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 _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 _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 _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 _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 _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, 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, 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 _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 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 _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 _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 _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 _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 _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box.
"""
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=4, setAsDefault=True, minimum=2, maximum=8, decimals=0, singleStep=1
)
self.smoothingCheckBox = PM_CheckBox(pmGroupBox, text="Smoothing", setAsDefault=True)
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 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 _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 _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 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 _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 )
class test_connectWithState_PM( ExampleCommand1_PM):
# does not use GBC; at least Done & Cancel should work
title = "test connectWithState"
def _addGroupBoxes(self):
"""Add the groupboxes for this Property Manager."""
self.pmGroupBox1 = PM_GroupBox( self, title = "settings")
self._loadGroupBox1(self.pmGroupBox1)
self.pmGroupBox2 = PM_GroupBox( self, title = "commands")
self._loadGroupBox2(self.pmGroupBox2)
return
_sMaxCylinderHeight = 20 ### TODO: ask the stateref for this
def _loadGroupBox1(self, pmGroupBox):
"""Load widgets into groupbox 1 (passed as pmGroupBox)."""
# cylinder height (a double, stored as a preferences value)
cylinderHeight_stateref = Preferences_StateRef_double(
CYLINDER_HEIGHT_PREFS_KEY,
CYLINDER_HEIGHT_DEFAULT_VALUE )
### TODO: ask model object for this ref; this code should not need to know what kind it is (from prefs or model)
self.cylinderHeightSpinbox = \
PM_DoubleSpinBox( pmGroupBox,
label = "cylinder height:",
## value = CYLINDER_HEIGHT_DEFAULT_VALUE,
## # guess: default value or initial value (guess they can't be distinguished -- bug -- yes, doc confirms)
## setAsDefault = True,
### TODO: get all the following from the stateref, whenever the connection to state is made
minimum = 3,
maximum = self._sMaxCylinderHeight,
singleStep = 0.25,
decimals = self._sCoordinateDecimals,
suffix = ' ' + self._sCoordinateUnits )
# REVIEW: is it ok that the above will set some wrong defaultValue,
# to be immediately corrected by the following connection with state?
self.cylinderHeightSpinbox.connectWithState(
cylinderHeight_stateref,
debug_metainfo = True
)
# ==
# cylinder width (a double, stored in the command object,
# defined there using the State macro -- note, this is not yet a good
# enough example for state stored in a Node)
cylinderWidth_stateref = ObjAttr_StateRef( self.commandrun, 'cylinderWidth')
## TEMPORARY: just make sure it's defined in there
junk = cylinderWidth_stateref.defaultValue
self.cylinderWidthSpinbox = \
PM_DoubleSpinBox( pmGroupBox,
label = "cylinder width:",
## value = defaultValue,
## setAsDefault = True,
## ### REVISE: the default value should come from the cylinderWidth_stateref
# (and so, probably, should min, max, step, units...)
minimum = 0.1,
maximum = 15.0,
singleStep = 0.1,
decimals = self._sCoordinateDecimals,
suffix = ' ' + self._sCoordinateUnits )
self.cylinderWidthSpinbox.connectWithState(
cylinderWidth_stateref,
debug_metainfo = True )
# ==
# cylinder round caps (boolean)
cylinderRoundCaps_stateref = Preferences_StateRef( CYLINDER_ROUND_CAPS_PREFS_KEY,
CYLINDER_ROUND_CAPS_DEFAULT_VALUE ) ### TODO: get from model
## TEMPORARY: just make sure it's defined in there
junk = cylinderRoundCaps_stateref.defaultValue
self.cylinderRoundCapsCheckbox = PM_CheckBox(pmGroupBox, text = 'round caps on cylinder')
## self.cylinderRoundCapsCheckbox.setDefaultValue(CYLINDER_ROUND_CAPS_DEFAULT_VALUE)
## # note: setDefaultValue is an extension to the PM_CheckBox API, not yet finalized
self.cylinderRoundCapsCheckbox.connectWithState(
cylinderRoundCaps_stateref,
debug_metainfo = True )
# ==
# cylinder vertical or horizontal (boolean)
cylinderVertical_stateref = ObjAttr_StateRef( self.commandrun, 'cylinderVertical' )
self.cylinderVerticalCheckbox = PM_CheckBox(pmGroupBox, text = 'cylinder is vertical')
## self.cylinderVerticalCheckbox.setDefaultValue(CYLINDER_VERTICAL_DEFAULT_VALUE)
## ### REVISE: the default value should come from the stateref
self.cylinderVerticalCheckbox.connectWithState(
cylinderVertical_stateref,
debug_metainfo = True )
return # from _loadGroupBox1
def _loadGroupBox2(self, pmGroupBox): ### RENAME button attrs
self.startButton = \
PM_PushButton( pmGroupBox,
label = "",
text = "Bigger",
spanWidth = False ) ###BUG: button spans PM width, in spite of this setting
self.startButton.setAction( self.button_Bigger, cmdname = "Bigger")
self.stopButton = \
PM_PushButton( pmGroupBox,
label = "",
text = "Smaller",
spanWidth = False )
self.stopButton.setAction( self.button_Smaller, cmdname = "Smaller")
return
def button_Bigger(self):
self.commandrun.cmd_Bigger()
def button_Smaller(self):
self.commandrun.cmd_Smaller()
def _addWhatsThisText(self):
"""What's This text for some of the widgets in the Property Manager."""
self.cylinderHeightSpinbox.setWhatsThis("cylinder height (stored in prefs)")
self.cylinderWidthSpinbox.setWhatsThis("cylinder width (stored as State in the command object)")
return
pass # end of class
class NanotubeGeneratorPropertyManager(PM_Dialog):
"""
The NanotubeGeneratorPropertyManager class provides a Property Manager
for the "Build > Nanotube" command.
"""
# The title that appears in the property manager header.
title = "Nanotube"
# The name of this property manager. This will be set to
# the name of the PropMgr (this) object via setObjectName().
pmName = title
# The relative path to PNG file that appears in the header.
iconPath = "ui/actions/Tools/Build Structures/Nanotube.png"
def __init__(self):
"""Construct the Graphene Property Manager.
"""
PM_Dialog.__init__(self, self.pmName, self.iconPath, self.title)
#@self.addGroupBoxes()
#@self.add_whats_this_text()
self.updateMessageGroupBox()
def updateMessageGroupBox(self):
msg = ""
# A (4, 4) tube is stable, but a (3, 3) has not been seen in
# isolation. Circumference of a (4, 4) tube is about 6.93.
xOffset = self.n + self.m * math.cos(math.pi/3.0)
yOffset = self.m * math.sin(math.pi/3.0)
circumference = math.sqrt(xOffset * xOffset + yOffset * yOffset)
if (circumference < 6.5):
msg = "Warning: Small diameter nanotubes may be unstable, \
and may give unexpected results when minimized.<p>"
msg = msg + "Edit the Nanotube parameters and select <b>Preview</b> to \
preview the structure. Click <b>Done</b> to insert it into the model."
# This causes the "Message" box to be displayed as well.
# setAsDefault=True causes this message to be reset whenever
# this PropMgr is (re)displayed via show(). Mark 2007-06-01.
self.MessageGroupBox.insertHtmlMessage(msg, setAsDefault=True)
def _addGroupBoxes(self):
"""
Add the 3 group boxes to the Nanotube Property Manager dialog.
"""
self.pmGroupBox1 = \
PM_GroupBox( self,
title = "Nanotube Parameters" )
self.pmGroupBox2 = \
PM_GroupBox( self,
title = "Nanotube Distortion" )
self.pmGroupBox3 = \
PM_GroupBox( self,
title = "Multi-Walled Nanotubes" )
# Add group box widgets.
self._loadGroupBox1(self.pmGroupBox1)
self._loadGroupBox2(self.pmGroupBox2)
self._loadGroupBox3(self.pmGroupBox3)
def _loadGroupBox1(self, inPmGroupBox):
"""
Load widgets in group box 1.
"""
memberChoices = ["Carbon", "Boron Nitride"]
self.typeComboBox= \
PM_ComboBox( inPmGroupBox,
label = "Type :",
choices = memberChoices,
index = 0,
setAsDefault = True,
spanWidth = False )
self.connect( self.typeComboBox,
SIGNAL("currentIndexChanged(int)"),
self.nt_type_changed)
self.lengthField = \
PM_DoubleSpinBox( inPmGroupBox,
label = "Length :",
value = 20.0,
setAsDefault = True,
minimum = 1.0,
maximum = 1000.0,
singleStep = 1.0,
decimals = 3,
suffix = " Angstroms" )
self.n = 5
self.chiralityNSpinBox = \
PM_SpinBox( inPmGroupBox,
label = "Chirality (n) :",
value = self.n,
setAsDefault = True )
self.connect(self.chiralityNSpinBox,
SIGNAL("valueChanged(int)"),
self.chirality_fixup)
self.m = 5
self.chiralityMSpinBox = \
PM_SpinBox( inPmGroupBox,
label = "Chirality (m) :",
value = self.m,
setAsDefault = True )
self.connect(self.chiralityMSpinBox,
SIGNAL("valueChanged(int)"),
self.chirality_fixup)
self.bondLengthField = \
PM_DoubleSpinBox( inPmGroupBox,
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( inPmGroupBox,
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 _loadGroupBox3(self, inPmGroupBox):
"""
Load widgets in group box 3.
"""
# "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.mwntSpacingField = \
PM_DoubleSpinBox( inPmGroupBox,
label = "Spacing :",
value = 2.46,
setAsDefault = True,
minimum = 1.0,
maximum = 10.0,
singleStep = 0.1,
decimals = 3,
suffix = " Angstroms" )
def _addWhatsThisText(self):
"""
What's This text for widgets in this Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_NanotubeGeneratorPropertyManager
whatsThis_NanotubeGeneratorPropertyManager(self)
def _addToolTipText(self):
"""
Tool Tip text for widgets in this Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_NanotubeGeneratorPropertyManager
ToolTip_NanotubeGeneratorPropertyManager(self)
def chirality_fixup(self, spinBoxValueJunk = None):
"""
Slot for several validators for different parameters.
This gets called each time a user types anything into a widget or
changes a spinbox.
@param spinBoxValueJunk: This is the Spinbox value from the valueChanged
signal. It is not used. We just want to know
that the spinbox value has changed.
@type spinBoxValueJunk: double or None
"""
if not hasattr(self, 'n'):
print_compact_traceback("Bug: no attr 'n' ") # mark 2007-05-24
return
n_previous = int(self.n)
m_previous = int(self.m)
n = self.chiralityNSpinBox.value()
m = self.chiralityMSpinBox.value()
# Two restrictions to maintain
# n >= 2
# 0 <= m <= n
if n < 2:
n = 2
if m != self.m:
# The user changed m. If m became larger than n, make n bigger.
if m > n:
n = m
elif n != self.n:
# The user changed n. If n became smaller than m, make m smaller.
if m > n:
m = n
self.chiralityNSpinBox.setValue(n)
self.chiralityMSpinBox.setValue(m)
self.m, self.n = m, n
self.updateMessageGroupBox()
def nt_type_changed(self, idx):
"""
Slot for Nanotube Type combobox.
Update the bond length field when the type changes.
"""
self.bondLengthField.setValue(ntBondLengths[idx])
class DnaStrand_PropertyManager( DnaOrCnt_PropertyManager):
"""
The DnaStrand_PropertyManager class provides a Property Manager
for the DnaStrand_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 = "DnaStrand Properties"
pmName = title
iconPath = "ui/actions/Properties Manager/Strand.png"
def __init__( self, win, editCommand ):
"""
Constructor for the Build DNA 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
self.sequenceEditor = None
self._numberOfBases = 0
self._conformation = 'B-DNA'
self.duplexRise = 3.18
self.basesPerTurn = 10
self.dnaModel = 'PAM3'
_superclass.__init__( self,
win,
editCommand)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
self._loadSequenceEditor()
msg = "Use resize handles to resize the strand. Use sequence editor"\
"to assign a new sequence or the current one to a file."
self.updateMessage(msg)
def _addGroupBoxes( self ):
"""
Add the DNA 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 = "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 _loadSequenceEditor(self):
"""
Temporary code that shows the Sequence editor ..a doc widget docked
at the bottom of the mainwindow. The implementation is going to change
before 'rattleSnake' product release.
As of 2007-11-20: This feature (sequence editor) is waiting
for the ongoing dna model work to complete.
"""
self.sequenceEditor = self.win.createDnaSequenceEditorIfNeeded()
self.sequenceEditor.hide()
def _loadDisplayOptionsGroupBox(self, pmGroupBox):
"""
Overrides superclass method.
Also loads the color chooser widget.
"""
self._loadColorChooser(pmGroupBox)
_superclass._loadDisplayOptionsGroupBox(self, pmGroupBox)
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 ,
dnaStrandEditCommand_showCursorTextCheckBox_prefs_key)
def _params_for_creating_cursorTextCheckBoxes(self):
"""
Returns params needed to create various cursor text checkboxes connected
to prefs_keys that allow custom cursor texts.
@return: A list containing tuples in the following format:
('checkBoxTextString' , preference_key). PM_PrefsCheckBoxes
uses this data to create checkboxes with the the given names and
connects them to the provided preference keys. (Note that
PM_PrefsCheckBoxes puts thes within a GroupBox)
@rtype: list
@see: PM_PrefsCheckBoxes
@see: self._loadDisplayOptionsGroupBox where this list is used.
@see: Superclass method which is overridden here --
DnaOrCnt_PropertyManager._params_for_creating_cursorTextCheckBoxes()
"""
params = \
[ #Format: (" checkbox text", prefs_key)
("Number of bases",
dnaStrandEditCommand_cursorTextCheckBox_numberOfBases_prefs_key),
("Number of bases to be changed",
dnaStrandEditCommand_cursorTextCheckBox_changedBases_prefs_key)
]
return params
def getParameters(self):
numberOfBases = self.numberOfBasesSpinBox.value()
dnaForm = self._conformation
dnaModel = self.dnaModel
basesPerTurn = self.basesPerTurn
duplexRise = self.duplexRise
color = self._colorChooser.getColor()
return (numberOfBases,
dnaForm,
dnaModel,
basesPerTurn,
duplexRise,
color
)
def setParameters(self, params):
"""
This is usually called when you are editing an existing structure.
Some property manager ui elements then display the information
obtained from the object being edited.
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?
"""
#Set the duplex rise and bases per turn spinbox values.
numberOfBases, \
dnaForm, \
dnaModel, \
basesPerTurn, \
duplexRise, \
color = params
if numberOfBases is not None:
self.numberOfBasesSpinBox.setValue(numberOfBases)
if dnaForm is not None:
self._conformation = dnaForm
if dnaModel is not None:
self.dnaModel = dnaModel
if duplexRise is not None:
self.duplexRiseDoubleSpinBox.setValue(duplexRise)
if basesPerTurn is not None:
self.basesPerTurnDoubleSpinBox.setValue(basesPerTurn)
if color is not None:
self._colorChooser.setColor(color)
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
"""
#TODO: This is a temporary fix for a bug. When you invoke a temporary
# mode Entering such a temporary mode keeps the signals of
#PM from the previous mode connected (
#but while exiting that temporary mode and reentering the
#previous mode, it atucally reconnects the signal! This gives rise to
#lots of bugs. This needs more general fix in Temporary mode API.
# -- Ninad 2008-01-09 (similar comment exists in MovePropertyManager.py
if isConnect and self.isAlreadyConnected:
if debug_flags.atom_debug:
print_compact_stack("warning: attempt to connect widgets"\
"in this PM that are already connected." )
return
if not isConnect and self.isAlreadyDisconnected:
if debug_flags.atom_debug:
print_compact_stack("warning: attempt to disconnect widgets"\
"in this PM that are already disconnected.")
return
self.isAlreadyConnected = isConnect
self.isAlreadyDisconnected = not isConnect
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
if self.sequenceEditor:
self.sequenceEditor.connect_or_disconnect_signals(isConnect)
_superclass.connect_or_disconnect_signals(self, isConnect)
change_connect(self.disableStructHighlightingCheckbox,
SIGNAL('stateChanged(int)'),
self.change_struct_highlightPolicy)
change_connect(self.showCursorTextCheckBox,
SIGNAL('stateChanged(int)'),
self._update_state_of_cursorTextGroupBox)
def model_changed(self):
"""
@see: DnaStrand_EditCommand.model_changed()
@see: DnaStrand_EditCommand.hasResizableStructure()
"""
isStructResizable, why_not = self.editCommand.hasResizableStructure()
if not isStructResizable:
#disable all widgets
if self._pmGroupBox1.isEnabled():
self._pmGroupBox1.setEnabled(False)
msg1 = ("Viewing properties of %s <br>") %(self.editCommand.struct.name)
msg2 = redmsg("DnaStrand is not resizable. Reason: %s"%(why_not))
self.updateMessage(msg1 + msg2)
else:
if not self._pmGroupBox1.isEnabled():
self._pmGroupBox1.setEnabled(True)
msg1 = ("Viewing properties of %s <br>") %(self.editCommand.struct.name)
msg2 = "Use resize handles to resize the strand. Use sequence editor"\
"to assign a new sequence or the current one to a file."
self.updateMessage(msg1 + msg2)
def show(self):
"""
Show this PM
As of 2007-11-20, it also shows the Sequence Editor widget and hides
the history widget. This implementation may change in the near future
This method also retrives the name information from the
editCommand's structure for its name line edit field.
@see: DnaStrand_EditCommand.getStructureName()
@see: self.close()
"""
_superclass.show(self)
self._showSequenceEditor()
if self.editCommand is not None:
name = self.editCommand.getStructureName()
if name is not None:
self.nameLineEdit.setText(name)
def close(self):
"""
Close this property manager.
Also sets the name of the self.editCommand's structure to the one
displayed in the line edit field.
@see self.show()
@see: DnaSegment_EditCommand.setStructureName
"""
if self.editCommand is not None:
name = str(self.nameLineEdit.text())
self.editCommand.setStructureName(name)
if self.sequenceEditor:
self.sequenceEditor.close()
_superclass.close(self)
def _showSequenceEditor(self):
if self.sequenceEditor:
if not self.sequenceEditor.isVisible():
#Show the sequence editor
#ATTENTION: the sequence editor also closes (temporarily) the
#reports dockwidget (if visible) Its state is later restored when
#the sequuence Editor is closed.
self.sequenceEditor.show()
self.updateSequence()
def updateSequence(self):
"""
Update the sequence string in the sequence editor
@see: DnaSequenceEditor.setSequence()
@see DnaSequenceEditor._determine_complementSequence()
@see: DnaSequenceEditor.setComplementSequence()
@see: DnaStrand.getStrandSequenceAndItsComplement()
"""
#Read in the strand sequence of the selected strand and
#show it in the text edit in the sequence editor.
##strand = self.strandListWidget.getPickedItem()
if not self.editCommand.hasValidStructure():
return
strand = self.editCommand.struct
titleString = 'Sequence Editor for ' + strand.name
self.sequenceEditor.setWindowTitle(titleString)
sequenceString, complementSequenceString = strand.getStrandSequenceAndItsComplement()
if sequenceString:
sequenceString = QString(sequenceString)
sequenceString = sequenceString.toUpper()
#Set the initial sequence (read in from the file)
self.sequenceEditor.setSequence(sequenceString)
#Set the initial complement sequence for DnaSequence editor.
#do this independently because 'complementSequenceString' may have
#some characters (such as * ) that denote a missing base on the
#complementary strand. this information is used by the sequence
#editor. See DnaSequenceEditor._determine_complementSequence()
#for more details. See also bug 2787
self.sequenceEditor.setComplementSequence(complementSequenceString)
def change_struct_highlightPolicy(self,checkedState = False):
"""
Change the 'highlight policy' of the structure being edited
(i.e. self.editCommand.struct) .
@param checkedState: The checked state of the checkbox that says
'Don't highlight while editing DNA'. So, it
its True, the structure being edited won't get
highlighted.
@see: DnaStrand.setHighlightPolicy for more comments
"""
if self.editCommand and self.editCommand.hasValidStructure():
highlight = not checkedState
self.editCommand.struct.setHighlightPolicy(highlight = highlight)
def _addWhatsThisText(self):
"""
Add what's this text.
Abstract method.
"""
pass
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 _loadGroupBox3(self, pmGroupBox):
"""
Load widgets in the grid plane group box.
@param pmGroupBox: The grid group box in the PM.
@type pmGroupBox: L{PM_GroupBox}
"""
self.gridPlaneCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Show grid",
widgetColumn = 0,
setAsDefault = True,
spanWidth = True
)
connect_checkbox_with_boolean_pref(
self.gridPlaneCheckBox ,
PlanePM_showGrid_prefs_key)
self.gpXSpacingDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "X Spacing:",
value = 4.000,
setAsDefault = True,
minimum = 1.00,
maximum = 200.0,
decimals = 3,
singleStep = 1.0,
spanWidth = False)
self.gpYSpacingDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Y Spacing:",
value = 4.000,
setAsDefault = True,
minimum = 1.00,
maximum = 200.0,
decimals = 3,
singleStep = 1.0,
spanWidth = False)
lineTypeChoices = [ 'Dotted (default)',
'Dashed',
'Solid' ]
self.gpLineTypeComboBox = \
PM_ComboBox( pmGroupBox ,
label = "Line type:",
choices = lineTypeChoices,
setAsDefault = True)
hhColorList = [ black, orange, red, magenta,
cyan, blue, white, yellow, gray ]
hhColorNames = [ "Black (default)", "Orange", "Red", "Magenta",
"Cyan", "Blue", "White", "Yellow", "Other color..." ]
self.gpColorTypeComboBox = \
PM_ColorComboBox( pmGroupBox,
colorList = hhColorList,
colorNames = hhColorNames,
color = black )
self.pmGroupBox5 = PM_GroupBox( pmGroupBox )
self.gpDisplayLabels =\
PM_CheckBox( self.pmGroupBox5,
text = "Display labels",
widgetColumn = 0,
state = Qt.Unchecked,
setAsDefault = True,
spanWidth = True )
originChoices = [ 'Lower left (default)',
'Upper left',
'Lower right',
'Upper right' ]
self.gpOriginComboBox = \
PM_ComboBox( self.pmGroupBox5 ,
label = "Origin:",
choices = originChoices,
setAsDefault = True )
positionChoices = [ 'Origin axes (default)',
'Plane perimeter' ]
self.gpPositionComboBox = \
PM_ComboBox( self.pmGroupBox5 ,
label = "Position:",
choices = positionChoices,
setAsDefault = True)
self._showHideGPWidgets()
if env.prefs[PlanePM_showGridLabels_prefs_key]:
self.displayLabels = True
self.gpOriginComboBox.setEnabled( True )
self.gpPositionComboBox.setEnabled( True )
else:
self.displayLabels = False
self.gpOriginComboBox.setEnabled( False )
self.gpPositionComboBox.setEnabled( False )
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 _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
class InsertNanotube_PropertyManager(DnaOrCnt_PropertyManager):
"""
The InsertNanotube_PropertyManager class provides a Property Manager
for the B{Build > Nanotube > CNT} command.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
"""
title = "Insert Nanotube"
pmName = title
iconPath = "ui/actions/Tools/Build Structures/InsertNanotube.png"
def __init__(self, win, editCommand):
"""
Constructor for the Nanotube property manager.
"""
self.endPoint1 = None
self.endPoint2 = None
self.nanotube = Nanotube() # A 5x5 CNT.
_superclass.__init__(self, win, editCommand)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_CANCEL_BUTTON | \
PM_WHATS_THIS_BUTTON)
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.ntTypeComboBox,
SIGNAL("currentIndexChanged(const QString&)"),
self._ntTypeComboBoxChanged)
change_connect(self.chiralityNSpinBox, SIGNAL("valueChanged(int)"),
self._chiralityFixup)
change_connect(self.chiralityMSpinBox, SIGNAL("valueChanged(int)"),
self._chiralityFixup)
change_connect(self.endingsComboBox,
SIGNAL("currentIndexChanged(const QString&)"),
self._endingsComboBoxChanged)
# This spin box is currently hidden.
change_connect(self.bondLengthDoubleSpinBox,
SIGNAL("valueChanged(double)"), self._bondLengthChanged)
change_connect(self.showCursorTextCheckBox,
SIGNAL('stateChanged(int)'),
self._update_state_of_cursorTextGroupBox)
def ok_btn_clicked(self):
"""
Slot for the OK button
"""
if self.editCommand:
self.editCommand.preview_or_finalize_structure(previewing=False)
##env.history.message(self.editCommand.logMessage)
self.win.toolsDone()
def cancel_btn_clicked(self):
"""
Slot for the Cancel button.
"""
if self.editCommand:
self.editCommand.cancelStructure()
self.win.toolsCancel()
def _update_widgets_in_PM_before_show(self):
"""
Update various widgets in this Property manager.
Overrides MotorPropertyManager._update_widgets_in_PM_before_show.
The various widgets , (e.g. spinboxes) will get values from the
structure for which this propMgr is constructed for
(self.editcCntroller.struct)
@see: MotorPropertyManager._update_widgets_in_PM_before_show
@see: self.show where it is called.
"""
pass
def getFlyoutActionList(self):
"""
Returns custom actionlist that will be used in a specific mode
or editing a feature etc Example: while in movie mode,
the _createFlyoutToolBar method calls this.
"""
#'allActionsList' returns all actions in the flyout toolbar
#including the subcontrolArea actions
allActionsList = []
#Action List for subcontrol Area buttons.
#In this mode there is really no subcontrol area.
#We will treat subcontrol area same as 'command area'
#(subcontrol area buttons will have an empty list as their command area
#list). We will set the Comamnd Area palette background color to the
#subcontrol area.
subControlAreaActionList = []
self.exitEditCommandAction.setChecked(True)
subControlAreaActionList.append(self.exitEditCommandAction)
separator = QAction(self.w)
separator.setSeparator(True)
subControlAreaActionList.append(separator)
allActionsList.extend(subControlAreaActionList)
#Empty actionlist for the 'Command Area'
commandActionLists = []
#Append empty 'lists' in 'commandActionLists equal to the
#number of actions in subControlArea
for i in range(len(subControlAreaActionList)):
lst = []
commandActionLists.append(lst)
params = (subControlAreaActionList, commandActionLists, allActionsList)
return params
def _addGroupBoxes(self):
"""
Add the Insert Nanotube Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox(self, title="Endpoints")
self._loadGroupBox1(self._pmGroupBox1)
self._pmGroupBox1.hide()
self._pmGroupBox2 = PM_GroupBox(self, title="Parameters")
self._loadGroupBox2(self._pmGroupBox2)
self._displayOptionsGroupBox = PM_GroupBox(self,
title="Display Options")
self._loadDisplayOptionsGroupBox(self._displayOptionsGroupBox)
self._pmGroupBox3 = PM_GroupBox(self, title="Nanotube Distortion")
self._loadGroupBox3(self._pmGroupBox3)
self._pmGroupBox3.hide() #@ Temporary.
self._pmGroupBox4 = PM_GroupBox(self, title="Multi-Walled CNTs")
self._loadGroupBox4(self._pmGroupBox4)
self._pmGroupBox4.hide() #@ Temporary.
self._pmGroupBox5 = PM_GroupBox(self, title="Advanced Options")
self._loadGroupBox5(self._pmGroupBox5)
self._pmGroupBox5.hide() #@ Temporary.
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 1.
"""
#Following toolbutton facilitates entering a temporary NanotubeLineMode
#to create a CNT using endpoints of the specified line.
self.specifyCntLineButton = PM_ToolButton(
pmGroupBox,
text="Specify Endpoints",
iconPath="ui/actions/Properties Manager/Pencil.png",
spanWidth=True)
self.specifyCntLineButton.setCheckable(True)
self.specifyCntLineButton.setAutoRaise(True)
self.specifyCntLineButton.setToolButtonStyle(
Qt.ToolButtonTextBesideIcon)
#EndPoint1 and endPoint2 coordinates. These widgets are hidden
# as of 2007- 12 - 05
self._endPoint1SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
label="End Point 1")
self.x1SpinBox = self._endPoint1SpinBoxes.xSpinBox
self.y1SpinBox = self._endPoint1SpinBoxes.ySpinBox
self.z1SpinBox = self._endPoint1SpinBoxes.zSpinBox
self._endPoint2SpinBoxes = PM_CoordinateSpinBoxes(pmGroupBox,
label="End Point 2")
self.x2SpinBox = self._endPoint2SpinBoxes.xSpinBox
self.y2SpinBox = self._endPoint2SpinBoxes.ySpinBox
self.z2SpinBox = self._endPoint2SpinBoxes.zSpinBox
self._endPoint1SpinBoxes.hide()
self._endPoint2SpinBoxes.hide()
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in group box 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, inPmGroupBox):
"""
Load widgets in group box 3.
"""
self.zDistortionDoubleSpinBox = \
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.xyDistortionDoubleSpinBox = \
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 _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 _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 _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,
insertNanotubeEditCommand_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",
insertNanotubeEditCommand_cursorTextCheckBox_length_prefs_key ),
("Angle",
insertNanotubeEditCommand_cursorTextCheckBox_angle_prefs_key )
]
return params
def _addToolTipText(self):
"""
Tool Tip text for widgets in the Insert Nanotube Property Manager.
"""
pass
def _setEndPoints(self):
"""
Set the two endpoints of the nanotube using the values from the
X, Y, Z coordinate spinboxes in the property manager.
@note: The group box containing the 2 sets of XYZ spin boxes are
currently hidden.
"""
# First endpoint (origin) of nanotube
x1 = self.x1SpinBox.value()
y1 = self.y1SpinBox.value()
z1 = self.z1SpinBox.value()
# Second endpoint (direction vector/axis) of nanotube.
x2 = self.x2SpinBox.value()
y2 = self.y2SpinBox.value()
z2 = self.z2SpinBox.value()
if not self.endPoint1:
self.endPoint1 = V(x1, y1, z1)
if not self.endPoint2:
self.endPoint2 = V(x2, y2, z2)
self.nanotube.setEndPoints(self.endPoint1, self.endPoint2)
# Need arg "recompute=True", which will recompute the second
# endpoint (endPoint2) using the nanotube rise.
def getParameters(self):
"""
Return the parameters from this property manager to be used to create
the nanotube.
@return: A nanotube instance with its attrs set to the current
parameters in the property manager.
@rtype: L{Nanotube}
@see: L{InsertNanotube_EditCommand._gatherParameters} where this is used
"""
self._setEndPoints()
return (self.nanotube)
def _ntTypeComboBoxChanged(self, type):
"""
Slot for the Type combobox. It is called whenever the
Type choice is changed.
@param inIndex: The new index.
@type inIndex: int
"""
self.nanotube.setType(str(type))
print "Bond Length =", self.nanotube.getBondLength()
self.bondLengthDoubleSpinBox.setValue(self.nanotube.getBondLength())
#self.bondLengthDoubleSpinBox.setValue(ntBondLengths[inIndex])
def _bondLengthChanged(self, bondLength):
"""
Slot for the B{Bond Length} spinbox.
"""
self.nanotube.setBondLength(bondLength)
self.updateNanotubeDiameter()
return
def _chiralityFixup(self, spinBoxValueJunk=None):
"""
Slot for several validators for different parameters.
This gets called whenever the user changes the n, m chirality values.
@param spinBoxValueJunk: This is the Spinbox value from the valueChanged
signal. It is not used. We just want to know
that the spinbox value has changed.
@type spinBoxValueJunk: double or None
"""
_n, _m = self.nanotube.setChirality(self.chiralityNSpinBox.value(),
self.chiralityMSpinBox.value())
#self.n, self.m = self.nanotube.getChirality()
self.connect_or_disconnect_signals(isConnect=False)
self.chiralityNSpinBox.setValue(_n)
self.chiralityMSpinBox.setValue(_m)
self.connect_or_disconnect_signals(isConnect=True)
self.updateNanotubeDiameter()
def updateNanotubeDiameter(self):
"""
Update the nanotube Diameter lineEdit widget.
"""
diameterText = "%-7.4f Angstroms" % (self.nanotube.getDiameter())
self.ntDiameterLineEdit.setText(diameterText)
# ntRiseDoubleSpinBox is currently hidden.
self.ntRiseDoubleSpinBox.setValue(self.nanotube.getRise())
def _endingsComboBoxChanged(self, endings):
"""
Slot for the B{Ending} combobox.
@param endings: The option's text.
@type endings: string
"""
self.nanotube.setEndings(str(endings))
return
def _addWhatsThisText(self):
"""
What's This text for widgets in this Property Manager.
"""
whatsThis_InsertNanotube_PropertyManager(self)
return
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 _loadGroupBox1(self, inPmGroupBox):
"""
Load widgets in group box 1.
"""
memberChoices = ["Carbon", "Boron Nitride"]
self.typeComboBox= \
PM_ComboBox( inPmGroupBox,
label = "Type :",
choices = memberChoices,
index = 0,
setAsDefault = True,
spanWidth = False )
self.connect( self.typeComboBox,
SIGNAL("currentIndexChanged(int)"),
self.nt_type_changed)
self.lengthField = \
PM_DoubleSpinBox( inPmGroupBox,
label = "Length :",
value = 20.0,
setAsDefault = True,
minimum = 1.0,
maximum = 1000.0,
singleStep = 1.0,
decimals = 3,
suffix = " Angstroms" )
self.n = 5
self.chiralityNSpinBox = \
PM_SpinBox( inPmGroupBox,
label = "Chirality (n) :",
value = self.n,
setAsDefault = True )
self.connect(self.chiralityNSpinBox,
SIGNAL("valueChanged(int)"),
self.chirality_fixup)
self.m = 5
self.chiralityMSpinBox = \
PM_SpinBox( inPmGroupBox,
label = "Chirality (m) :",
value = self.m,
setAsDefault = True )
self.connect(self.chiralityMSpinBox,
SIGNAL("valueChanged(int)"),
self.chirality_fixup)
self.bondLengthField = \
PM_DoubleSpinBox( inPmGroupBox,
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( inPmGroupBox,
label = "Endings :",
choices = endingChoices,
index = 0,
setAsDefault = True,
spanWidth = False )
class BackrubProteinSim_PropertyManager(Command_PropertyManager):
"""
The BackrubProteinSim_PropertyManager class provides a Property Manager
for the B{Fixed backbone Protein Sequence Design} command on the flyout toolbar in the
Build > Protein > Simulate 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 = "Backrub Motion"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildProtein/Backrub.png"
def __init__( self, command ):
"""
Constructor for the property manager.
"""
_superclass.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
msg = "Choose various parameters from below to design an optimized" \
" protein sequence with Rosetta with backrub motion allowed."
self.updateMessage(msg)
def connect_or_disconnect_signals(self, isConnect = True):
"""
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.ex1Checkbox, SIGNAL("stateChanged(int)"), self.update_ex1)
change_connect(self.ex1aroCheckbox, SIGNAL("stateChanged(int)"), self.update_ex1aro)
change_connect(self.ex2Checkbox, SIGNAL("stateChanged(int)"), self.update_ex2)
change_connect(self.ex2aroOnlyCheckbox, SIGNAL("stateChanged(int)"), self.update_ex2aro_only)
change_connect(self.ex3Checkbox, SIGNAL("stateChanged(int)"), self.update_ex3)
change_connect(self.ex4Checkbox, SIGNAL("stateChanged(int)"), self.update_ex4)
change_connect(self.rotOptCheckbox, SIGNAL("stateChanged(int)"), self.update_rot_opt)
change_connect(self.tryBothHisTautomersCheckbox, SIGNAL("stateChanged(int)"), self.update_try_both_his_tautomers)
change_connect(self.softRepDesignCheckbox, SIGNAL("stateChanged(int)"), self.update_soft_rep_design)
change_connect(self.useElecRepCheckbox, SIGNAL("stateChanged(int)"), self.update_use_elec_rep)
change_connect(self.norepackDisulfCheckbox, SIGNAL("stateChanged(int)"), self.update_norepack_disulf)
#signal slot connections for the push buttons
change_connect(self.okButton, SIGNAL("clicked()"), self.runRosettaBackrubSim)
return
#Protein Display methods
def show(self):
"""
Shows the Property Manager. Exends superclass method.
"""
self.sequenceEditor = self.win.createProteinSequenceEditorIfNeeded()
self.sequenceEditor.hide()
#update the min and max residues spinbox max values based on the length
#of the current protein
numResidues = self._getNumResiduesForCurrentProtein()
if numResidues == 0:
self.minresSpinBox.setMaximum(numResidues + 2)
self.maxresSpinBox.setMaximum(numResidues + 2)
else:
self.minresSpinBox.setMaximum(numResidues)
self.maxresSpinBox.setMaximum(numResidues)
_superclass.show(self)
return
def _addGroupBoxes( self ):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox2 = PM_GroupBox( self,
title = "Backrub Specific Parameters")
self._loadGroupBox2( self._pmGroupBox2 )
self._pmGroupBox1 = PM_GroupBox( self,
title = "Rosetta Sequence Design Parameters")
self._loadGroupBox1( self._pmGroupBox1 )
return
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 _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 _getNumResiduesForCurrentProtein(self):
"""
Get number of residues for the current protein
"""
_current_protein = self.win.assy.getSelectedProteinChunk()
if _current_protein:
return len(_current_protein.protein.get_sequence_string())
return 0
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.numSimSpinBox = PM_SpinBox( pmGroupBox,
labelColumn = 0,
label = "Number of trials:",
minimum = 1000,
maximum = 1000000,
singleStep = 1000,
setAsDefault = False,
spanWidth = False)
self.ex1Checkbox = PM_CheckBox(pmGroupBox,
text = "Expand rotamer library for chi1 angle",
state = Qt.Unchecked,
setAsDefault = False,
widgetColumn = 0,
spanWidth = True)
self.ex1aroCheckbox = PM_CheckBox(pmGroupBox,
text = "Use large chi1 library for aromatic residues",
state = Qt.Unchecked,
setAsDefault = False,
widgetColumn = 0,
spanWidth = True)
self.ex2Checkbox = PM_CheckBox(pmGroupBox,
text = "Expand rotamer library for chi2 angle",
state = Qt.Unchecked,
setAsDefault = False,
widgetColumn = 0,
spanWidth = True)
self.ex2aroOnlyCheckbox = PM_CheckBox(pmGroupBox,
text = "Use large chi2 library only for aromatic residues",
state = Qt.Unchecked,
setAsDefault = False,
widgetColumn = 0,
spanWidth = True)
self.ex3Checkbox = PM_CheckBox(pmGroupBox,
text = "Expand rotamer library for chi3 angle",
state = Qt.Unchecked,
setAsDefault = False,
widgetColumn = 0,
spanWidth = True)
self.ex4Checkbox = PM_CheckBox(pmGroupBox,
text ="Expand rotamer library for chi4 angle",
state = Qt.Unchecked,
setAsDefault = False,
widgetColumn = 0,
spanWidth = True)
self.rotOptCheckbox = PM_CheckBox(pmGroupBox,
text ="Optimize one-body energy",
state = Qt.Unchecked,
setAsDefault = False,
widgetColumn = 0,
spanWidth = True)
self.tryBothHisTautomersCheckbox = PM_CheckBox(pmGroupBox,
text ="Try both histidine tautomers",
state = Qt.Unchecked,
setAsDefault = False,
widgetColumn = 0,
spanWidth = True)
self.softRepDesignCheckbox = PM_CheckBox(pmGroupBox,
text ="Use softer Lennard-Jones repulsive term",
state = Qt.Unchecked,
setAsDefault = False,
widgetColumn = 0,
spanWidth = True)
self.useElecRepCheckbox = PM_CheckBox(pmGroupBox,
text ="Use electrostatic repulsion",
state = Qt.Unchecked,
setAsDefault = False,
widgetColumn = 0,
spanWidth = True)
self.norepackDisulfCheckbox = PM_CheckBox(pmGroupBox,
text ="Don't re-pack disulphide bonds",
state = Qt.Unchecked,
setAsDefault = False,
widgetColumn = 0,
spanWidth = True)
self.otherCommandLineOptions = PM_TextEdit(pmGroupBox,
label = "Command line options:",
spanWidth = True)
self.otherCommandLineOptions.setFixedHeight(80)
self.okButton = PM_PushButton( pmGroupBox,
text = "Run Rosetta",
setAsDefault = True,
spanWidth = True)
return
def update_ex1(self, state):
"""
Update the command text edit depending on the state of the update_ex1
checkbox
@param state:state of the update_ex1 checkbox
@type state: int
"""
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
if self.ex1Checkbox.isChecked() == True:
otherOptionsText = otherOptionsText + ' -ex1 '
else:
otherOptionsText = otherOptionsText.replace(' -ex1 ', '')
self.otherCommandLineOptions.setText(otherOptionsText)
return
def update_ex1aro(self, state):
"""
Update the command text edit depending on the state of the update_ex1aro
checkbox
@param state:state of the update_ex1aro checkbox
@type state: int
"""
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
if self.ex1aroCheckbox.isChecked() == True:
otherOptionsText = otherOptionsText + ' -ex1aro '
else:
otherOptionsText = otherOptionsText.replace(' -ex1aro ', '')
self.otherCommandLineOptions.setText(otherOptionsText)
return
def update_ex2(self, state):
"""
Update the command text edit depending on the state of the update_ex2
checkbox
@param state:state of the update_ex2 checkbox
@type state: int
"""
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
if self.ex2Checkbox.isChecked() == True:
otherOptionsText = otherOptionsText + ' -ex2 '
else:
otherOptionsText = otherOptionsText.replace(' -ex2 ', '')
self.otherCommandLineOptions.setText(otherOptionsText)
return
def update_ex2aro_only(self, state):
"""
Update the command text edit depending on the state of the update_ex2aro_only
checkbox
@param state:state of the update_ex2aro_only checkbox
@type state: int
"""
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
if self.ex2aroOnlyCheckbox.isChecked() == True:
otherOptionsText = otherOptionsText + ' -ex2aro_only '
else:
otherOptionsText = otherOptionsText.replace(' -ex2aro_only ', '')
self.otherCommandLineOptions.setText(otherOptionsText)
return
def update_ex3(self, state):
"""
Update the command text edit depending on the state of the update_ex3
checkbox
@param state:state of the update_ex3 checkbox
@type state: int
"""
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
if self.ex3Checkbox.isChecked() == True:
otherOptionsText = otherOptionsText + ' -ex3 '
else:
otherOptionsText = otherOptionsText.replace(' -ex3 ', '')
self.otherCommandLineOptions.setText(otherOptionsText)
return
def update_ex4(self, state):
"""
Update the command text edit depending on the state of the update_ex4
checkbox
@param state:state of the update_ex4 checkbox
@type state: int
"""
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
if self.ex4Checkbox.isChecked() == True:
otherOptionsText = otherOptionsText + ' -ex4 '
else:
otherOptionsText = otherOptionsText.replace(' -ex4 ', '')
self.otherCommandLineOptions.setText(otherOptionsText)
return
def update_rot_opt(self, state):
"""
Update the command text edit depending on the state of the update_rot_opt
checkbox
@param state:state of the update_rot_opt checkbox
@type state: int
"""
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
if self.rotOptCheckbox.isChecked() == True:
otherOptionsText = otherOptionsText + ' -rot_opt '
else:
otherOptionsText = otherOptionsText.replace(' -rot_opt ', '')
self.otherCommandLineOptions.setText(otherOptionsText)
return
def update_try_both_his_tautomers(self, state):
"""
Update the command text edit depending on the state of the update_try_both_his_tautomers
checkbox
@param state:state of the update_try_both_his_tautomers checkbox
@type state: int
"""
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
if self.tryBothHisTautomersCheckbox.isChecked() == True:
otherOptionsText = otherOptionsText + ' -try_both_his_tautomers '
else:
otherOptionsText = otherOptionsText.replace(' -try_both_his_tautomers ', '')
self.otherCommandLineOptions.setText(otherOptionsText)
return
def update_soft_rep_design(self, state):
"""
Update the command text edit depending on the state of the update_soft_rep_design
checkbox
@param state:state of the update_soft_rep_design checkbox
@type state: int
"""
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
if self.softRepDesignCheckbox.isChecked() == True:
otherOptionsText = otherOptionsText + ' -soft_rep_design '
else:
otherOptionsText = otherOptionsText.replace(' -soft_rep_design ', '')
self.otherCommandLineOptions.setText(otherOptionsText)
return
def update_use_elec_rep(self, state):
"""
Update the command text edit depending on the state of the update_use_elec_rep
checkbox
@param state:state of the update_use_elec_rep checkbox
@type state: int
"""
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
if self.useElecRepCheckbox.isChecked() == True:
otherOptionsText = otherOptionsText + ' -use_electrostatic_repulsion '
else:
otherOptionsText = otherOptionsText.replace(' -use_electrostatic_repulsion ', '')
self.otherCommandLineOptions.setText(otherOptionsText)
return
def update_norepack_disulf(self, state):
"""
Update the command text edit depending on the state of the update_no_repack
checkbox
@param state:state of the update_no_repack checkbox
@type state: int
"""
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
if self.norepackDisulfCheckbox.isChecked() == True:
otherOptionsText = otherOptionsText + ' -norepack_disulf '
else:
otherOptionsText = otherOptionsText.replace(' -norepack_disulf ', '')
self.otherCommandLineOptions.setText(otherOptionsText)
return
def runRosettaBackrubSim(self):
"""
Get all the parameters from the PM and run a rosetta simulation
"""
proteinChunk = self.win.assy.getSelectedProteinChunk()
if not proteinChunk:
msg = "You must select a single protein to run a Rosetta <i>Backrub</i> simulation."
self.updateMessage(msg)
return
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
numSim = self.numSimSpinBox.value()
argList = [numSim, otherOptionsText, proteinChunk.name]
backrubSpecificArgList = self.getBackrubSpecificArgumentList()
from simulation.ROSETTA.rosetta_commandruns import rosettaSetup_CommandRun
if argList[0] > 0:
env.prefs[rosetta_backrub_enabled_prefs_key] = True
cmdrun = rosettaSetup_CommandRun(self.win, argList, "BACKRUB_PROTEIN_SEQUENCE_DESIGN", backrubSpecificArgList)
cmdrun.run()
return
def getBackrubSpecificArgumentList(self):
"""
get list of backrub specific parameters from PM
"""
listOfArgs = []
bond_angle_weight = str(self.bondAngleWeightSimSpinBox.value())
listOfArgs.append('-bond_angle_weight')
listOfArgs.append( bond_angle_weight)
if self.bondAngleParamComboBox.currentIndex() == 0:
bond_angle_params = 'bond_angle_amber_rosetta'
else:
bond_angle_params = 'bond_angle_charmm_rosetta'
listOfArgs.append('-bond_angle_params')
listOfArgs.append(bond_angle_params)
only_bb = str(self.onlybbSpinBox.value())
listOfArgs.append('-only_bb')
listOfArgs.append( only_bb)
only_rot = str(self.onlyrotSpinBox.value())
listOfArgs.append('-only_rot')
listOfArgs.append( only_rot)
mc_temp = str(self.mctempSpinBox.value())
listOfArgs.append('-mc_temp')
listOfArgs.append( mc_temp)
min_res = self.minresSpinBox.value()
max_res = self.maxresSpinBox.value()
if max_res < min_res:
msg = redmsg("Maximum number of residues for rosetta simulation with backrub" \
" motion cannot be less than minimum number of residues."\
" Neglecting this parameter for this simulation.")
env.history.message("BACKRUB SIMULATION: " + msg)
else:
listOfArgs.append('-min_res')
listOfArgs.append( str(min_res))
listOfArgs.append('-max_res')
listOfArgs.append( str(max_res))
return listOfArgs
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
class DnaDisplayStyle_PropertyManager( Command_PropertyManager):
"""
The DnaDisplayStyle_PropertyManager class provides a Property Manager
for the B{Display Style} 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 = "Edit DNA Display Style"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildDna/EditDnaDisplayStyle.png"
def __init__( self, command ):
"""
Constructor for the property manager.
"""
self.currentWorkingDirectory = env.prefs[workingDirectory_prefs_key]
_superclass.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
msg = "Modify the DNA display settings below."
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
# Favorite buttons signal-slot connections.
change_connect( self.applyFavoriteButton,
SIGNAL("clicked()"),
self.applyFavorite)
change_connect( self.addFavoriteButton,
SIGNAL("clicked()"),
self.addFavorite)
change_connect( self.deleteFavoriteButton,
SIGNAL("clicked()"),
self.deleteFavorite)
change_connect( self.saveFavoriteButton,
SIGNAL("clicked()"),
self.saveFavorite)
change_connect( self.loadFavoriteButton,
SIGNAL("clicked()"),
self.loadFavorite)
# Current display settings groupbox.
change_connect( self.dnaRenditionComboBox,
SIGNAL("currentIndexChanged(int)"),
self.change_dnaRendition )
# Axis options.
change_connect( self.axisShapeComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleAxisShape )
change_connect( self.axisScaleDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.win.userPrefs.change_dnaStyleAxisScale )
change_connect( self.axisColorComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleAxisColor )
change_connect( self.axisEndingStyleComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleAxisEndingStyle )
# Strands options.
change_connect( self.strandsShapeComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleStrandsShape )
change_connect( self.strandsScaleDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.win.userPrefs.change_dnaStyleStrandsScale )
change_connect( self.strandsColorComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleStrandsColor )
change_connect( self.strandsArrowsComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleStrandsArrows )
# Structs options.
change_connect( self.strutsShapeComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleStrutsShape )
change_connect( self.strutsScaleDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.win.userPrefs.change_dnaStyleStrutsScale )
change_connect( self.strutsColorComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleStrutsColor )
# Nucleotides options.
change_connect( self.nucleotidesShapeComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleBasesShape )
change_connect( self.nucleotidesScaleDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.win.userPrefs.change_dnaStyleBasesScale )
change_connect( self.nucleotidesColorComboBox,
SIGNAL("currentIndexChanged(int)"),
self.win.userPrefs.change_dnaStyleBasesColor )
connect_checkbox_with_boolean_pref(
self.dnaStyleBasesDisplayLettersCheckBox,
dnaStyleBasesDisplayLetters_prefs_key)
# Dna Strand labels option.
change_connect( self.standLabelColorComboBox,
SIGNAL("currentIndexChanged(int)"),
self.change_dnaStrandLabelsDisplay )
def show(self):
"""
Shows the Property Manager. Extends superclass method
"""
_superclass.show(self)
#@REVIEW: Is it safe to do the follwoing before calling superclass.show()?
#-- Ninad 2008-10-02
# Force the Global Display Style to "DNA Cylinder" so the user
# can see the display style setting effects on any DNA in the current
# model. The current global display style will be restored when leaving
# this command (via self.close()).
self.originalDisplayStyle = self.o.displayMode
# TODO: rename that public attr of GLPane (widely used)
# from displayMode to displayStyle. [bruce 080910 comment]
self.o.setGlobalDisplayStyle(diDNACYLINDER)
# Update all PM widgets, .
# note: It is important to update the widgets by blocking the
# 'signals'. If done in the reverse order, it will generate signals
#when updating the PM widgets (via updateDnaDisplayStyleWidgets()),
#causing unneccessary repaints of the model view.
self.updateDnaDisplayStyleWidgets(blockSignals = True)
def close(self):
"""
Closes the Property Manager. Extends superclass method.
"""
_superclass.close(self)
# Restore the original global display style.
self.o.setGlobalDisplayStyle(self.originalDisplayStyle)
def _addGroupBoxes( self ):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self,
title = "Favorites")
self._loadGroupBox1( self._pmGroupBox1 )
self._pmGroupBox2 = PM_GroupBox( self,
title = "Current Display Settings")
self._loadGroupBox2( self._pmGroupBox2 )
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
# Other info
# Not only loads the factory default settings but also all the favorite
# files stored in the ~/Nanorex/Favorites/DnaDisplayStyle directory
favoriteChoices = ['Factory default settings']
#look for all the favorite files in the favorite folder and add them to
# the list
from platform_dependent.PlatformDependent import find_or_make_Nanorex_subdir
_dir = find_or_make_Nanorex_subdir('Favorites/DnaDisplayStyle')
for file in os.listdir(_dir):
fullname = os.path.join( _dir, file)
if os.path.isfile(fullname):
if fnmatch.fnmatch( file, "*.txt"):
# leave the extension out
favoriteChoices.append(file[0:len(file)-4])
self.favoritesComboBox = \
PM_ComboBox( pmGroupBox,
choices = favoriteChoices,
spanWidth = True)
self.favoritesComboBox.setWhatsThis(
"""<b> List of Favorites </b>
<p>
Creates a list of favorite DNA display styles. Once favorite
styles have been added to the list using the Add Favorite button,
the list will display the chosen favorites.
To change the current favorite, select a current favorite from
the list, and push the Apply Favorite button.""")
# PM_ToolButtonRow ===============
# Button list to create a toolbutton row.
# Format:
# - QToolButton, buttonId, buttonText,
# - iconPath,
# - tooltip, shortcut, column
BUTTON_LIST = [
( "QToolButton", 1, "APPLY_FAVORITE",
"ui/actions/Properties Manager/ApplyFavorite.png",
"Apply Favorite", "", 0),
( "QToolButton", 2, "ADD_FAVORITE",
"ui/actions/Properties Manager/AddFavorite.png",
"Add Favorite", "", 1),
( "QToolButton", 3, "DELETE_FAVORITE",
"ui/actions/Properties Manager/DeleteFavorite.png",
"Delete Favorite", "", 2),
( "QToolButton", 4, "SAVE_FAVORITE",
"ui/actions/Properties Manager/SaveFavorite.png",
"Save Favorite", "", 3),
( "QToolButton", 5, "LOAD_FAVORITE",
"ui/actions/Properties Manager/LoadFavorite.png",
"Load Favorite", \
"", 4)
]
self.favsButtonGroup = \
PM_ToolButtonRow( pmGroupBox,
title = "",
buttonList = BUTTON_LIST,
spanWidth = True,
isAutoRaise = False,
isCheckable = False,
setAsDefault = True,
)
self.favsButtonGroup.buttonGroup.setExclusive(False)
self.applyFavoriteButton = self.favsButtonGroup.getButtonById(1)
self.addFavoriteButton = self.favsButtonGroup.getButtonById(2)
self.deleteFavoriteButton = self.favsButtonGroup.getButtonById(3)
self.saveFavoriteButton = self.favsButtonGroup.getButtonById(4)
self.loadFavoriteButton = self.favsButtonGroup.getButtonById(5)
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 _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 _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 _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 updateDnaDisplayStyleWidgets( self , blockSignals = False):
"""
Updates all the DNA Display style widgets based on the current pref keys
values.
@param blockSignals: If its set to True, the set* methods of the
the widgets (currently only PM_ Spinboxes and
ComboBoxes) won't emit a signal.
@type blockSignals: bool
@see: self.show() where this method is called.
@see: PM_Spinbox.setValue()
@see: PM_ComboBox.setCurrentIndex()
@note: This should be called each time the PM is displayed (see show()).
"""
self.dnaRenditionComboBox.setCurrentIndex(
env.prefs[dnaRendition_prefs_key],
blockSignals = blockSignals )
self.axisShapeComboBox.setCurrentIndex(
env.prefs[dnaStyleAxisShape_prefs_key], blockSignals = blockSignals)
self.axisScaleDoubleSpinBox.setValue(
env.prefs[dnaStyleAxisScale_prefs_key], blockSignals = blockSignals)
self.axisColorComboBox.setCurrentIndex(
env.prefs[dnaStyleAxisColor_prefs_key], blockSignals = blockSignals)
self.axisEndingStyleComboBox.setCurrentIndex(
env.prefs[dnaStyleAxisEndingStyle_prefs_key], blockSignals = blockSignals)
self.strandsShapeComboBox.setCurrentIndex(
env.prefs[dnaStyleStrandsShape_prefs_key], blockSignals = blockSignals)
self.strandsScaleDoubleSpinBox.setValue(
env.prefs[dnaStyleStrandsScale_prefs_key], blockSignals = blockSignals)
self.strandsColorComboBox.setCurrentIndex(
env.prefs[dnaStyleStrandsColor_prefs_key], blockSignals = blockSignals)
self.strandsArrowsComboBox.setCurrentIndex(
env.prefs[dnaStyleStrandsArrows_prefs_key], blockSignals = blockSignals)
self.strutsShapeComboBox.setCurrentIndex(
env.prefs[dnaStyleStrutsShape_prefs_key], blockSignals = blockSignals)
self.strutsScaleDoubleSpinBox.setValue(
env.prefs[dnaStyleStrutsScale_prefs_key], blockSignals = blockSignals)
self.strutsColorComboBox.setCurrentIndex(
env.prefs[dnaStyleStrutsColor_prefs_key], blockSignals = blockSignals)
self.nucleotidesShapeComboBox.setCurrentIndex(
env.prefs[dnaStyleBasesShape_prefs_key], blockSignals = blockSignals)
self.nucleotidesScaleDoubleSpinBox.setValue(
env.prefs[dnaStyleBasesScale_prefs_key], blockSignals = blockSignals)
self.nucleotidesColorComboBox.setCurrentIndex(
env.prefs[dnaStyleBasesColor_prefs_key], blockSignals = blockSignals)
# DNA Strand label combobox.
if env.prefs[dnaStrandLabelsEnabled_prefs_key]:
_dnaStrandColorItem = env.prefs[dnaStrandLabelsColorMode_prefs_key] + 1
else:
_dnaStrandColorItem = 0
self.standLabelColorComboBox.setCurrentIndex(
_dnaStrandColorItem, blockSignals = blockSignals)
def change_dnaStrandLabelsDisplay(self, mode):
"""
Changes DNA Strand labels display (and color) mode.
@param mode: The display mode:
- 0 = hide all labels
- 1 = show (same color as chunk)
- 2 = show (black)
- 3 = show (white)
- 4 = show (custom color...)
@type mode: int
"""
if mode == 4:
self.win.userPrefs.change_dnaStrandLabelsColor()
if mode == 0:
#@ Fix this at the same time I (we) remove the DNA display style
# prefs options from the Preferences dialog. --Mark 2008-05-13
self.win.userPrefs.toggle_dnaDisplayStrandLabelsGroupBox(False)
else:
self.win.userPrefs.toggle_dnaDisplayStrandLabelsGroupBox(True)
self.win.userPrefs.change_dnaStrandLabelsColorMode(mode - 1)
def applyFavorite(self):
"""
Apply the DNA display style settings stored in the current favorite
(selected in the combobox) to the current DNA display style settings.
"""
# Rules and other info:
# The user has to press the button related to this method when he loads
# a previously saved favorite file
current_favorite = self.favoritesComboBox.currentText()
if current_favorite == 'Factory default settings':
env.prefs.restore_defaults(dnaDisplayStylePrefsList)
else:
favfilepath = getFavoritePathFromBasename(current_favorite)
loadFavoriteFile(favfilepath)
self.updateDnaDisplayStyleWidgets()
return
def addFavorite(self):
"""
Adds a new favorite to the user's list of favorites.
"""
# Rules and other info:
# - The new favorite is defined by the current DNA display style
# settings.
# - The user is prompted to type in a name for the new
# favorite.
# - The DNA display style settings are written to a file in a special
# directory on the disk
# (i.e. $HOME/Nanorex/Favorites/DnaDisplayStyle/$FAV_NAME.fav).
# - The name of the new favorite is added to the list of favorites in
# the combobox, which becomes the current option.
# Existence of a favorite with the same name is checked in the above
# mentioned location and if a duplicate exists, then the user can either
# overwrite and provide a new name.
# Prompt user for a favorite name to add.
from widgets.simple_dialogs import grab_text_line_using_dialog
ok1, name = \
grab_text_line_using_dialog(
title = "Add new favorite",
label = "favorite name:",
iconPath = "ui/actions/Properties Manager/AddFavorite.png",
default = "" )
if ok1:
# check for duplicate files in the
# $HOME/Nanorex/Favorites/DnaDisplayStyle/ directory
fname = getFavoritePathFromBasename( name )
if os.path.exists(fname):
#favorite file already exists!
_ext= ".txt"
ret = QMessageBox.warning( self, "Warning!",
"The favorite file \"" + name + _ext + "\"already exists.\n"
"Do you want to overwrite the existing file?",
"&Overwrite", "&Cancel", "",
0, # Enter == button 0
1) # Escape == button 1
if ret == 0:
#overwrite favorite file
ok2, text = writeDnaDisplayStyleSettingsToFavoritesFile(name)
indexOfDuplicateItem = self.favoritesComboBox.findText(name)
self.favoritesComboBox.removeItem(indexOfDuplicateItem)
print "Add Favorite: removed duplicate favorite item."
else:
env.history.message("Add Favorite: cancelled overwriting favorite item.")
return
else:
ok2, text = writeDnaDisplayStyleSettingsToFavoritesFile(name)
else:
# User cancelled.
return
if ok2:
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
msg = "New favorite [%s] added." % (text)
else:
msg = "Can't add favorite [%s]: %s" % (name, text) # text is reason why not
env.history.message(msg)
return
def deleteFavorite(self):
"""
Deletes the current favorite from the user's personal list of favorites
(and from disk, only in the favorites folder though).
@note: Cannot delete "Factory default settings".
"""
currentIndex = self.favoritesComboBox.currentIndex()
currentText = self.favoritesComboBox.currentText()
if currentIndex == 0:
msg = "Cannot delete '%s'." % currentText
else:
self.favoritesComboBox.removeItem(currentIndex)
# delete file from the disk
deleteFile= getFavoritePathFromBasename( currentText )
os.remove(deleteFile)
msg = "Deleted favorite named [%s].\n" \
"and the favorite file [%s.txt]." \
% (currentText, currentText)
env.history.message(msg)
return
def saveFavorite(self):
"""
Writes the current favorite (selected in the combobox) to a file, any
where in the disk that
can be given to another NE1 user (i.e. as an email attachment).
"""
cmd = greenmsg("Save Favorite File: ")
env.history.message(greenmsg("Save Favorite File:"))
current_favorite = self.favoritesComboBox.currentText()
favfilepath = getFavoritePathFromBasename(current_favorite)
#Check to see if favfilepath exists first
if not os.path.exists(favfilepath):
msg = "%s does not exist" % favfilepath
env.history.message(cmd + msg)
return
formats = \
"Favorite (*.txt);;"\
"All Files (*.*)"
directory = self.currentWorkingDirectory
saveLocation = directory + "/" + current_favorite + ".txt"
fn = QFileDialog.getSaveFileName(
self,
"Save Favorite As", # caption
saveLocation, #where to save
formats, # file format options
QString("Favorite (*.txt)") # selectedFilter
)
if not fn:
env.history.message(cmd + "Cancelled")
else:
dir, fil = os.path.split(str(fn))
self.setCurrentWorkingDirectory(dir)
saveFavoriteFile(str(fn), favfilepath)
return
def setCurrentWorkingDirectory(self, dir = None):
if os.path.isdir(dir):
self.currentWorkingDirectory = dir
self._setWorkingDirectoryInPrefsDB(dir)
else:
self.currentWorkingDirectory = getDefaultWorkingDirectory()
def _setWorkingDirectoryInPrefsDB(self, workdir = None):
"""
[private method]
Set the working directory in the user preferences database.
@param workdir: The fullpath directory to write to the user pref db.
If I{workdir} is None (default), there is no change.
@type workdir: string
"""
if not workdir:
return
workdir = str(workdir)
if os.path.isdir(workdir):
workdir = os.path.normpath(workdir)
env.prefs[workingDirectory_prefs_key] = workdir # Change pref in prefs db.
else:
msg = "[" + workdir + "] is not a directory. Working directory was not changed."
env.history.message( redmsg(msg))
return
def loadFavorite(self):
"""
Prompts the user to choose a "favorite file" (i.e. *.txt) from disk to
be added to the personal favorites list.
"""
# If the file already exists in the favorites folder then the user is
# given the option of overwriting it or renaming it
env.history.message(greenmsg("Load Favorite File:"))
formats = \
"Favorite (*.txt);;"\
"All Files (*.*)"
directory = self.currentWorkingDirectory
if directory == '':
directory= getDefaultWorkingDirectory()
fname = QFileDialog.getOpenFileName(self,
"Choose a file to load",
directory,
formats)
if not fname:
env.history.message("User cancelled loading file.")
return
else:
dir, fil = os.path.split(str(fname))
self.setCurrentWorkingDirectory(dir)
canLoadFile=loadFavoriteFile(fname)
if canLoadFile == 1:
#get just the name of the file for loading into the combobox
favName = os.path.basename(str(fname))
name = favName[0:len(favName)-4]
indexOfDuplicateItem = self.favoritesComboBox.findText(name)
#duplicate exists in combobox
if indexOfDuplicateItem != -1:
ret = QMessageBox.warning( self, "Warning!",
"The favorite file \"" + name +
"\"already exists.\n"
"Do you want to overwrite the existing file?",
"&Overwrite", "&Rename", "&Cancel",
0, # Enter == button 0
1 # button 1
)
if ret == 0:
self.favoritesComboBox.removeItem(indexOfDuplicateItem)
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
ok2, text = writeDnaDisplayStyleSettingsToFavoritesFile(name)
msg = "Overwrote favorite [%s]." % (text)
env.history.message(msg)
elif ret == 1:
# add new item to favorites folder as well as combobox
self.addFavorite()
else:
#reset the display setting values to factory default
factoryIndex = self.favoritesComboBox.findText(
'Factory default settings')
self.favoritesComboBox.setCurrentIndex(factoryIndex)
env.prefs.restore_defaults(dnaDisplayStylePrefsList)
env.history.message("Cancelled overwriting favorite file.")
return
else:
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
msg = "Loaded favorite [%s]." % (name)
env.history.message(msg)
self.updateDnaDisplayStyleWidgets()
return
def change_dnaRendition(self, rendition):
"""
Sets the DNA rendition to 3D or one of the optional 2D styles.
@param rendition: The rendition mode, where:
- 0 = 3D (default)
- 1 = 2D with base letters
- 2 = 2D ball and stick
- 3 = 2D ladder
@type rendition: int
"""
if rendition == 0:
_enabled_flag = True
else:
_enabled_flag = False
self.dnaComponentComboBox.setEnabled(_enabled_flag)
self.dnaComponentStackedWidget.setEnabled(_enabled_flag)
self.standLabelColorComboBox.setEnabled(_enabled_flag)
env.prefs[dnaRendition_prefs_key] = rendition
self.o.gl_update() # Force redraw
return
def _addWhatsThisText( self ):
"""
What's This text for widgets in the DNA Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import WhatsThis_EditDnaDisplayStyle_PropertyManager
WhatsThis_EditDnaDisplayStyle_PropertyManager(self)
def _addToolTipText(self):
"""
Tool Tip text for widgets in the DNA Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_EditDnaDisplayStyle_PropertyManager
ToolTip_EditDnaDisplayStyle_PropertyManager(self)
class PM_Dialog_with_example_widgets( PM_Dialog):
"""
[private] PM_Dialog with some PM widgets common to several examples here
"""
# NOTE: contains some code copied (and perhaps modified) from AtomGeneratorDialog.py
# these class constants should be defined by each specific PM subclass
# (we don't define them here, since we want errors to occur if you don't override them)
# title = "title"
# pmName = "pm" + title
# iconPath = "path-to-some-icon.png"
#k all needed?
_sMinCoordinateValue = -30.0
_sMaxCoordinateValue = 30.0
_sStepCoordinateValue = 0.1
_sCoordinateDecimals = 4
_sCoordinateUnit = 'Angstrom'
_sCoordinateUnits = _sCoordinateUnit + 's'
_sElementSymbolList = ["H","O","C","S"]
def __init__(self):
PM_Dialog.__init__( self, self.pmName, self.iconPath, self.title )
msg = "Example command created at %s" % time.asctime()
# This causes the "Message" box to be displayed as well.
self.MessageGroupBox.insertHtmlMessage( msg, setAsDefault = False )
return
def _addGroupBoxes(self):
"""
Add group boxes to this Property Manager.
"""
self.pmGroupBox1 = PM_GroupBox( self, title = "Atom Parameters" )
self._loadGroupBox1(self.pmGroupBox1)
return
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 _addWhatsThisText(self):
"""
What's This text for some of the widgets in the Property Manager.
"""
self.xCoordinateField.setWhatsThis("<b>x</b><p>: The x-coordinate (up to </p>"
+ str( self._sMaxCoordinateValue )
+ self._sCoordinateUnits
+ ") of the Atom in "
+ self._sCoordinateUnits + '.')
pass # end of class PM_Dialog_with_example_widgets
def _loadGroupBox1(self, pmGroupBox):
"""Load widgets into groupbox 1 (passed as pmGroupBox)."""
# cylinder height (a double, stored as a preferences value)
cylinderHeight_stateref = Preferences_StateRef_double(
CYLINDER_HEIGHT_PREFS_KEY,
CYLINDER_HEIGHT_DEFAULT_VALUE )
### TODO: ask model object for this ref; this code should not need to know what kind it is (from prefs or model)
self.cylinderHeightSpinbox = \
PM_DoubleSpinBox( pmGroupBox,
label = "cylinder height:",
## value = CYLINDER_HEIGHT_DEFAULT_VALUE,
## # guess: default value or initial value (guess they can't be distinguished -- bug -- yes, doc confirms)
## setAsDefault = True,
### TODO: get all the following from the stateref, whenever the connection to state is made
minimum = 3,
maximum = self._sMaxCylinderHeight,
singleStep = 0.25,
decimals = self._sCoordinateDecimals,
suffix = ' ' + self._sCoordinateUnits )
# REVIEW: is it ok that the above will set some wrong defaultValue,
# to be immediately corrected by the following connection with state?
self.cylinderHeightSpinbox.connectWithState(
cylinderHeight_stateref,
debug_metainfo = True
)
# ==
# cylinder width (a double, stored in the command object,
# defined there using the State macro -- note, this is not yet a good
# enough example for state stored in a Node)
cylinderWidth_stateref = ObjAttr_StateRef( self.commandrun, 'cylinderWidth')
## TEMPORARY: just make sure it's defined in there
junk = cylinderWidth_stateref.defaultValue
self.cylinderWidthSpinbox = \
PM_DoubleSpinBox( pmGroupBox,
label = "cylinder width:",
## value = defaultValue,
## setAsDefault = True,
## ### REVISE: the default value should come from the cylinderWidth_stateref
# (and so, probably, should min, max, step, units...)
minimum = 0.1,
maximum = 15.0,
singleStep = 0.1,
decimals = self._sCoordinateDecimals,
suffix = ' ' + self._sCoordinateUnits )
self.cylinderWidthSpinbox.connectWithState(
cylinderWidth_stateref,
debug_metainfo = True )
# ==
# cylinder round caps (boolean)
cylinderRoundCaps_stateref = Preferences_StateRef( CYLINDER_ROUND_CAPS_PREFS_KEY,
CYLINDER_ROUND_CAPS_DEFAULT_VALUE ) ### TODO: get from model
## TEMPORARY: just make sure it's defined in there
junk = cylinderRoundCaps_stateref.defaultValue
self.cylinderRoundCapsCheckbox = PM_CheckBox(pmGroupBox, text = 'round caps on cylinder')
## self.cylinderRoundCapsCheckbox.setDefaultValue(CYLINDER_ROUND_CAPS_DEFAULT_VALUE)
## # note: setDefaultValue is an extension to the PM_CheckBox API, not yet finalized
self.cylinderRoundCapsCheckbox.connectWithState(
cylinderRoundCaps_stateref,
debug_metainfo = True )
# ==
# cylinder vertical or horizontal (boolean)
cylinderVertical_stateref = ObjAttr_StateRef( self.commandrun, 'cylinderVertical' )
self.cylinderVerticalCheckbox = PM_CheckBox(pmGroupBox, text = 'cylinder is vertical')
## self.cylinderVerticalCheckbox.setDefaultValue(CYLINDER_VERTICAL_DEFAULT_VALUE)
## ### REVISE: the default value should come from the stateref
self.cylinderVerticalCheckbox.connectWithState(
cylinderVertical_stateref,
debug_metainfo = True )
return # from _loadGroupBox1
class ProteinDisplayStyle_PropertyManager(Command_PropertyManager):
"""
The ProteinDisplayStyle_PropertyManager class provides a Property Manager
for the B{Display Style} command on the flyout toolbar in the
Build > Protein 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 = "Edit Protein Display Style"
pmName = title
iconPath = "ui/actions/Edit/EditProteinDisplayStyle.png"
def __init__( self, command ):
"""
Constructor for the property manager.
"""
self.currentWorkingDirectory = env.prefs[workingDirectory_prefs_key]
_superclass.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
msg = "Modify the protein display settings below."
self.updateMessage(msg)
def connect_or_disconnect_signals(self, isConnect = True):
"""
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
# Favorite buttons signal-slot connections.
change_connect( self.applyFavoriteButton,
SIGNAL("clicked()"),
self.applyFavorite)
change_connect( self.addFavoriteButton,
SIGNAL("clicked()"),
self.addFavorite)
change_connect( self.deleteFavoriteButton,
SIGNAL("clicked()"),
self.deleteFavorite)
change_connect( self.saveFavoriteButton,
SIGNAL("clicked()"),
self.saveFavorite)
change_connect( self.loadFavoriteButton,
SIGNAL("clicked()"),
self.loadFavorite)
#Display group box signal slot connections
change_connect(self.proteinStyleComboBox,
SIGNAL("currentIndexChanged(int)"),
self.changeProteinDisplayStyle)
change_connect(self.smoothingCheckBox,
SIGNAL("stateChanged(int)"),
self.smoothProteinDisplay)
change_connect(self.scaleComboBox,
SIGNAL("currentIndexChanged(int)"),
self.changeProteinDisplayScale)
change_connect(self.splineDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.changeProteinSplineValue)
change_connect(self.scaleFactorDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.changeProteinScaleFactor)
#color groupbox
change_connect(self.proteinComponentComboBox,
SIGNAL("currentIndexChanged(int)"),
self.chooseProteinComponent)
change_connect(self.proteinAuxComponentComboBox,
SIGNAL("currentIndexChanged(int)"),
self.chooseAuxilliaryProteinComponent)
change_connect(self.customColorComboBox,
SIGNAL("editingFinished()"),
self.chooseCustomColor)
change_connect(self.auxColorComboBox,
SIGNAL("editingFinished()"),
self.chooseAuxilliaryColor)
#change_connect(self.discColorCheckBox,
# SIGNAL("stateChanged(int)"),
# self.setDiscreteColors)
change_connect(self.helixColorComboBox,
SIGNAL("editingFinished()"),
self.chooseHelixColor)
change_connect(self.strandColorComboBox,
SIGNAL("editingFinished()"),
self.chooseStrandColor)
change_connect(self.coilColorComboBox,
SIGNAL("editingFinished()"),
self.chooseCoilColor)
#Protein Display methods
def changeProteinDisplayStyle(self, idx):
"""
Change protein display style
@param idx: index of the protein display style combo box
@type idx: int
"""
env.prefs[proteinStyle_prefs_key] = idx
return
def changeProteinDisplayQuality(self, idx):
env.prefs[proteinStyleQuality_prefs_key] = idx
return
def smoothProteinDisplay(self, state):
"""
Smoooth protein display.
@param state: state of the smooth protein display check box.
@type state: int
"""
if state == Qt.Checked:
env.prefs[proteinStyleSmooth_prefs_key] = True
else:
env.prefs[proteinStyleSmooth_prefs_key] = False
return
def changeProteinDisplayScale(self, idx):
"""
Change protein display scale
@param idx: index of the protein display scaling choices combo box
@type idx: int
"""
env.prefs[proteinStyleScaling_prefs_key] = idx
return
def changeProteinSplineValue(self, val):
"""
Change protein display resolution
@param val: value in the protein display resolution double spinbox
@type val: double
"""
env.prefs[proteinStyleQuality_prefs_key] = val
return
def changeProteinScaleFactor(self, val):
"""
Change protein display scale factor
@param val: value in the protein display scale factor double spinbox
@type val: double
"""
env.prefs[proteinStyleScaleFactor_prefs_key] = val
return
def chooseProteinComponent(self, idx):
"""
Choose protein component to set the color of
@param idx: index of the protein component choices combo box
@type idx: int
"""
env.prefs[proteinStyleColors_prefs_key] = idx
return
def chooseAuxilliaryProteinComponent(self, idx):
"""
Choose auxilliary protein component to set the color of
@param idx: index of the auxilliary protein component choices combo box
@type idx: int
"""
env.prefs[proteinStyleAuxColors_prefs_key] = idx - 1
return
def chooseCustomColor(self):
"""
Choose custom color of the chosen protein component
"""
color = self.customColorComboBox.getColor()
env.prefs[proteinStyleCustomColor_prefs_key] = color
return
def chooseAuxilliaryColor(self):
"""
Choose custom color of the chosen auxilliary protein component
"""
color = self.auxColorComboBox.getColor()
env.prefs[proteinStyleAuxCustomColor_prefs_key] = color
return
def chooseHelixColor(self):
"""
Choose helix color
"""
color = self.helixColorComboBox.getColor()
env.prefs[proteinStyleHelixColor_prefs_key] = color
return
def chooseStrandColor(self):
"""
Choose strand color
"""
color = self.strandColorComboBox.getColor()
env.prefs[proteinStyleStrandColor_prefs_key] = color
return
def chooseCoilColor(self):
"""
Choose coil color
"""
color = self.coilColorComboBox.getColor()
env.prefs[proteinStyleCoilColor_prefs_key] = color
return
def setDiscreteColors(self, state):
"""
Set discrete colors.
@param state: state of the set discrete colors check box.
@type state: int
"""
if state == Qt.Checked:
env.prefs[proteinStyleColorsDiscrete_prefs_key] = True
else:
env.prefs[proteinStyleColorsDiscrete_prefs_key] = False
return
def show_OLD(self):
"""
Shows the Property Manager.Extends superclass method.
"""
#@REVIEW: See comment in CompareProteins_PropertyManager
self.sequenceEditor = self.win.createProteinSequenceEditorIfNeeded()
self.sequenceEditor.hide()
self.updateProteinDisplayStyleWidgets()
_superclass.show(self)
def show(self):
"""
Shows the Property Manager. Extends superclass method
"""
_superclass.show(self)
#@REVIEW: Is it safe to do the follwoing before calling superclass.show()?
#-- Ninad 2008-10-02
# Force the Global Display Style to "DNA Cylinder" so the user
# can see the display style setting effects on any DNA in the current
# model. The current global display style will be restored when leaving
# this command (via self.close()).
self.originalDisplayStyle = self.o.displayMode
# TODO: rename that public attr of GLPane (widely used)
# from displayMode to displayStyle. [bruce 080910 comment]
self.o.setGlobalDisplayStyle(diPROTEIN)
# Update all PM widgets, .
# note: It is important to update the widgets by blocking the
# 'signals'. If done in the reverse order, it will generate signals
#when updating the PM widgets (via updateDnaDisplayStyleWidgets()),
#causing unneccessary repaints of the model view.
self.updateProteinDisplayStyleWidgets()#@@@ blockSignals = True)
return
def close(self):
"""
Closes the Property Manager. Extends superclass method.
"""
_superclass.close(self)
# Restore the original global display style.
self.o.setGlobalDisplayStyle(self.originalDisplayStyle)
return
def _addGroupBoxes( self ):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self,
title = "Favorites")
self._loadGroupBox1( self._pmGroupBox1 )
self._pmGroupBox2 = PM_GroupBox( self,
title = "Display")
self._loadGroupBox2( self._pmGroupBox2 )
self._pmGroupBox3 = PM_GroupBox( self,
title = "Color")
self._loadGroupBox3( self._pmGroupBox3 )
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
@param pmGroupBox: group box that contains various favorite buttons
@see: L{PM_GroupBox}
"""
# Other info
# Not only loads the factory default settings but also all the favorite
# files stored in the ~/Nanorex/Favorites/ProteinDisplayStyle directory
favoriteChoices = ['Factory default settings']
#look for all the favorite files in the favorite folder and add them to
# the list
from platform_dependent.PlatformDependent import find_or_make_Nanorex_subdir
_dir = find_or_make_Nanorex_subdir('Favorites/ProteinDisplayStyle')
for file in os.listdir(_dir):
fullname = os.path.join( _dir, file)
if os.path.isfile(fullname):
if fnmatch.fnmatch( file, "*.txt"):
# leave the extension out
favoriteChoices.append(file[0:len(file)-4])
self.favoritesComboBox = \
PM_ComboBox( pmGroupBox,
choices = favoriteChoices,
spanWidth = True)
self.favoritesComboBox.setWhatsThis(
"""<b> List of Favorites </b>
<p>
Creates a list of favorite Protein display styles. Once favorite
styles have been added to the list using the Add Favorite button,
the list will display the chosen favorites.
To change the current favorite, select a current favorite from
the list, and push the Apply Favorite button.""")
# PM_ToolButtonRow ===============
# Button list to create a toolbutton row.
# Format:
# - QToolButton, buttonId, buttonText,
# - iconPath,
# - tooltip, shortcut, column
BUTTON_LIST = [
( "QToolButton", 1, "APPLY_FAVORITE","ui/actions/Properties Manager/ApplyPeptideDisplayStyleFavorite.png",
"Apply Favorite", "", 0),
( "QToolButton", 2, "ADD_FAVORITE",
"ui/actions/Properties Manager/AddFavorite.png","Add Favorite", "", 1),
( "QToolButton", 3, "DELETE_FAVORITE", "ui/actions/Properties Manager/DeleteFavorite.png",
"Delete Favorite", "", 2),
( "QToolButton", 4, "SAVE_FAVORITE",
"ui/actions/Properties Manager/SaveFavorite.png",
"Save Favorite", "", 3),
( "QToolButton", 5, "LOAD_FAVORITE",
"ui/actions/Properties Manager/LoadFavorite.png",
"Load Favorite", \
"", 4)
]
self.favsButtonGroup = \
PM_ToolButtonRow( pmGroupBox,
title = "",
buttonList = BUTTON_LIST,
spanWidth = True,
isAutoRaise = False,
isCheckable = False,
setAsDefault = True,
)
self.favsButtonGroup.buttonGroup.setExclusive(False)
self.applyFavoriteButton = self.favsButtonGroup.getButtonById(1)
self.addFavoriteButton = self.favsButtonGroup.getButtonById(2)
self.deleteFavoriteButton = self.favsButtonGroup.getButtonById(3)
self.saveFavoriteButton = self.favsButtonGroup.getButtonById(4)
self.loadFavoriteButton = self.favsButtonGroup.getButtonById(5)
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.
@param pmGroupBox: group box that contains various color choices
@see: L{PM_GroupBox}
"""
colorChoices = ['Chunk', 'Chain', 'Order', 'Hydropathy', 'Polarity',
'Acidity', 'Size', 'Character', 'Number of contacts',
'Secondary structure type', 'Secondary structure order',
'B-factor', 'Occupancy', 'Custom']
self.proteinComponentComboBox = \
PM_ComboBox( pmGroupBox,
label = "Color by:",
choices = colorChoices,
setAsDefault = True)
colorList = [orange, yellow, red, magenta,
cyan, blue, white, black, gray]
colorNames = ["Orange(default)", "Yellow", "Red", "Magenta",
"Cyan", "Blue", "White", "Black", "Other color..."]
self.customColorComboBox = \
PM_ColorComboBox(pmGroupBox,
colorList = colorList,
colorNames = colorNames,
label = "Custom:",
color = orange,
setAsDefault = True)
colorChoices1 = [ 'Same as main color', 'Lighter', 'Darker',
'Gray', 'Custom']
self.proteinAuxComponentComboBox = \
PM_ComboBox( pmGroupBox,
label = "Aux:",
choices = colorChoices1,
setAsDefault = True)
colorListAux = [orange, yellow, red, magenta,cyan, blue, white, black, gray]
colorNamesAux = ["Orange(default)", "Yellow", "Red", "Magenta", "Cyan",
"Blue", "White", "Black", "Other color..."]
self.auxColorComboBox = \
PM_ColorComboBox(pmGroupBox,
colorList = colorListAux,
colorNames = colorNamesAux,
label = "Custom aux:",
color = gray,
setAsDefault = True)
#self.discColorCheckBox = \
# PM_CheckBox( pmGroupBox,
# text = "Discretize colors",
# setAsDefault = True
# )
#
colorListHelix = [red, yellow, gray, magenta,
cyan, blue, white, black, orange]
colorNamesHelix = ["Red(default)", "Yellow", "Gray", "Magenta",
"Cyan", "Blue", "White", "Black", "Other color..."]
self.helixColorComboBox = \
PM_ColorComboBox(pmGroupBox,
colorList = colorListHelix,
colorNames = colorNamesHelix,
label = "Helix:",
color = red,
setAsDefault = True)
colorListStrand = [cyan, yellow, gray, magenta,
red, blue, white, black, orange]
colorNamesStrand = ["Cyan(default)", "Yellow", "Gray", "Magenta",
"Red", "Blue", "White", "Black", "Other color..."]
self.strandColorComboBox = \
PM_ColorComboBox(pmGroupBox,
colorList = colorListStrand,
colorNames = colorNamesStrand,
label = "Strand:",
color = cyan,
setAsDefault = True)
self.coilColorComboBox = \
PM_ColorComboBox(pmGroupBox,
colorList = colorListAux,
colorNames = colorNamesAux,
label = "Coil:",
color = orange,
setAsDefault = True)
def updateProteinDisplayStyleWidgets( self ):
"""
Updates all the Protein Display style widgets based on the current pref keys
values
"""
self.proteinStyleComboBox.setCurrentIndex(env.prefs[proteinStyle_prefs_key])
self.splineDoubleSpinBox.setValue(env.prefs[proteinStyleQuality_prefs_key])
if env.prefs[proteinStyleSmooth_prefs_key] == True:
self.smoothingCheckBox.setCheckState(Qt.Checked)
else:
self.smoothingCheckBox.setCheckState(Qt.Unchecked)
self.scaleComboBox.setCurrentIndex(env.prefs[proteinStyleScaling_prefs_key])
self.scaleFactorDoubleSpinBox.setValue(env.prefs[proteinStyleScaleFactor_prefs_key])
self.proteinComponentComboBox.setCurrentIndex(env.prefs[proteinStyleColors_prefs_key])
self.customColorComboBox.setColor(env.prefs[proteinStyleCustomColor_prefs_key])
self.proteinAuxComponentComboBox.setCurrentIndex(env.prefs[proteinStyleAuxColors_prefs_key])
self.auxColorComboBox.setColor(env.prefs[proteinStyleAuxCustomColor_prefs_key])
#if env.prefs[proteinStyleColorsDiscrete_prefs_key] == True:
# self.discColorCheckBox.setCheckState(Qt.Checked)
#else:
# self.discColorCheckBox.setCheckState(Qt.Unchecked)
self.helixColorComboBox.setColor(env.prefs[proteinStyleHelixColor_prefs_key])
self.strandColorComboBox.setColor(env.prefs[proteinStyleStrandColor_prefs_key])
self.coilColorComboBox.setColor(env.prefs[proteinStyleCoilColor_prefs_key])
return
def applyFavorite(self):
"""
Apply a favorite to the current display chosen in the favorites combo box
"""
current_favorite = self.favoritesComboBox.currentText()
if current_favorite == 'Factory default settings':
env.prefs.restore_defaults(proteinDisplayStylePrefsList)
else:
favfilepath = getFavoritePathFromBasename(current_favorite)
loadFavoriteFile(favfilepath)
self.updateProteinDisplayStyleWidgets()
return
def addFavorite(self):
"""
create and add favorite to favorites directory and favorites combo box
in PM
@note: Rules and other info:
- The new favorite is defined by the current Protein display style
settings.
- The user is prompted to type in a name for the new
favorite.
- The Protein display style settings are written to a file in a special
directory on the disk
(i.e. $HOME/Nanorex/Favorites/ProteinDisplayStyle/$FAV_NAME.txt).
- The name of the new favorite is added to the list of favorites in
the combobox, which becomes the current option.
Existence of a favorite with the same name is checked in the above
mentioned location and if a duplicate exists, then the user can either
overwrite and provide a new name.
"""
# Prompt user for a favorite name to add.
from widgets.simple_dialogs import grab_text_line_using_dialog
ok1, name = \
grab_text_line_using_dialog(
title = "Add new favorite",
label = "favorite name:",
iconPath = "ui/actions/Properties Manager/AddFavorite.png",
default = "" )
if ok1:
# check for duplicate files in the
# $HOME/Nanorex/Favorites/DnaDisplayStyle/ directory
fname = getFavoritePathFromBasename( name )
if os.path.exists(fname):
#favorite file already exists!
_ext= ".txt"
ret = QMessageBox.warning( self, "Warning!",
"The favorite file \"" + name + _ext + "\"already exists.\n"
"Do you want to overwrite the existing file?",
"&Overwrite", "&Cancel", "",
0, # Enter == button 0
1) # Escape == button 1
if ret == 0:
#overwrite favorite file
ok2, text = writeProteinDisplayStyleSettingsToFavoritesFile(name)
indexOfDuplicateItem = self.favoritesComboBox.findText(name)
self.favoritesComboBox.removeItem(indexOfDuplicateItem)
print "Add Favorite: removed duplicate favorite item."
else:
env.history.message("Add Favorite: cancelled overwriting favorite item.")
return
else:
ok2, text = writeProteinDisplayStyleSettingsToFavoritesFile(name)
else:
# User cancelled.
return
if ok2:
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
msg = "New favorite [%s] added." % (text)
else:
msg = "Can't add favorite [%s]: %s" % (name, text) # text is reason why not
env.history.message(msg)
return
def deleteFavorite(self):
"""
Delete favorite file from the favorites directory
"""
currentIndex = self.favoritesComboBox.currentIndex()
currentText = self.favoritesComboBox.currentText()
if currentIndex == 0:
msg = "Cannot delete '%s'." % currentText
else:
self.favoritesComboBox.removeItem(currentIndex)
# delete file from the disk
deleteFile= getFavoritePathFromBasename( currentText )
os.remove(deleteFile)
msg = "Deleted favorite named [%s].\n" \
"and the favorite file [%s.txt]." \
% (currentText, currentText)
env.history.message(msg)
return
def saveFavorite(self):
"""
Save favorite file in a user chosen location
"""
cmd = greenmsg("Save Favorite File: ")
env.history.message(greenmsg("Save Favorite File:"))
current_favorite = self.favoritesComboBox.currentText()
favfilepath = getFavoritePathFromBasename(current_favorite)
formats = \
"Favorite (*.txt);;"\
"All Files (*.*)"
directory = self.currentWorkingDirectory
saveLocation = directory + "/" + current_favorite + ".txt"
fn = QFileDialog.getSaveFileName(
self,
"Save Favorite As", # caption
favfilepath, #where to save
formats, # file format options
QString("Favorite (*.txt)") # selectedFilter
)
if not fn:
env.history.message(cmd + "Cancelled")
else:
dir, fil = os.path.split(str(fn))
self.setCurrentWorkingDirectory(dir)
saveFavoriteFile(str(fn), favfilepath)
return
def setCurrentWorkingDirectory(self, dir = None):
"""
Set dir as current working diretcory
@param dir: dirname
@type dir: str
"""
if os.path.isdir(dir):
self.currentWorkingDirectory = dir
self._setWorkingDirectoryInPrefsDB(dir)
else:
self.currentWorkingDirectory = getDefaultWorkingDirectory()
return
def _setWorkingDirectoryInPrefsDB(self, workdir = None):
"""
Set workdir as current working diretcory in prefDB
@param workdir: dirname
@type workdir: str
"""
if not workdir:
return
workdir = str(workdir)
if os.path.isdir(workdir):
workdir = os.path.normpath(workdir)
env.prefs[workingDirectory_prefs_key] = workdir # Change pref in prefs db.
else:
msg = "[" + workdir + "] is not a directory. Working directory was not changed."
env.history.message( redmsg(msg))
return
def loadFavorite(self):
"""
Load a favorite file
"""
# If the file already exists in the favorites folder then the user is
# given the option of overwriting it or renaming it
env.history.message(greenmsg("Load Favorite File:"))
formats = \
"Favorite (*.txt);;"\
"All Files (*.*)"
directory = self.currentWorkingDirectory
if directory == '':
directory= getDefaultWorkingDirectory()
fname = QFileDialog.getOpenFileName(self,
"Choose a file to load",
directory,
formats)
if not fname:
env.history.message("User cancelled loading file.")
return
else:
dir, fil = os.path.split(str(fname))
self.setCurrentWorkingDirectory(dir)
canLoadFile=loadFavoriteFile(fname)
if canLoadFile == 1:
#get just the name of the file for loading into the combobox
favName = os.path.basename(str(fname))
name = favName[0:len(favName)-4]
indexOfDuplicateItem = self.favoritesComboBox.findText(name)
#duplicate exists in combobox
if indexOfDuplicateItem != -1:
ret = QMessageBox.warning( self, "Warning!",
"The favorite file \"" + name +
"\"already exists.\n"
"Do you want to overwrite the existing file?",
"&Overwrite", "&Rename", "&Cancel",
0, # Enter == button 0
1 # button 1
)
if ret == 0:
self.favoritesComboBox.removeItem(indexOfDuplicateItem)
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
ok2, text = writeProteinDisplayStyleSettingsToFavoritesFile(name)
msg = "Overwrote favorite [%s]." % (text)
env.history.message(msg)
elif ret == 1:
# add new item to favorites folder as well as combobox
self.addFavorite()
else:
#reset the display setting values to factory default
factoryIndex = self.favoritesComboBox.findText(
'Factory default settings')
self.favoritesComboBox.setCurrentIndex(factoryIndex)
env.prefs.restore_defaults(proteinDisplayStylePrefsList)
env.history.message("Cancelled overwriting favorite file.")
return
else:
self.favoritesComboBox.addItem(name)
_lastItem = self.favoritesComboBox.count()
self.favoritesComboBox.setCurrentIndex(_lastItem - 1)
msg = "Loaded favorite [%s]." % (name)
env.history.message(msg)
self.updateProteinDisplayStyleWidgets()
return
def _addWhatsThisText( self ):
"""
Add what's this text for this PM
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import WhatsThis_EditDnaDisplayStyle_PropertyManager
WhatsThis_EditDnaDisplayStyle_PropertyManager(self)
def _addToolTipText(self):
"""
Add tool tip text to all widgets.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_EditProteinDisplayStyle_PropertyManager
ToolTip_EditProteinDisplayStyle_PropertyManager(self)
class AtomGeneratorPropertyManager(PM_Dialog):
""" Implements user interface to specify properties of an atom """
# The title that appears in the property manager header.
title = "Insert Atom"
# 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 PNG file that appears in the header.
iconPath = "ui/actions/Command Toolbar/BuildAtoms/InsertAtom.png"
# Jeff 20070530:
# Private static variables (prefixed with '_s') are used to assure consistency
# between related widgets and simplify code revision.
# Example: The unit for coordinates is specified by _sCoordinateUnit. All
# widgets related to coordinates should refer to _sCoordinateUnit rather than
# hardcoding the unit for each coordinate widget. The advantage comes when
# a later revision uses different units (or chosen possibly via a user
# preference), the value of only _sCoordinateUnit (not blocks of code)
# needs to be changed. All related widgets follow the new choice for units.
_sMinCoordinateValue = -30.0
_sMaxCoordinateValue = 30.0
_sStepCoordinateValue = 0.1
_sCoordinateDecimals = 3
_sCoordinateUnit = 'Angstrom'
_sCoordinateUnits = _sCoordinateUnit + 's'
def __init__(self):
"""
Construct the Atom Property Manager.
"""
PM_Dialog.__init__( self, self.pmName, self.iconPath, self.title )
self.addGroupBoxes()
self.add_whats_this_text()
msg = "Edit the Atom parameters and select <b>Preview</b> to \
preview the structure. Click <b>Done</b> to insert the atom \
into the model."
# This causes the "Message" box to be displayed as well.
self.MessageGroupBox.insertHtmlMessage( msg, setAsDefault = False )
def getCartesianCoordinates(self):
"""
Gets the cartesian coordinates for the position of the atom
specified in the coordinate spin boxes of the Atom Generator
property manager.
"""
return ( self.xCoordinateField.value,
self.yCoordinateField.value,
self.zCoordinateField.value )
def getMinCoordinateValue(self):
"""
Get the minimum value allowed in the coordinate spin boxes
of the Atom Generator property manager.
"""
return self.sel_sMinCoordinateValue
def getMaxCoordinateValue(self):
"""
Get the maximum value allowed in the coordinate
spin boxes of the Atom Generator property manager.
"""
return self._sMaxCoordinateValue
def getStepCoordinateValue(self):
"""
Get the value by which a coordinate increases/decreases
when the user clicks an arrow of a coordinate spin box
in the Atom Generator property manager.
"""
return self._sStepCoordinateValue
def getCoordinateDecimals(self):
"""
Get the number of decimal places given for a value in a
coordinate spin box in the Atom Generator property manager.
"""
return self._sStepCoordinateValue
def getCoordinateUnit(self):
"""
Get the unit (of measure) for the coordinates of the
generated atom's position.
"""
return self._sCoordinateUnit
def setCartesianCoordinates( self, inX, inY, inZ ):
"""
Set the cartesian coordinates for the position of the atom
specified in the coordinate spin boxes of the Atom Generator
property manager.
"""
# We may want to restrict
self.xCoordinateField.value = inX
self.yCoordinateField.value = inY
self.zCoordinateField.value = inZ
def setMinCoordinateValue( self, inMin ):
"""
Set the minimum value allowed in the coordinate spin boxes
of the Atom Generator property manager.
"""
self._sMinCoordinateValue = inMin
def setMaxCoordinateValue( self, inMax ):
"""
Set the maximum value allowed in the coordinate
spin boxes of the Atom Generator property manager.
"""
self._sMaxCoordinateValue = inMax
def setStepCoordinateValue( self, inStep ):
"""
Set the value by which a coordinate increases/decreases
when the user clicks an arrow of a coordinate spin box
in the Atom Generator property manager.
"""
self._sStepCoordinateValue = inStep
def setCoordinateDecimals( self, inDecimals ):
"""
Set the number of decimal places given for a value in a
coordinate spin box in the Atom Generator property manager.
"""
self._sStepCoordinateValue = inDecimals
def setCoordinateUnit( self, inUnit ):
"""
Set the unit(s) (of measure) for the coordinates of the
generated atom's position.
"""
self._sCoordinateUnit = inUnit
self._sCoordinateUnits = inUnit + 's'
def addGroupBoxes(self):
"""
Add the 1 groupbox for the Atom Property Manager.
"""
self.pmGroupBox1 = \
PM_GroupBox( self,
title = "Atom Position" )
self.loadGroupBox1(self.pmGroupBox1)
self.pmElementChooser = PM_ElementChooser(self)
AddTestGroupBoxes = True # For testing. Mark 2007-05-24
if not AddTestGroupBoxes: # Add test widgets to their own groupbox.
return
"""
self.testGroupBox1 = \
PM_GroupBox( self,
title = "Test Widgets1" )
self.loadTestWidgets1(self.testGroupBox1)
self.pmLineEditGroupBox = \
PM_GroupBox( self,
title = "PM_LineEdit Widgets" )
self.loadLineEditGroupBox(self.pmLineEditGroupBox)
"""
"""
self.radioButtonGroupBox = \
PM_GroupBox( self,
title = "PM_RadioButtons" )
self.loadRadioButtonGroupBox(self.radioButtonGroupBox)
self.pmToolButtonGroupBox = \
PM_GroupBox( self,
title = "MMKit Widget" )
self.loadToolButtonGroupBox(self.pmToolButtonGroupBox)
"""
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 add_whats_this_text(self):
"""
What's This... text for some of the widgets in the
Atom Property Manager.
:Jeff 2007-05-30:
"""
self.xCoordinateField.setWhatsThis("<b>x</b><p>: The x-coordinate (up "\
"to </p>" \
+ str( self._sMaxCoordinateValue ) \
+ self._sCoordinateUnits \
+ ") of the Atom in " \
+ self._sCoordinateUnits + '.')
self.yCoordinateField.setWhatsThis("<b>y</b><p>: The y-coordinate (up" \
"to </p>"\
+ str( self._sMaxCoordinateValue ) \
+ self._sCoordinateUnits \
+ ") of the Atom in " \
+ self._sCoordinateUnits + '.')
self.zCoordinateField.setWhatsThis("<b>z</b><p>: The z-coordinate (up" \
"to </p>" \
+ str( self._sMaxCoordinateValue )
+ self._sCoordinateUnits \
+ ") of the Atom in "
+ self._sCoordinateUnits + '.')
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 loadLineEditGroupBox(self, inPmGroupBox):
"""
Load PM_LineEdit test widgets in group box.
"""
self.lineEdit1 = \
PM_LineEdit( inPmGroupBox,
label = "Name:",
text = "RotaryMotor-1",
setAsDefault = True,
spanWidth = False)
self.lineEdit2 = \
PM_LineEdit( inPmGroupBox,
label = ":Name",
labelColumn = 1,
text = "RotaryMotor-1",
setAsDefault = True,
spanWidth = False)
self.lineEdit3 = \
PM_LineEdit( inPmGroupBox,
label = "LineEdit (spanWidth = True):",
text = "RotaryMotor-1",
setAsDefault = False,
spanWidth = True)
def loadCheckBoxGroupBox(self, inPmGroupBox):
"""
Load PM_CheckBox test widgets in group box.
"""
self.checkBoxGroupBox = \
PM_GroupBox( inPmGroupBox,
title = "<b> PM_CheckBox examples</b>" )
self.checkBox1 = \
PM_CheckBox( self.checkBoxGroupBox,
text = "Widget on left:",
widgetColumn = 1,
state = Qt.Checked,
setAsDefault = True,
)
self.checkBox2 = \
PM_CheckBox( self.checkBoxGroupBox,
text = "Widget on right",
widgetColumn = 1,
state = Qt.Checked,
setAsDefault = True,
)
def loadRadioButtonGroupBox(self, inPmGroupBox):
"""
Test for PM_RadioButtonGroupBox.
"""
#from PyQt4.Qt import QButtonGroup
#self.radioButtonGroup = QButtonGroup()
#self.radioButtonGroup.setExclusive(True)
self.radioButton1 = \
PM_RadioButton( inPmGroupBox,
label = "Display PM_CheckBox group box",
spanWidth = False)
self.radioButton2 = \
PM_RadioButton( inPmGroupBox,
label = "Display PM_ComboBox group box",
spanWidth = False)
self.radioButton3 = \
PM_RadioButton( inPmGroupBox,
label = "Display PM_DoubleSpinBox group box",
spanWidth = False)
self.radioButton4 = \
PM_RadioButton( inPmGroupBox,
label = "Display PM_PushButton group box",
spanWidth = False)
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in the image group box.
@param pmGroupBox: The image group box in the PM.
@type pmGroupBox: L{PM_GroupBox}
"""
self.imageDisplayCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Display image",
widgetColumn = 0,
state = Qt.Unchecked,
setAsDefault = True,
spanWidth = True
)
self.imageDisplayFileChooser = \
PM_FileChooser(pmGroupBox,
label = 'Image file:',
text = '' ,
spanWidth = True,
filter = "PNG (*.png);;"\
"All Files (*.*)"
)
self.imageDisplayFileChooser.setEnabled(False)
# add change image properties button
BUTTON_LIST = [
( "QToolButton", 1, "+90",
"ui/actions/Properties Manager/RotateImage+90.png",
"+90", "", 0),
( "QToolButton", 2, "-90",
"ui/actions/Properties Manager/RotateImage-90.png",
"-90", "", 1),
( "QToolButton", 3, "FLIP",
"ui/actions/Properties Manager/FlipImageVertical.png",
"Flip", "", 2),
( "QToolButton", 4, "MIRROR",
"ui/actions/Properties Manager/FlipImageHorizontal.png",
"Mirror", "", 3)
]
#image change button groupbox
self.pmGroupBox2 = PM_GroupBox(pmGroupBox, title = "Modify Image")
self.imageChangeButtonGroup = \
PM_ToolButtonRow( self.pmGroupBox2,
title = "",
buttonList = BUTTON_LIST,
spanWidth = True,
isAutoRaise = False,
isCheckable = False,
setAsDefault = True,
)
self.imageChangeButtonGroup.buttonGroup.setExclusive(False)
self.plusNinetyButton = self.imageChangeButtonGroup.getButtonById(1)
self.minusNinetyButton = self.imageChangeButtonGroup.getButtonById(2)
self.flipButton = self.imageChangeButtonGroup.getButtonById(3)
self.mirrorButton = self.imageChangeButtonGroup.getButtonById(4)
# buttons enabled when a valid image is loaded
self.mirrorButton.setEnabled(False)
self.plusNinetyButton.setEnabled(False)
self.minusNinetyButton.setEnabled(False)
self.flipButton.setEnabled(False)
self.heightfieldDisplayCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Create 3D relief",
widgetColumn = 0,
state = Qt.Unchecked,
setAsDefault = True,
spanWidth = True
)
self.heightfieldHQDisplayCheckBox = \
PM_CheckBox( pmGroupBox,
text = "High quality",
widgetColumn = 0,
state = Qt.Unchecked,
setAsDefault = True,
spanWidth = True
)
self.heightfieldTextureCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Use texture",
widgetColumn = 0,
state = Qt.Checked,
setAsDefault = True,
spanWidth = True
)
self.vScaleSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
label = " Vertical scale:",
value = 1.0,
setAsDefault = True,
minimum = -1000.0, # -1000 A
maximum = 1000.0, # 1000 A
singleStep = 0.1,
decimals = 1,
suffix = ' Angstroms')
self.heightfieldDisplayCheckBox.setEnabled(False)
self.heightfieldHQDisplayCheckBox.setEnabled(False)
self.heightfieldTextureCheckBox.setEnabled(False)
self.vScaleSpinBox.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)
class PlanePropertyManager(EditCommand_PM):
"""
The PlanePropertyManager class provides a Property Manager for a
(reference) Plane.
"""
# The title that appears in the Property Manager header.
title = "Plane"
# 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/Insert/Reference Geometry/Plane.png"
def __init__(self, command):
"""
Construct the Plane Property Manager.
@param plane: The plane.
@type plane: L{Plane}
"""
#see self.connect_or_disconnect_signals for comment about this flag
self.isAlreadyConnected = False
self.isAlreadyDisconnected = False
self.gridColor = black
self.gridXSpacing = 4.0
self.gridYSpacing = 4.0
self.gridLineType = 3
self.displayLabels = False
self.originLocation = PLANE_ORIGIN_LOWER_LEFT
self.displayLabelStyle = LABELS_ALONG_ORIGIN
EditCommand_PM.__init__( self, command)
# Hide Preview and Restore defaults buttons
self.hideTopRowButtons(PM_RESTORE_DEFAULTS_BUTTON)
def _addGroupBoxes(self):
"""
Add the 1st group box to the Property Manager.
"""
# Placement Options radio button list to create radio button list.
# Format: buttonId, buttonText, tooltip
PLACEMENT_OPTIONS_BUTTON_LIST = [ \
( 0, "Parallel to screen", "Parallel to screen" ),
( 1, "Through selected atoms", "Through selected atoms" ),
( 2, "Offset to a plane", "Offset to a plane" ),
( 3, "Custom", "Custom" )
]
self.pmPlacementOptions = \
PM_RadioButtonList( self,
title = "Placement Options",
buttonList = PLACEMENT_OPTIONS_BUTTON_LIST,
checkedId = 3 )
self.pmGroupBox1 = PM_GroupBox(self, title = "Parameters")
self._loadGroupBox1(self.pmGroupBox1)
#image groupbox
self.pmGroupBox2 = PM_GroupBox(self, title = "Image")
self._loadGroupBox2(self.pmGroupBox2)
#grid plane groupbox
self.pmGroupBox3 = PM_GroupBox(self, title = "Grid")
self._loadGroupBox3(self.pmGroupBox3)
def _loadGroupBox3(self, pmGroupBox):
"""
Load widgets in the grid plane group box.
@param pmGroupBox: The grid group box in the PM.
@type pmGroupBox: L{PM_GroupBox}
"""
self.gridPlaneCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Show grid",
widgetColumn = 0,
setAsDefault = True,
spanWidth = True
)
connect_checkbox_with_boolean_pref(
self.gridPlaneCheckBox ,
PlanePM_showGrid_prefs_key)
self.gpXSpacingDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "X Spacing:",
value = 4.000,
setAsDefault = True,
minimum = 1.00,
maximum = 200.0,
decimals = 3,
singleStep = 1.0,
spanWidth = False)
self.gpYSpacingDoubleSpinBox = \
PM_DoubleSpinBox( pmGroupBox,
label = "Y Spacing:",
value = 4.000,
setAsDefault = True,
minimum = 1.00,
maximum = 200.0,
decimals = 3,
singleStep = 1.0,
spanWidth = False)
lineTypeChoices = [ 'Dotted (default)',
'Dashed',
'Solid' ]
self.gpLineTypeComboBox = \
PM_ComboBox( pmGroupBox ,
label = "Line type:",
choices = lineTypeChoices,
setAsDefault = True)
hhColorList = [ black, orange, red, magenta,
cyan, blue, white, yellow, gray ]
hhColorNames = [ "Black (default)", "Orange", "Red", "Magenta",
"Cyan", "Blue", "White", "Yellow", "Other color..." ]
self.gpColorTypeComboBox = \
PM_ColorComboBox( pmGroupBox,
colorList = hhColorList,
colorNames = hhColorNames,
color = black )
self.pmGroupBox5 = PM_GroupBox( pmGroupBox )
self.gpDisplayLabels =\
PM_CheckBox( self.pmGroupBox5,
text = "Display labels",
widgetColumn = 0,
state = Qt.Unchecked,
setAsDefault = True,
spanWidth = True )
originChoices = [ 'Lower left (default)',
'Upper left',
'Lower right',
'Upper right' ]
self.gpOriginComboBox = \
PM_ComboBox( self.pmGroupBox5 ,
label = "Origin:",
choices = originChoices,
setAsDefault = True )
positionChoices = [ 'Origin axes (default)',
'Plane perimeter' ]
self.gpPositionComboBox = \
PM_ComboBox( self.pmGroupBox5 ,
label = "Position:",
choices = positionChoices,
setAsDefault = True)
self._showHideGPWidgets()
if env.prefs[PlanePM_showGridLabels_prefs_key]:
self.displayLabels = True
self.gpOriginComboBox.setEnabled( True )
self.gpPositionComboBox.setEnabled( True )
else:
self.displayLabels = False
self.gpOriginComboBox.setEnabled( False )
self.gpPositionComboBox.setEnabled( False )
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
"""
#TODO: Fix for bug: When you invoke a temporary mode
# entering such a temporary mode keeps the signals of
#PM from the previous mode connected (
#but while exiting that temporary mode and reentering the
#previous mode, it actually reconnects the signal! This gives rise to
#lots of bugs. This needs more general fix in Temporary mode API.
# -- Ninad 2008-01-09 (similar comment exists in MovePropertyManager.py
#UPDATE: (comment copied and modifief from BuildNanotube_PropertyManager.
#The general problem still remains -- Ninad 2008-06-25
if isConnect and self.isAlreadyConnected:
if debug_flags.atom_debug:
print_compact_stack("warning: attempt to connect widgets"\
"in this PM that are already connected." )
return
if not isConnect and self.isAlreadyDisconnected:
if debug_flags.atom_debug:
print_compact_stack("warning: attempt to disconnect widgets"\
"in this PM that are already disconnected.")
return
self.isAlreadyConnected = isConnect
self.isAlreadyDisconnected = not isConnect
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.pmPlacementOptions.buttonGroup,
SIGNAL("buttonClicked(int)"),
self.changePlanePlacement)
change_connect(self.widthDblSpinBox,
SIGNAL("valueChanged(double)"),
self.change_plane_width)
change_connect(self.heightDblSpinBox,
SIGNAL("valueChanged(double)"),
self.change_plane_height)
change_connect(self.aspectRatioCheckBox,
SIGNAL("stateChanged(int)"),
self._enableAspectRatioSpinBox)
#signal slot connection for imageDisplayCheckBox
change_connect(self.imageDisplayCheckBox,
SIGNAL("stateChanged(int)"),
self.toggleFileChooserBehavior)
#signal slot connection for imageDisplayFileChooser
change_connect(self.imageDisplayFileChooser.lineEdit,
SIGNAL("editingFinished()"),
self.update_imageFile)
#signal slot connection for heightfieldDisplayCheckBox
change_connect(self.heightfieldDisplayCheckBox,
SIGNAL("stateChanged(int)"),
self.toggleHeightfield)
#signal slot connection for heightfieldHQDisplayCheckBox
change_connect(self.heightfieldHQDisplayCheckBox,
SIGNAL("stateChanged(int)"),
self.toggleHeightfieldHQ)
#signal slot connection for heightfieldTextureCheckBox
change_connect(self.heightfieldTextureCheckBox,
SIGNAL("stateChanged(int)"),
self.toggleTexture)
#signal slot connection for vScaleSpinBox
change_connect(self.vScaleSpinBox,
SIGNAL("valueChanged(double)"),
self.change_vertical_scale)
change_connect(self.plusNinetyButton,
SIGNAL("clicked()"),
self.rotate_90)
change_connect(self.minusNinetyButton,
SIGNAL("clicked()"),
self.rotate_neg_90)
change_connect(self.flipButton,
SIGNAL("clicked()"),
self.flip_image)
change_connect(self.mirrorButton,
SIGNAL("clicked()"),
self.mirror_image)
change_connect(self.gridPlaneCheckBox,
SIGNAL("stateChanged(int)"),
self.displayGridPlane)
change_connect(self.gpXSpacingDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.changeXSpacingInGP)
change_connect(self.gpYSpacingDoubleSpinBox,
SIGNAL("valueChanged(double)"),
self.changeYSpacingInGP)
change_connect( self.gpLineTypeComboBox,
SIGNAL("currentIndexChanged(int)"),
self.changeLineTypeInGP )
change_connect( self.gpColorTypeComboBox,
SIGNAL("editingFinished()"),
self.changeColorTypeInGP )
change_connect( self.gpDisplayLabels,
SIGNAL("stateChanged(int)"),
self.displayLabelsInGP )
change_connect( self.gpOriginComboBox,
SIGNAL("currentIndexChanged(int)"),
self.changeOriginInGP )
change_connect( self.gpPositionComboBox,
SIGNAL("currentIndexChanged(int)"),
self.changePositionInGP )
self._connect_checkboxes_to_global_prefs_keys()
return
def _connect_checkboxes_to_global_prefs_keys(self):
"""
"""
connect_checkbox_with_boolean_pref(
self.gridPlaneCheckBox ,
PlanePM_showGrid_prefs_key)
connect_checkbox_with_boolean_pref(
self.gpDisplayLabels,
PlanePM_showGridLabels_prefs_key)
def changePositionInGP(self, idx):
"""
Change Display of origin Labels (choices are along origin edges or along
the plane perimeter.
@param idx: Current index of the change grid label position combo box
@type idx: int
"""
if idx == 0:
self.displayLabelStyle = LABELS_ALONG_ORIGIN
elif idx == 1:
self.displayLabelStyle = LABELS_ALONG_PLANE_EDGES
else:
print "Invalid index", idx
return
def changeOriginInGP(self, idx):
"""
Change Display of origin Labels based on the location of the origin
@param idx: Current index of the change origin position combo box
@type idx: int
"""
if idx == 0:
self.originLocation = PLANE_ORIGIN_LOWER_LEFT
elif idx ==1:
self.originLocation = PLANE_ORIGIN_UPPER_LEFT
elif idx == 2:
self.originLocation = PLANE_ORIGIN_LOWER_RIGHT
elif idx == 3:
self.originLocation = PLANE_ORIGIN_UPPER_RIGHT
else:
print "Invalid index", idx
return
def displayLabelsInGP(self, state):
"""
Choose to show or hide grid labels
@param state: State of the Display Label Checkbox
@type state: boolean
"""
if env.prefs[PlanePM_showGridLabels_prefs_key]:
self.gpOriginComboBox.setEnabled(True)
self.gpPositionComboBox.setEnabled(True)
self.displayLabels = True
self.originLocation = PLANE_ORIGIN_LOWER_LEFT
self.displayLabelStyle = LABELS_ALONG_ORIGIN
else:
self.gpOriginComboBox.setEnabled(False)
self.gpPositionComboBox.setEnabled(False)
self.displayLabels = False
return
def changeColorTypeInGP(self):
"""
Change Color of grid
"""
self.gridColor = self.gpColorTypeComboBox.getColor()
return
def changeLineTypeInGP(self, idx):
"""
Change line type in grid
@param idx: Current index of the Line type combo box
@type idx: int
"""
#line_type for actually drawing the grid is: 0=None, 1=Solid, 2=Dashed" or 3=Dotted
if idx == 0:
self.gridLineType = 3
if idx == 1:
self.gridLineType = 2
if idx == 2:
self.gridLineType = 1
return
def changeYSpacingInGP(self, val):
"""
Change Y spacing on the grid
@param val:value of Y spacing
@type val: double
"""
self.gridYSpacing = float(val)
return
def changeXSpacingInGP(self, val):
"""
Change X spacing on the grid
@param val:value of X spacing
@type val: double
"""
self.gridXSpacing = float(val)
return
def displayGridPlane(self, state):
"""
Display or hide grid based on the state of the checkbox
@param state: State of the Display Label Checkbox
@type state: boolean
"""
self._showHideGPWidgets()
if self.gridPlaneCheckBox.isChecked():
env.prefs[PlanePM_showGrid_prefs_key] = True
self._makeGridPlane()
else:
env.prefs[PlanePM_showGrid_prefs_key] = False
return
def _makeGridPlane(self):
"""
Show grid on the plane
"""
#get all the grid related values in here
self.gridXSpacing = float(self.gpXSpacingDoubleSpinBox.value())
self.gridYSpacing = float(self.gpYSpacingDoubleSpinBox.value())
#line_type for actually drawing the grid is: 0=None, 1=Solid, 2=Dashed" or 3=Dotted
idx = self.gpLineTypeComboBox.currentIndex()
self.changeLineTypeInGP(idx)
self.gridColor = self.gpColorTypeComboBox.getColor()
return
def _showHideGPWidgets(self):
"""
Enable Disable grid related widgets based on the state of the show grid
checkbox.
"""
if self.gridPlaneCheckBox.isChecked():
self.gpXSpacingDoubleSpinBox.setEnabled(True)
self.gpYSpacingDoubleSpinBox.setEnabled(True)
self.gpLineTypeComboBox.setEnabled(True)
self.gpColorTypeComboBox.setEnabled(True)
self.gpDisplayLabels.setEnabled(True)
else:
self.gpXSpacingDoubleSpinBox.setEnabled(False)
self.gpXSpacingDoubleSpinBox.setEnabled(False)
self.gpYSpacingDoubleSpinBox.setEnabled(False)
self.gpLineTypeComboBox.setEnabled(False)
self.gpColorTypeComboBox.setEnabled(False)
self.gpDisplayLabels.setEnabled(False)
return
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in the image group box.
@param pmGroupBox: The image group box in the PM.
@type pmGroupBox: L{PM_GroupBox}
"""
self.imageDisplayCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Display image",
widgetColumn = 0,
state = Qt.Unchecked,
setAsDefault = True,
spanWidth = True
)
self.imageDisplayFileChooser = \
PM_FileChooser(pmGroupBox,
label = 'Image file:',
text = '' ,
spanWidth = True,
filter = "PNG (*.png);;"\
"All Files (*.*)"
)
self.imageDisplayFileChooser.setEnabled(False)
# add change image properties button
BUTTON_LIST = [
( "QToolButton", 1, "+90",
"ui/actions/Properties Manager/RotateImage+90.png",
"+90", "", 0),
( "QToolButton", 2, "-90",
"ui/actions/Properties Manager/RotateImage-90.png",
"-90", "", 1),
( "QToolButton", 3, "FLIP",
"ui/actions/Properties Manager/FlipImageVertical.png",
"Flip", "", 2),
( "QToolButton", 4, "MIRROR",
"ui/actions/Properties Manager/FlipImageHorizontal.png",
"Mirror", "", 3)
]
#image change button groupbox
self.pmGroupBox2 = PM_GroupBox(pmGroupBox, title = "Modify Image")
self.imageChangeButtonGroup = \
PM_ToolButtonRow( self.pmGroupBox2,
title = "",
buttonList = BUTTON_LIST,
spanWidth = True,
isAutoRaise = False,
isCheckable = False,
setAsDefault = True,
)
self.imageChangeButtonGroup.buttonGroup.setExclusive(False)
self.plusNinetyButton = self.imageChangeButtonGroup.getButtonById(1)
self.minusNinetyButton = self.imageChangeButtonGroup.getButtonById(2)
self.flipButton = self.imageChangeButtonGroup.getButtonById(3)
self.mirrorButton = self.imageChangeButtonGroup.getButtonById(4)
# buttons enabled when a valid image is loaded
self.mirrorButton.setEnabled(False)
self.plusNinetyButton.setEnabled(False)
self.minusNinetyButton.setEnabled(False)
self.flipButton.setEnabled(False)
self.heightfieldDisplayCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Create 3D relief",
widgetColumn = 0,
state = Qt.Unchecked,
setAsDefault = True,
spanWidth = True
)
self.heightfieldHQDisplayCheckBox = \
PM_CheckBox( pmGroupBox,
text = "High quality",
widgetColumn = 0,
state = Qt.Unchecked,
setAsDefault = True,
spanWidth = True
)
self.heightfieldTextureCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Use texture",
widgetColumn = 0,
state = Qt.Checked,
setAsDefault = True,
spanWidth = True
)
self.vScaleSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
label = " Vertical scale:",
value = 1.0,
setAsDefault = True,
minimum = -1000.0, # -1000 A
maximum = 1000.0, # 1000 A
singleStep = 0.1,
decimals = 1,
suffix = ' Angstroms')
self.heightfieldDisplayCheckBox.setEnabled(False)
self.heightfieldHQDisplayCheckBox.setEnabled(False)
self.heightfieldTextureCheckBox.setEnabled(False)
self.vScaleSpinBox.setEnabled(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.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 _addWhatsThisText(self):
"""
What's This text for some of the widgets in this Property Manager.
@note: Many PM widgets are still missing their "What's This" text.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_PlanePropertyManager
whatsThis_PlanePropertyManager(self)
def toggleFileChooserBehavior(self, checked):
"""
Enables FileChooser and displays image when checkbox is checked otherwise
not
"""
self.imageDisplayFileChooser.lineEdit.emit(SIGNAL("editingFinished()"))
if checked == Qt.Checked:
self.imageDisplayFileChooser.setEnabled(True)
elif checked == Qt.Unchecked:
self.imageDisplayFileChooser.setEnabled(False)
# if an image is already displayed, that's need to be hidden as well
else:
pass
self.command.struct.glpane.gl_update()
def toggleHeightfield(self, checked):
"""
Enables 3D relief drawing mode.
"""
if self.command and self.command.struct:
plane = self.command.struct
plane.display_heightfield = checked
if checked:
self.heightfieldHQDisplayCheckBox.setEnabled(True)
self.heightfieldTextureCheckBox.setEnabled(True)
self.vScaleSpinBox.setEnabled(True)
plane.computeHeightfield()
else:
self.heightfieldHQDisplayCheckBox.setEnabled(False)
self.heightfieldTextureCheckBox.setEnabled(False)
self.vScaleSpinBox.setEnabled(False)
plane.heightfield = None
plane.glpane.gl_update()
def toggleHeightfieldHQ(self, checked):
"""
Enables high quality rendering in 3D relief mode.
"""
if self.command and self.command.struct:
plane = self.command.struct
plane.heightfield_hq = checked
plane.computeHeightfield()
plane.glpane.gl_update()
def toggleTexture(self, checked):
"""
Enables texturing in 3D relief mode.
"""
if self.command and self.command.struct:
plane = self.command.struct
plane.heightfield_use_texture = checked
# It is not necessary to re-compute the heightfield coordinates
# at this point, they are re-computed whenever the "3D relief image"
# checkbox is set.
plane.glpane.gl_update()
def update_spinboxes(self):
"""
Update the width and height spinboxes.
@see: Plane.resizeGeometry()
This typically gets called when the plane is resized from the
3D workspace (which marks assy as modified) .So, update the spinboxes
that represent the Plane's width and height, but do no emit 'valueChanged'
signal when the spinbox value changes.
@see: Plane.resizeGeometry()
@see: self._update_UI_do_updates()
@see: Plane_EditCommand.command_update_internal_state()
"""
# blockSignals = True make sure that spinbox.valueChanged()
# signal is not emitted after calling spinbox.setValue(). This is done
#because the spinbox valu changes as a result of resizing the plane
#from the 3D workspace.
if self.command.hasValidStructure():
self.heightDblSpinBox.setValue(self.command.struct.height,
blockSignals = True)
self.widthDblSpinBox.setValue(self.command.struct.width,
blockSignals = True)
def update_imageFile(self):
"""
Loads image file if path is valid
"""
# Update buttons and checkboxes.
self.mirrorButton.setEnabled(False)
self.plusNinetyButton.setEnabled(False)
self.minusNinetyButton.setEnabled(False)
self.flipButton.setEnabled(False)
self.heightfieldDisplayCheckBox.setEnabled(False)
self.heightfieldHQDisplayCheckBox.setEnabled(False)
self.heightfieldTextureCheckBox.setEnabled(False)
self.vScaleSpinBox.setEnabled(False)
plane = self.command.struct
# Delete current image and heightfield
plane.deleteImage()
plane.heightfield = None
plane.display_image = self.imageDisplayCheckBox.isChecked()
if plane.display_image:
imageFile = str(self.imageDisplayFileChooser.lineEdit.text())
from model.Plane import checkIfValidImagePath
validPath = checkIfValidImagePath(imageFile)
if validPath:
from PIL import Image
# Load image from file
plane.image = Image.open(imageFile)
plane.loadImage(imageFile)
# Compute the relief image
plane.computeHeightfield()
if plane.image:
self.mirrorButton.setEnabled(True)
self.plusNinetyButton.setEnabled(True)
self.minusNinetyButton.setEnabled(True)
self.flipButton.setEnabled(True)
self.heightfieldDisplayCheckBox.setEnabled(True)
if plane.display_heightfield:
self.heightfieldHQDisplayCheckBox.setEnabled(True)
self.heightfieldTextureCheckBox.setEnabled(True)
self.vScaleSpinBox.setEnabled(True)
def show(self):
"""
Show the Plane Property Manager.
"""
EditCommand_PM.show(self)
#It turns out that if updateCosmeticProps is called before
#EditCommand_PM.show, the 'preview' properties are not updated
#when you are editing an existing plane. Don't know the cause at this
#time, issue is trivial. So calling it in the end -- Ninad 2007-10-03
if self.command.struct:
plane = self.command.struct
plane.updateCosmeticProps(previewing = True)
if plane.imagePath:
self.imageDisplayFileChooser.setText(plane.imagePath)
self.imageDisplayCheckBox.setChecked(plane.display_image)
#Make sure that the plane placement option is always set to
#'Custom' when the Plane PM is shown. This makes sure that bugs like
#2949 won't occur. Let the user change the plane placement option
#explicitely
button = self.pmPlacementOptions.getButtonById(3)
button.setChecked(True)
def setParameters(self, params):
"""
"""
width, height, gridColor, gridLineType, \
gridXSpacing, gridYSpacing, originLocation, \
displayLabelStyle = params
# blockSignals = True flag makes sure that the
# spinbox.valueChanged()
# signal is not emitted after calling spinbox.setValue().
self.widthDblSpinBox.setValue(width, blockSignals = True)
self.heightDblSpinBox.setValue(height, blockSignals = True)
self.win.glpane.gl_update()
self.gpColorTypeComboBox.setColor(gridColor)
self.gridLineType = gridLineType
self.gpXSpacingDoubleSpinBox.setValue(gridXSpacing)
self.gpYSpacingDoubleSpinBox.setValue(gridYSpacing)
self.gpOriginComboBox.setCurrentIndex(originLocation)
self.gpPositionComboBox.setCurrentIndex(displayLabelStyle)
def getCurrrentDisplayParams(self):
"""
Returns a tuple containing current display parameters such as current
image path and grid display params.
@see: Plane_EditCommand.command_update_internal_state() which uses this
to decide whether to modify the structure (e.g. because of change in the
image path or display parameters.)
"""
imagePath = self.imageDisplayFileChooser.text
gridColor = self.gpColorTypeComboBox.getColor()
return (imagePath, gridColor, self.gridLineType,
self.gridXSpacing, self.gridYSpacing,
self.originLocation, self.displayLabelStyle)
def getParameters(self):
"""
"""
width = self.widthDblSpinBox.value()
height = self.heightDblSpinBox.value()
gridColor = self.gpColorTypeComboBox.getColor()
params = (width, height, gridColor, self.gridLineType,
self.gridXSpacing, self.gridYSpacing, self.originLocation,
self.displayLabelStyle)
return params
def change_plane_width(self, newWidth):
"""
Slot for width spinbox in the Property Manager.
@param newWidth: width in Angstroms.
@type newWidth: float
"""
if self.aspectRatioCheckBox.isChecked():
self.command.struct.width = newWidth
self.command.struct.height = self.command.struct.width / \
self.aspectRatioSpinBox.value()
self.update_spinboxes()
else:
self.change_plane_size()
self._updateAspectRatio()
def change_plane_height(self, newHeight):
"""
Slot for height spinbox in the Property Manager.
@param newHeight: height in Angstroms.
@type newHeight: float
"""
if self.aspectRatioCheckBox.isChecked():
self.command.struct.height = newHeight
self.command.struct.width = self.command.struct.height * \
self.aspectRatioSpinBox.value()
self.update_spinboxes()
else:
self.change_plane_size()
self._updateAspectRatio()
def change_plane_size(self, gl_update = True):
"""
Slot to change the Plane's width and height.
@param gl_update: Forces an update of the glpane.
@type gl_update: bool
"""
self.command.struct.width = self.widthDblSpinBox.value()
self.command.struct.height = self.heightDblSpinBox.value()
if gl_update:
self.command.struct.glpane.gl_update()
def change_vertical_scale(self, scale):
"""
Changes vertical scaling of the heightfield.
"""
if self.command and self.command.struct:
plane = self.command.struct
plane.heightfield_scale = scale
plane.computeHeightfield()
plane.glpane.gl_update()
def changePlanePlacement(self, buttonId):
"""
Slot to change the placement of the plane depending upon the
option checked in the "Placement Options" group box of the PM.
@param buttonId: The button id of the selected radio button (option).
@type buttonId: int
"""
if buttonId == 0:
msg = "Create a Plane parallel to the screen. "\
"With <b>Parallel to Screen</b> plane placement option, the "\
"center of the plane is always (0,0,0)"
self.updateMessage(msg)
self.command.placePlaneParallelToScreen()
elif buttonId == 1:
msg = "Create a Plane with center coinciding with the common center "\
"of <b> 3 or more selected atoms </b>. If exactly 3 atoms are "\
"selected, the Plane will pass through those atoms."
self.updateMessage(msg)
self.command.placePlaneThroughAtoms()
if self.command.logMessage:
env.history.message(self.command.logMessage)
elif buttonId == 2:
msg = "Create a Plane at an <b>offset</b> to the selected plane "\
"indicated by the direction arrow. "\
"you can click on the direction arrow to reverse its direction."
self.updateMessage(msg)
self.command.placePlaneOffsetToAnother()
if self.command.logMessage:
env.history.message(self.command.logMessage)
elif buttonId == 3:
#'Custom' plane placement. Do nothing (only update message box)
# Fixes bug 2439
msg = "Create a plane with a <b>Custom</b> plane placement. "\
"The plane is placed parallel to the screen, with "\
"center at (0, 0, 0). User can then modify the plane placement."
self.updateMessage(msg)
def _enableAspectRatioSpinBox(self, enable):
"""
Slot for "Maintain Aspect Ratio" checkbox which enables or disables
the Aspect Ratio spin box.
@param enable: True = enable, False = disable.
@type enable: bool
"""
self.aspectRatioSpinBox.setEnabled(enable)
def _updateAspectRatio(self):
"""
Updates the Aspect Ratio spin box based on the current width and height.
"""
aspectRatio = self.command.struct.width / self.command.struct.height
self.aspectRatioSpinBox.setValue(aspectRatio)
def _update_UI_do_updates(self):
"""
Overrides superclass method.
@see: Command_PropertyManager._update_UI_do_updates() for documentation.
@see: Plane.resizeGeometry()
@see: self.update_spinboxes()
@see: Plane_EditCommand.command_update_internal_state()
"""
#This typically gets called when the plane is resized from the
#3D workspace (which marks assy as modified) . So, update the spinboxes
#that represent the Plane's width and height.
self.update_spinboxes()
def update_props_if_needed_before_closing(self):
"""
This updates some cosmetic properties of the Plane (e.g. fill color,
border color, etc.) before closing the Property Manager.
"""
# Example: The Plane Property Manager is open and the user is
# 'previewing' the plane. Now the user clicks on "Build > Atoms"
# to invoke the next command (without clicking "Done").
# This calls openPropertyManager() which replaces the current PM
# with the Build Atoms PM. Thus, it creates and inserts the Plane
# that was being previewed. Before the plane is permanently inserted
# into the part, it needs to change some of its cosmetic properties
# (e.g. fill color, border color, etc.) which distinguishes it as
# a new plane in the part. This function changes those properties.
# ninad 2007-06-13
#called in updatePropertyManager in MWsemeantics.py --(Partwindow class)
EditCommand_PM.update_props_if_needed_before_closing(self)
#Don't draw the direction arrow when the object is finalized.
if self.command.struct and \
self.command.struct.offsetParentGeometry:
dirArrow = self.command.struct.offsetParentGeometry.directionArrow
dirArrow.setDrawRequested(False)
def updateMessage(self, msg = ''):
"""
Updates the message box with an informative message
@param message: Message to be displayed in the Message groupbox of
the property manager
@type message: string
"""
self.MessageGroupBox.insertHtmlMessage(msg,
setAsDefault = False,
minLines = 5)
def rotate_90(self):
"""
Rotate the image clockwise.
"""
if self.command.hasValidStructure():
self.command.struct.rotateImage(0)
return
def rotate_neg_90(self):
"""
Rotate the image counterclockwise.
"""
if self.command.hasValidStructure():
self.command.struct.rotateImage(1)
return
def flip_image(self):
"""
Flip the image horizontally.
"""
if self.command.hasValidStructure():
self.command.struct.mirrorImage(1)
return
def mirror_image(self):
"""
Flip the image vertically.
"""
if self.command.hasValidStructure():
self.command.struct.mirrorImage(0)
return
class BackrubProteinSim_PropertyManager(Command_PropertyManager):
"""
The BackrubProteinSim_PropertyManager class provides a Property Manager
for the B{Fixed backbone Protein Sequence Design} command on the flyout toolbar in the
Build > Protein > Simulate 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 = "Backrub Motion"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildProtein/Backrub.png"
def __init__(self, command):
"""
Constructor for the property manager.
"""
_superclass.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
msg = "Choose various parameters from below to design an optimized" \
" protein sequence with Rosetta with backrub motion allowed."
self.updateMessage(msg)
def connect_or_disconnect_signals(self, isConnect=True):
"""
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.ex1Checkbox, SIGNAL("stateChanged(int)"),
self.update_ex1)
change_connect(self.ex1aroCheckbox, SIGNAL("stateChanged(int)"),
self.update_ex1aro)
change_connect(self.ex2Checkbox, SIGNAL("stateChanged(int)"),
self.update_ex2)
change_connect(self.ex2aroOnlyCheckbox, SIGNAL("stateChanged(int)"),
self.update_ex2aro_only)
change_connect(self.ex3Checkbox, SIGNAL("stateChanged(int)"),
self.update_ex3)
change_connect(self.ex4Checkbox, SIGNAL("stateChanged(int)"),
self.update_ex4)
change_connect(self.rotOptCheckbox, SIGNAL("stateChanged(int)"),
self.update_rot_opt)
change_connect(self.tryBothHisTautomersCheckbox,
SIGNAL("stateChanged(int)"),
self.update_try_both_his_tautomers)
change_connect(self.softRepDesignCheckbox, SIGNAL("stateChanged(int)"),
self.update_soft_rep_design)
change_connect(self.useElecRepCheckbox, SIGNAL("stateChanged(int)"),
self.update_use_elec_rep)
change_connect(self.norepackDisulfCheckbox,
SIGNAL("stateChanged(int)"),
self.update_norepack_disulf)
#signal slot connections for the push buttons
change_connect(self.okButton, SIGNAL("clicked()"),
self.runRosettaBackrubSim)
return
#Protein Display methods
def show(self):
"""
Shows the Property Manager. Exends superclass method.
"""
self.sequenceEditor = self.win.createProteinSequenceEditorIfNeeded()
self.sequenceEditor.hide()
#update the min and max residues spinbox max values based on the length
#of the current protein
numResidues = self._getNumResiduesForCurrentProtein()
if numResidues == 0:
self.minresSpinBox.setMaximum(numResidues + 2)
self.maxresSpinBox.setMaximum(numResidues + 2)
else:
self.minresSpinBox.setMaximum(numResidues)
self.maxresSpinBox.setMaximum(numResidues)
_superclass.show(self)
return
def _addGroupBoxes(self):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox2 = PM_GroupBox(self,
title="Backrub Specific Parameters")
self._loadGroupBox2(self._pmGroupBox2)
self._pmGroupBox1 = PM_GroupBox(
self, title="Rosetta Sequence Design Parameters")
self._loadGroupBox1(self._pmGroupBox1)
return
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 _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 _getNumResiduesForCurrentProtein(self):
"""
Get number of residues for the current protein
"""
_current_protein = self.win.assy.getSelectedProteinChunk()
if _current_protein:
return len(_current_protein.protein.get_sequence_string())
return 0
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.numSimSpinBox = PM_SpinBox(pmGroupBox,
labelColumn=0,
label="Number of trials:",
minimum=1000,
maximum=1000000,
singleStep=1000,
setAsDefault=False,
spanWidth=False)
self.ex1Checkbox = PM_CheckBox(
pmGroupBox,
text="Expand rotamer library for chi1 angle",
state=Qt.Unchecked,
setAsDefault=False,
widgetColumn=0,
spanWidth=True)
self.ex1aroCheckbox = PM_CheckBox(
pmGroupBox,
text="Use large chi1 library for aromatic residues",
state=Qt.Unchecked,
setAsDefault=False,
widgetColumn=0,
spanWidth=True)
self.ex2Checkbox = PM_CheckBox(
pmGroupBox,
text="Expand rotamer library for chi2 angle",
state=Qt.Unchecked,
setAsDefault=False,
widgetColumn=0,
spanWidth=True)
self.ex2aroOnlyCheckbox = PM_CheckBox(
pmGroupBox,
text="Use large chi2 library only for aromatic residues",
state=Qt.Unchecked,
setAsDefault=False,
widgetColumn=0,
spanWidth=True)
self.ex3Checkbox = PM_CheckBox(
pmGroupBox,
text="Expand rotamer library for chi3 angle",
state=Qt.Unchecked,
setAsDefault=False,
widgetColumn=0,
spanWidth=True)
self.ex4Checkbox = PM_CheckBox(
pmGroupBox,
text="Expand rotamer library for chi4 angle",
state=Qt.Unchecked,
setAsDefault=False,
widgetColumn=0,
spanWidth=True)
self.rotOptCheckbox = PM_CheckBox(pmGroupBox,
text="Optimize one-body energy",
state=Qt.Unchecked,
setAsDefault=False,
widgetColumn=0,
spanWidth=True)
self.tryBothHisTautomersCheckbox = PM_CheckBox(
pmGroupBox,
text="Try both histidine tautomers",
state=Qt.Unchecked,
setAsDefault=False,
widgetColumn=0,
spanWidth=True)
self.softRepDesignCheckbox = PM_CheckBox(
pmGroupBox,
text="Use softer Lennard-Jones repulsive term",
state=Qt.Unchecked,
setAsDefault=False,
widgetColumn=0,
spanWidth=True)
self.useElecRepCheckbox = PM_CheckBox(
pmGroupBox,
text="Use electrostatic repulsion",
state=Qt.Unchecked,
setAsDefault=False,
widgetColumn=0,
spanWidth=True)
self.norepackDisulfCheckbox = PM_CheckBox(
pmGroupBox,
text="Don't re-pack disulphide bonds",
state=Qt.Unchecked,
setAsDefault=False,
widgetColumn=0,
spanWidth=True)
self.otherCommandLineOptions = PM_TextEdit(
pmGroupBox, label="Command line options:", spanWidth=True)
self.otherCommandLineOptions.setFixedHeight(80)
self.okButton = PM_PushButton(pmGroupBox,
text="Run Rosetta",
setAsDefault=True,
spanWidth=True)
return
def update_ex1(self, state):
"""
Update the command text edit depending on the state of the update_ex1
checkbox
@param state:state of the update_ex1 checkbox
@type state: int
"""
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
if self.ex1Checkbox.isChecked() == True:
otherOptionsText = otherOptionsText + ' -ex1 '
else:
otherOptionsText = otherOptionsText.replace(' -ex1 ', '')
self.otherCommandLineOptions.setText(otherOptionsText)
return
def update_ex1aro(self, state):
"""
Update the command text edit depending on the state of the update_ex1aro
checkbox
@param state:state of the update_ex1aro checkbox
@type state: int
"""
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
if self.ex1aroCheckbox.isChecked() == True:
otherOptionsText = otherOptionsText + ' -ex1aro '
else:
otherOptionsText = otherOptionsText.replace(' -ex1aro ', '')
self.otherCommandLineOptions.setText(otherOptionsText)
return
def update_ex2(self, state):
"""
Update the command text edit depending on the state of the update_ex2
checkbox
@param state:state of the update_ex2 checkbox
@type state: int
"""
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
if self.ex2Checkbox.isChecked() == True:
otherOptionsText = otherOptionsText + ' -ex2 '
else:
otherOptionsText = otherOptionsText.replace(' -ex2 ', '')
self.otherCommandLineOptions.setText(otherOptionsText)
return
def update_ex2aro_only(self, state):
"""
Update the command text edit depending on the state of the update_ex2aro_only
checkbox
@param state:state of the update_ex2aro_only checkbox
@type state: int
"""
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
if self.ex2aroOnlyCheckbox.isChecked() == True:
otherOptionsText = otherOptionsText + ' -ex2aro_only '
else:
otherOptionsText = otherOptionsText.replace(' -ex2aro_only ', '')
self.otherCommandLineOptions.setText(otherOptionsText)
return
def update_ex3(self, state):
"""
Update the command text edit depending on the state of the update_ex3
checkbox
@param state:state of the update_ex3 checkbox
@type state: int
"""
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
if self.ex3Checkbox.isChecked() == True:
otherOptionsText = otherOptionsText + ' -ex3 '
else:
otherOptionsText = otherOptionsText.replace(' -ex3 ', '')
self.otherCommandLineOptions.setText(otherOptionsText)
return
def update_ex4(self, state):
"""
Update the command text edit depending on the state of the update_ex4
checkbox
@param state:state of the update_ex4 checkbox
@type state: int
"""
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
if self.ex4Checkbox.isChecked() == True:
otherOptionsText = otherOptionsText + ' -ex4 '
else:
otherOptionsText = otherOptionsText.replace(' -ex4 ', '')
self.otherCommandLineOptions.setText(otherOptionsText)
return
def update_rot_opt(self, state):
"""
Update the command text edit depending on the state of the update_rot_opt
checkbox
@param state:state of the update_rot_opt checkbox
@type state: int
"""
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
if self.rotOptCheckbox.isChecked() == True:
otherOptionsText = otherOptionsText + ' -rot_opt '
else:
otherOptionsText = otherOptionsText.replace(' -rot_opt ', '')
self.otherCommandLineOptions.setText(otherOptionsText)
return
def update_try_both_his_tautomers(self, state):
"""
Update the command text edit depending on the state of the update_try_both_his_tautomers
checkbox
@param state:state of the update_try_both_his_tautomers checkbox
@type state: int
"""
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
if self.tryBothHisTautomersCheckbox.isChecked() == True:
otherOptionsText = otherOptionsText + ' -try_both_his_tautomers '
else:
otherOptionsText = otherOptionsText.replace(
' -try_both_his_tautomers ', '')
self.otherCommandLineOptions.setText(otherOptionsText)
return
def update_soft_rep_design(self, state):
"""
Update the command text edit depending on the state of the update_soft_rep_design
checkbox
@param state:state of the update_soft_rep_design checkbox
@type state: int
"""
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
if self.softRepDesignCheckbox.isChecked() == True:
otherOptionsText = otherOptionsText + ' -soft_rep_design '
else:
otherOptionsText = otherOptionsText.replace(
' -soft_rep_design ', '')
self.otherCommandLineOptions.setText(otherOptionsText)
return
def update_use_elec_rep(self, state):
"""
Update the command text edit depending on the state of the update_use_elec_rep
checkbox
@param state:state of the update_use_elec_rep checkbox
@type state: int
"""
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
if self.useElecRepCheckbox.isChecked() == True:
otherOptionsText = otherOptionsText + ' -use_electrostatic_repulsion '
else:
otherOptionsText = otherOptionsText.replace(
' -use_electrostatic_repulsion ', '')
self.otherCommandLineOptions.setText(otherOptionsText)
return
def update_norepack_disulf(self, state):
"""
Update the command text edit depending on the state of the update_no_repack
checkbox
@param state:state of the update_no_repack checkbox
@type state: int
"""
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
if self.norepackDisulfCheckbox.isChecked() == True:
otherOptionsText = otherOptionsText + ' -norepack_disulf '
else:
otherOptionsText = otherOptionsText.replace(
' -norepack_disulf ', '')
self.otherCommandLineOptions.setText(otherOptionsText)
return
def runRosettaBackrubSim(self):
"""
Get all the parameters from the PM and run a rosetta simulation
"""
proteinChunk = self.win.assy.getSelectedProteinChunk()
if not proteinChunk:
msg = "You must select a single protein to run a Rosetta <i>Backrub</i> simulation."
self.updateMessage(msg)
return
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
numSim = self.numSimSpinBox.value()
argList = [numSim, otherOptionsText, proteinChunk.name]
backrubSpecificArgList = self.getBackrubSpecificArgumentList()
from simulation.ROSETTA.rosetta_commandruns import rosettaSetup_CommandRun
if argList[0] > 0:
env.prefs[rosetta_backrub_enabled_prefs_key] = True
cmdrun = rosettaSetup_CommandRun(
self.win, argList, "BACKRUB_PROTEIN_SEQUENCE_DESIGN",
backrubSpecificArgList)
cmdrun.run()
return
def getBackrubSpecificArgumentList(self):
"""
get list of backrub specific parameters from PM
"""
listOfArgs = []
bond_angle_weight = str(self.bondAngleWeightSimSpinBox.value())
listOfArgs.append('-bond_angle_weight')
listOfArgs.append(bond_angle_weight)
if self.bondAngleParamComboBox.currentIndex() == 0:
bond_angle_params = 'bond_angle_amber_rosetta'
else:
bond_angle_params = 'bond_angle_charmm_rosetta'
listOfArgs.append('-bond_angle_params')
listOfArgs.append(bond_angle_params)
only_bb = str(self.onlybbSpinBox.value())
listOfArgs.append('-only_bb')
listOfArgs.append(only_bb)
only_rot = str(self.onlyrotSpinBox.value())
listOfArgs.append('-only_rot')
listOfArgs.append(only_rot)
mc_temp = str(self.mctempSpinBox.value())
listOfArgs.append('-mc_temp')
listOfArgs.append(mc_temp)
min_res = self.minresSpinBox.value()
max_res = self.maxresSpinBox.value()
if max_res < min_res:
msg = redmsg("Maximum number of residues for rosetta simulation with backrub" \
" motion cannot be less than minimum number of residues."\
" Neglecting this parameter for this simulation.")
env.history.message("BACKRUB SIMULATION: " + msg)
else:
listOfArgs.append('-min_res')
listOfArgs.append(str(min_res))
listOfArgs.append('-max_res')
listOfArgs.append(str(max_res))
return listOfArgs
class DnaGeneratorPropertyManager( PM_Dialog, DebugMenuMixin ):
"""
The DnaGeneratorPropertyManager class provides a Property Manager
for the "Build > Atoms" command.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
@ivar validSymbols: Miscellaneous symbols that may appear in the sequence
(but are ignored). The hyphen '-' is a special case
that must be dealt with individually; it is not
included because it can confuse regular expressions.
@type validSymbols: QString
"""
title = "DNA"
pmName = title
iconPath = "ui/actions/Tools/Build Structures/DNA.png"
validSymbols = QString(' <>~!@#%&_+`=$*()[]{}|^\'"\\.;:,/?')
# The following class variables guarantee the UI's menu items
# are synchronized with their action code. The arrays should
# not be changed, unless an item is removed or inserted.
# Changes should be made via only the _action... variables.
# e.g., Change _action_Complement from "Complement"
# to "Complement Sequences". The menu item will
# change and its related code will need no update.
_action_Complement = "Complement"
_action_Reverse = "Reverse"
_action_RemoveUnrecognized = 'Remove unrecognized letters'
_action_ConvertUnrecognized = 'Convert unrecognized letters to "N"'
_actionChoices = [ "Action",
"---",
_action_Complement,
_action_Reverse,
_action_RemoveUnrecognized,
_action_ConvertUnrecognized ]
_modeltype_PAM3 = "PAM3"
_modeltype_PAM5 = "PAM5"
_modeltype_Atomistic = "Atomistic" # deprecated
_modelChoices = [ _modeltype_PAM3,
_modeltype_PAM5 ]
def __init__( self ):
"""
Constructor for the DNA Generator property manager.
"""
PM_Dialog.__init__( self, self.pmName, self.iconPath, self.title )
DebugMenuMixin._init1( self )
msg = "Edit the DNA parameters and select <b>Preview</b> to \
preview the structure. Click <b>Done</b> to insert it into \
the model."
# This causes the "Message" box to be displayed as well.
# setAsDefault=True causes this message to be reset whenever
# this PM is (re)displayed via show(). Mark 2007-06-01.
self.MessageGroupBox.insertHtmlMessage( msg, setAsDefault = True )
def _addGroupBoxes( self ):
"""
Add the DNA Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self, title = "Strand Sequence" )
self._loadGroupBox1( self._pmGroupBox1 )
self._pmGroupBox2 = PM_GroupBox( self, title = "DNA Parameters" )
self._loadGroupBox2( self._pmGroupBox2 )
self._pmGroupBox3 = PM_GroupBox( self, title = "Endpoints" )
self._loadGroupBox3( self._pmGroupBox3 )
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.
"""
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 _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 _addWhatsThisText( self ):
"""
What's This text for some of the widgets in the
DNA Property Manager.
@note: Many PM widgets are still missing their "What's This" text.
"""
self.conformationComboBox.setWhatsThis("""<b>Conformation</b>
<p>There are three DNA geometries, A-DNA, B-DNA,
and Z-DNA. Only B-DNA and Z-DNA are currently supported.</p>""")
self.sequenceTextEdit.setWhatsThis("""<b>Strand Sequence</b>
<p>Type in the strand sequence you want to generate here (5' => 3')<br>
<br>
Recognized base letters:<br>
<br>
A = Adenosine<br>
C = Cytosine<br>
G = Guanosine<br>
T = Thymidine<br>
N = aNy base<br>
X = Unassigned<br>
<br>
Other base letters currently recognized:<br>
<br>
B = C,G, or T<br>
D = A,G, or T<br>
H = A,C, or T<br>
V = A,C, or G<br>
R = A or G (puRine)<br>
Y = C or T (pYrimidine)<br>
K = G or T (Keto)<br>
M = A or C (aMino)<br>
S = G or C (Strong -3H bonds)<br>
W = A or T (Weak - 2H bonds)<br>
</p>""")
self.actionsComboBox.setWhatsThis("""<b>Action</b>
<p>Select an action to perform on the sequence.</p>""")
def conformationComboBoxChanged( self, inIndex ):
"""
Slot for the Conformation combobox. It is called whenever the
Conformation choice is changed.
@param inIndex: The new index.
@type inIndex: int
"""
self.basesPerTurnComboBox.clear()
conformation = self.conformationComboBox.currentText()
if conformation == "B-DNA":
self.basesPerTurnComboBox.insertItem(0, "10.0")
self.basesPerTurnComboBox.insertItem(1, "10.5")
self.basesPerTurnComboBox.insertItem(2, "10.67")
#10.5 is the default value for Bases per turn.
#So set the current index to 1
self.basesPerTurnComboBox.setCurrentIndex(1)
elif conformation == "Z-DNA":
self.basesPerTurnComboBox.insertItem(0, "12.0")
elif inIndex == -1:
# Caused by clear(). This is tolerable for now. Mark 2007-05-24.
conformation = "B-DNA" # Workaround for "Restore Defaults".
pass
else:
msg = redmsg("conformationComboBoxChanged(): \
Error - unknown DNA conformation. Index = "+ inIndex)
env.history.message(msg)
self.duplexLengthSpinBox.setSingleStep(
self.getDuplexRise(conformation) )
def modelComboBoxChanged( self, inIndex ):
"""
Slot for the Model combobox. It is called whenever the
Model choice is changed.
@param inIndex: The new index.
@type inIndex: int
"""
conformation = self._modelChoices[ inIndex ]
self.disconnect( self.conformationComboBox,
SIGNAL("currentIndexChanged(int)"),
self.conformationComboBoxChanged )
self.conformationComboBox.clear() # Generates signal!
if conformation == self._modeltype_PAM3:
self.conformationComboBox.addItem("B-DNA")
elif conformation == self._modeltype_PAM5:
self.conformationComboBox.addItem("B-DNA")
elif conformation == self._modeltype_Atomistic:
self.conformationComboBox.addItem("B-DNA")
self.conformationComboBox.addItem("Z-DNA")
elif inIndex == -1:
# Caused by clear(). This is tolerable for now. Mark 2007-05-24.
pass
else:
msg = "Error - unknown model representation. Index = " + inIndex
env.history.message(redmsg(msg))
self.connect( self.conformationComboBox,
SIGNAL("currentIndexChanged(int)"),
self.conformationComboBoxChanged)
# GroupBox3 slots (and other methods) supporting the Strand Sequence groupbox.
def getDuplexRise( self, inConformation ):
"""
Return the 'rise' between base pairs of the
specified DNA type (conformation).
@param inConformation: The current conformation.
@type inConformation: int
"""
return dnaDict[str(inConformation)]['DuplexRise']
def synchronizeLengths( self ):
"""
Guarantees the values of the duplex length and strand length
spinboxes agree with the strand sequence (textedit).
"""
self.updateStrandLength()
self.updateDuplexLength()
return
# Added :jbirac 20070613:
def duplexLengthChanged( self, inDuplexLength ):
"""
Slot for the duplex length spinbox, called whenever the value of the
Duplex Length spinbox changes.
@param inDuplexLength: The duplex length.
@type inDuplexLength: float
"""
conformation = self.conformationComboBox.currentText()
duplexRise = self.getDuplexRise( conformation )
newStrandLength = inDuplexLength / duplexRise + 0.5
newStrandLength = int( newStrandLength )
self.strandLengthChanged( newStrandLength )
def updateDuplexLength( self ): # Added :jbirac 20070615:
"""
Update the Duplex Length spinbox; always the length of the
strand sequence multiplied by the 'rise' of the duplex. This
method is called by slots of other controls (i.e., this itself
is not a slot.)
"""
conformation = self.conformationComboBox.currentText()
newDuplexLength = self.getDuplexRise( conformation ) \
* self.getSequenceLength()
self.disconnect( self.duplexLengthSpinBox,
SIGNAL("valueChanged(double)"),
self.duplexLengthChanged)
self.duplexLengthSpinBox.setValue( newDuplexLength )
self.connect( self.duplexLengthSpinBox,
SIGNAL("valueChanged(double)"),
self.duplexLengthChanged)
# Renamed from length_changed :jbirac 20070613:
def strandLengthChanged( self, inStrandLength ):
"""
Slot for the Strand Length spin box, called whenever the value of the
Strand Length spin box changes.
@param inStrandLength: The number of bases in the strand sequence.
@type inStrandLength: int
"""
theSequence = self.getPlainSequence()
sequenceLen = len( theSequence )
lengthChange = inStrandLength - self.getSequenceLength()
# Preserve the cursor's position/selection
cursor = self.sequenceTextEdit.textCursor()
#cursorPosition = cursor.position()
selectionStart = cursor.selectionStart()
selectionEnd = cursor.selectionEnd()
if inStrandLength < 0:
return # Should never happen.
if lengthChange < 0:
# If length is less than the previous length,
# simply truncate the current sequence.
theSequence.chop( -lengthChange )
elif lengthChange > 0:
# If length has increased, add the correct number of base
# letters to the current strand sequence.
numNewBases = lengthChange
# Get current base selected in combobox.
chosenBase = 'X' # Unassigned.
basesToAdd = chosenBase * numNewBases
theSequence.append( basesToAdd )
else:
env.history.message(
orangemsg( "strandLengthChanged(): Length has not changed." ))
self.setSequence( theSequence )
return
# Renamed from updateLength :jbirac 20070613:
def updateStrandLength( self ):
"""
Update the Strand Length spinbox; always the length of the strand
sequence.
"""
self.disconnect( self.strandLengthSpinBox,
SIGNAL("valueChanged(int)"),
self.strandLengthChanged )
self.strandLengthSpinBox.setValue( self.getSequenceLength() )
self.connect( self.strandLengthSpinBox,
SIGNAL("valueChanged(int)"),
self.strandLengthChanged )
return
def sequenceChanged( self ):
"""
Slot for the Strand Sequence textedit widget.
Assumes the sequence changed directly by user's keystroke in the
textedit. Other methods...
"""
cursorPosition = self.getCursorPosition()
theSequence = self.getPlainSequence()
# Disconnect while we edit the sequence.
self.disconnect( self.sequenceTextEdit,
SIGNAL("textChanged()"),
self.sequenceChanged )
# How has the text changed?
if theSequence.length() == 0: # There is no sequence.
self.updateStrandLength()
self.updateDuplexLength()
else:
# Insert the sequence; it will be "stylized" by setSequence().
self.setSequence( theSequence )
# Reconnect to respond when the sequence is changed.
self.connect( self.sequenceTextEdit,
SIGNAL("textChanged()"),
self.sequenceChanged )
self.synchronizeLengths()
return
def getPlainSequence( self, inOmitSymbols = False ):
"""
Returns a plain text QString (without HTML stylization)
of the current sequence. All characters are preserved (unless
specified explicitly), including valid base letters, punctuation
symbols, whitespace and invalid letters.
@param inOmitSymbols: Omits characters listed in self.validSymbols.
@type inOmitSymbols: bool
@return: The current DNA sequence in the PM.
@rtype: QString
"""
outSequence = self.sequenceTextEdit.toPlainText()
if inOmitSymbols:
# This may look like a sloppy piece of code, but Qt's QRegExp
# class makes it pretty tricky to remove all punctuation.
theString = '[<>' \
+ str( QRegExp.escape(self.validSymbols) ) \
+ ']|-'
outSequence.remove(QRegExp( theString ))
return outSequence
def stylizeSequence( self, inSequence ):
"""
Converts a plain text string of a sequence (including optional
symbols) to an HTML rich text string.
@param inSequence: A DNA sequence.
@type inSequence: QString
@return: The sequence.
@rtype: QString
"""
outSequence = str(inSequence)
# Verify that all characters (bases) in the sequence are "valid".
invalidSequence = False
basePosition = 0
sequencePosition = 0
invalidStartTag = "<b><font color=black>"
invalidEndTag = "</b>"
previousChar = chr(1) # Null character; may be revised.
# Some characters must be substituted to preserve
# whitespace and tags in HTML code.
substituteDict = { ' ':' ', '<':'<', '>':'>' }
while basePosition < len(outSequence):
theSeqChar = outSequence[basePosition]
if ( theSeqChar in basesDict
or theSeqChar in self.validSymbols ):
# Close any preceding invalid sequence segment.
if invalidSequence == True:
outSequence = outSequence[:basePosition] \
+ invalidEndTag \
+ outSequence[basePosition:]
basePosition += len(invalidEndTag)
invalidSequence = False
# Color the valid characters.
if theSeqChar != previousChar:
# We only need to insert 'color' tags in places where
# the adjacent characters are different.
if theSeqChar in basesDict:
theTag = '<font color=' \
+ basesDict[ theSeqChar ]['Color'] \
+ '>'
elif not previousChar in self.validSymbols:
# The character is a 'valid' symbol to be greyed
# out. Only one 'color' tag is needed for a
# group of adjacent symbols.
theTag = '<font color=dimgrey>'
else:
theTag = ''
outSequence = outSequence[:basePosition] \
+ theTag + outSequence[basePosition:]
basePosition += len(theTag)
# Any <space> character must be substituted with an
# ASCII code tag because the HTML engine will collapse
# whitespace to a single <space> character; whitespace
# is truncated from the end of HTML by default.
# Also, many symbol characters must be substituted
# because they confuse the HTML syntax.
#if str( outSequence[basePosition] ) in substituteDict:
if outSequence[basePosition] in substituteDict:
#theTag = substituteDict[theSeqChar]
theTag = substituteDict[ outSequence[basePosition] ]
outSequence = outSequence[:basePosition] \
+ theTag \
+ outSequence[basePosition + 1:]
basePosition += len(theTag) - 1
else:
# The sequence character is invalid (but permissible).
# Tags (e.g., <b> and </b>) must be inserted at both the
# beginning and end of a segment of invalid characters.
if invalidSequence == False:
outSequence = outSequence[:basePosition] \
+ invalidStartTag \
+ outSequence[basePosition:]
basePosition += len(invalidStartTag)
invalidSequence = True
basePosition += 1
previousChar = theSeqChar
#basePosition += 1
# Specify that theSequence is definitely HTML format, because
# Qt can get confused between HTML and Plain Text.
outSequence = "<html>" + outSequence
outSequence += "</html>"
return outSequence
def setSequence( self,
inSequence,
inStylize = True,
inRestoreCursor = True ):
"""
Replace the current strand sequence with the new sequence text.
@param inSequence: The new sequence.
@type inSequence: QString
@param inStylize: If True, inSequence will be converted from a plain
text string (including optional symbols) to an HTML
rich text string.
@type inStylize: bool
@param inRestoreCursor: Not implemented yet.
@type inRestoreCursor: bool
@attention: Signals/slots must be managed before calling this method.
The textChanged() signal will be sent to any connected widgets.
"""
cursor = self.sequenceTextEdit.textCursor()
selectionStart = cursor.selectionStart()
selectionEnd = cursor.selectionEnd()
if inStylize:
inSequence = self.stylizeSequence( inSequence )
self.sequenceTextEdit.insertHtml( inSequence )
if inRestoreCursor:
cursor.setPosition( min(selectionStart, self.getSequenceLength()),
QTextCursor.MoveAnchor )
cursor.setPosition( min(selectionEnd, self.getSequenceLength()),
QTextCursor.KeepAnchor )
self.sequenceTextEdit.setTextCursor( cursor )
return
def getSequenceLength( self ):
"""
Returns the number of characters in
the strand sequence textedit widget.
"""
theSequence = self.getPlainSequence( inOmitSymbols = True )
outLength = theSequence.length()
return outLength
def getCursorPosition( self ):
"""
Returns the cursor position in the
strand sequence textedit widget.
"""
cursor = self.sequenceTextEdit.textCursor()
return cursor.position()
def cursorPosChanged( self ):
"""
Slot called when the cursor position changes.
"""
cursor = self.sequenceTextEdit.textCursor()
if 0:
env.history.message( greenmsg( "cursorPosChanged: Selection ("
+ str(cursor.selectionStart())
+ " thru "
+ str(cursor.selectionEnd())+')' ) )
return
def actionsComboBoxChanged( self, inIndex ):
"""
Slot for the Actions combobox. It is called whenever the
Action choice is changed.
@param inIndex: The index of the selected action choice.
@type inIndex: int
"""
if inIndex == 0: # Very important.
return
actionName = str(self.actionsComboBox.currentText())
self.actionsComboBox.setCurrentIndex( 0 ) # Generates signal!
self.invokeAction( actionName )
return
def invokeAction( self, inActionName ):
"""
Applies an action on the current sequence displayed in the PM.
@param inActionName: The action name.
@type inActionName: str
@return: The sequence after the action has been applied.
@rtype: str
"""
sequence, allKnown = self._getSequence()
outResult = ""
if inActionName == self._action_Complement:
outResult = getComplementSequence(sequence)
elif inActionName == self._action_Reverse:
outResult = getReverseSequence(sequence)
elif inActionName == self._action_ConvertUnrecognized:
outResult = replaceUnrecognized(sequence, replaceBase = 'N')
self.setSequence( outResult )
elif inActionName == self._action_RemoveUnrecognized:
outResult = replaceUnrecognized(sequence, replaceBase = '')
self.setSequence( outResult )
return
