceTextEdit.setCursorWidth(2)
self.sequenceTextEdit.setWordWrapMode(QTextOption.WrapAnywhere)
self.connect(self.sequenceTextEdit, SIGNAL("textChanged()"),
self.sequenceChanged)
self.connect(self.sequenceTextEdit, SIGNAL("cursorPositionChanged()"),
self.cursorPosChanged)
# Actions
self.actionsComboBox = \
PM_ComboBox( pmGroupBox,
label = '',
choices = self._actionChoices,
index = 0,
setAsDefault = True,
spanWidth = True )
# If SIGNAL("activate(const QString&)") is used, we get a TypeError.
# This is a bug that needs Bruce. Using currentIndexChanged(int) as
# a workaround, but there is still a bug when the "Reverse" action
# is selected. Mark 2007-08-15
self.connect(self.actionsComboBox, SIGNAL("currentIndexChanged(int)"),
self.actionsComboBoxChanged)
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box 2.
"""
_ntTypeChoices = ['Carbon', 'Boron Nitride']
self.ntTypeComboBox = \
PM_ComboBox( pmGroupBox,
label = "Type:",
choices = _ntTypeChoices,
setAsDefault = True)
self.ntRiseDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Rise:",
value = self.nanotube.getRise(),
setAsDefault = True,
minimum = 2.0,
maximum = 4.0,
decimals = 3,
singleStep = 0.01 )
self.ntRiseDoubleSpinBox.hide()
# Nanotube Length
self.ntLengthLineEdit = \
PM_LineEdit( pmGroupBox,
label = "Nanotube Length: ",
text = "0.0 Angstroms",
setAsDefault = False)
self.ntLengthLineEdit.setDisabled(True)
self.ntLengthLineEdit.hide()
# Nanotube diameter
self.ntDiameterLineEdit = \
PM_LineEdit( pmGroupBox,
label = "Diameter: ",
setAsDefault = False)
self.ntDiameterLineEdit.setDisabled(True)
self.updateNanotubeDiameter()
self.chiralityNSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Chirality (n):",
value = self.nanotube.getChiralityN(),
minimum = 2,
maximum = 100,
setAsDefault = True )
self.chiralityMSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Chirality (m):",
value = self.nanotube.getChiralityM(),
minimum = 0,
maximum = 100,
setAsDefault = True )
# How about having user prefs for CNT and BNNT bond lengths?
# I'm guessing that if the user wants to set these values, they will
# do it once and would like those bond length values persist forever.
# Need to discuss with others to determine if this spinbox comes out.
# --Mark 2008-03-29
self.bondLengthDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Bond length:",
value = self.nanotube.getBondLength(),
setAsDefault = True,
minimum = 1.0,
maximum = 3.0,
singleStep = 0.1,
decimals = 3,
suffix = " Angstroms" )
#self.bondLengthDoubleSpinBox.hide()
endingChoices = ["Hydrogen", "None"] # Removed:, "Nitrogen"]
self.endingsComboBox= \
PM_ComboBox( pmGroupBox,
label = "Endings:",
choices = endingChoices,
index = 0,
setAsDefault = True,
spanWidth = False )
def _loadGroupBox3(self, pmGroupBox):
"""
Load widgets in group box 3.
"""
self._endPoint1GroupBox = PM_GroupBox(pmGroupBox, title="Endpoint1")
self._endPoint2GroupBox = PM_GroupBox(pmGroupBox, title="Endpoint2")
# Point 1
self.x1SpinBox = \
PM_DoubleSpinBox( self._endPoint1GroupBox,
label = \
"ui/actions/Properties Manager/X_Coordinate.png",
value = 0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
self.y1SpinBox = \
PM_DoubleSpinBox( self._endPoint1GroupBox,
label = \
"ui/actions/Properties Manager/Y_Coordinate.png",
value = 0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
self.z1SpinBox = \
PM_DoubleSpinBox( self._endPoint1GroupBox,
label = \
"ui/actions/Properties Manager/Z_Coordinate.png",
value = 0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
# Point 2
self.x2SpinBox = \
PM_DoubleSpinBox( self._endPoint2GroupBox,
label = \
"ui/actions/Properties Manager/X_Coordinate.png",
value = 10.0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
self.y2SpinBox = \
PM_DoubleSpinBox( self._endPoint2GroupBox,
label = \
"ui/actions/Properties Manager/Y_Coordinate.png",
value = 0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
self.z2SpinBox = \
PM_DoubleSpinBox( self._endPoint2GroupBox,
label = \
"ui/actions/Properties Manager/Z_Coordinate.png",
value = 0,
setAsDefault = True,
minimum = -100.0,
maximum = 100.0,
decimals = 3,
suffix = ' Angstroms')
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.bondAngleWeightSimSpinBox = PM_DoubleSpinBox(
pmGroupBox,
labelColumn=0,
label="Bond angle weight:",
minimum=0.01,
decimals=2,
maximum=1.0,
singleStep=0.01,
value=1.0,
setAsDefault=False,
spanWidth=False)
bond_angle_param_list = ['Amber', 'Charmm']
self.bondAngleParamComboBox = PM_ComboBox(
pmGroupBox,
label="Bond angle parameters:",
choices=bond_angle_param_list,
setAsDefault=False)
self.onlybbSpinBox = PM_DoubleSpinBox(pmGroupBox,
labelColumn=0,
label="Only backbone rotation:",
minimum=0.01,
maximum=1.0,
value=0.75,
decimals=2,
singleStep=0.01,
setAsDefault=False,
spanWidth=False)
self.onlyrotSpinBox = PM_DoubleSpinBox(pmGroupBox,
labelColumn=0,
label="Only rotamer rotation:",
minimum=0.01,
maximum=1.0,
decimals=2,
value=0.25,
singleStep=0.01,
setAsDefault=False,
spanWidth=False)
self.mctempSpinBox = PM_DoubleSpinBox(
pmGroupBox,
labelColumn=0,
label="MC simulation temperature:",
minimum=0.1,
value=0.6,
maximum=1.0,
decimals=2,
singleStep=0.1,
setAsDefault=False,
spanWidth=False)
numResidues = self._getNumResiduesForCurrentProtein()
self.minresSpinBox = PM_SpinBox(pmGroupBox,
labelColumn=0,
label="Minimum number of residues:",
minimum=2,
maximum=numResidues,
singleStep=1,
setAsDefault=False,
spanWidth=False)
self.maxresSpinBox = PM_SpinBox(pmGroupBox,
labelColumn=0,
label="Maximum number of residues:",
minimum=2,
maximum=numResidues,
singleStep=1,
setAsDefault=False,
spanWidth=False)
if numResidues == 0:
self.minresSpinBox.setMaximum(numResidues + 2)
self.maxresSpinBox.setMaximum(numResidues + 2)
return
def _loadGroupBox1(self, inPmGroupBox):
"""
Load widgets in the group box.
"""
memberChoices = [
"Custom", "Alpha helix", "Beta strand", "Pi helix", "3_10 helix",
"Polyproline-II helix", "Fully extended"
]
self.aaTypeComboBox= \
PM_ComboBox( inPmGroupBox,
label = "Conformation:",
choices = memberChoices,
index = 1,
setAsDefault = True,
spanWidth = False )
self.connect(self.aaTypeComboBox, SIGNAL("currentIndexChanged(int)"),
self._aaTypeChanged)
self.phiAngleField = \
PM_DoubleSpinBox( inPmGroupBox,
label = "Phi angle:",
value = self.phi,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
singleStep = 1.0,
decimals = 1,
suffix = " degrees")
self.connect(self.phiAngleField, SIGNAL("valueChanged(double)"),
self._aaPhiAngleChanged)
self.phiAngleField.setEnabled(False)
self.psiAngleField = \
PM_DoubleSpinBox( inPmGroupBox,
label = "Psi angle:",
value = self.psi,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
singleStep = 1.0,
decimals = 1,
suffix = " degrees" )
self.connect(self.psiAngleField, SIGNAL("valueChanged(double)"),
self._aaPsiAngleChanged)
self.psiAngleField.setEnabled(False)
self.aaTypesButtonGroup = \
PM_ToolButtonGrid( inPmGroupBox,
buttonList = AA_BUTTON_LIST,
label = "Amino acids",
checkedId = self.current_amino_acid, # Glycine
setAsDefault = True )
self.connect(self.aaTypesButtonGroup.buttonGroup,
SIGNAL("buttonClicked(int)"), self._setAminoAcidType)
return
