def _load5PrimeEndArrowAndCustomColor(self, pmGroupBox):
"""
Loads 5' end custom color checkbox and color chooser dialog
"""
self.pmGroupBox2 = PM_GroupBox(pmGroupBox, title="5' end:")
self.arrowsOnFivePrimeEnds_checkBox = PM_CheckBox(
self.pmGroupBox2, text="Show arrowhead", widgetColumn=0, setAsDefault=True, spanWidth=True
)
prefs_key = self._prefs_key_arrowsOnFivePrimeEnds()
if env.prefs[prefs_key]:
self.arrowsOnFivePrimeEnds_checkBox.setCheckState(Qt.Checked)
else:
self.arrowsOnFivePrimeEnds_checkBox.setCheckState(Qt.Unchecked)
self.strandFivePrimeArrowheadsCustomColorCheckBox = PM_CheckBox(
self.pmGroupBox2, text="Display custom color", widgetColumn=0, setAsDefault=True, spanWidth=True
)
prefs_key = self._prefs_key_dnaStrandFivePrimeArrowheadsCustomColor()
self.fivePrimeEndColorChooser = PM_ColorComboBox(self.pmGroupBox2, color=env.prefs[prefs_key])
prefs_key = self._prefs_key_useCustomColorForFivePrimeArrowheads()
if env.prefs[prefs_key]:
self.strandFivePrimeArrowheadsCustomColorCheckBox.setCheckState(Qt.Checked)
self.fivePrimeEndColorChooser.show()
else:
self.strandFivePrimeArrowheadsCustomColorCheckBox.setCheckState(Qt.Unchecked)
self.fivePrimeEndColorChooser.hide()
return
def _loadGroupBox1(self, pmGroupBox):
"""
load widgets in groupbox1
"""
self._loadSegmentListWidget(pmGroupBox)
self.crossoversBetGivenSegmentsOnly_checkBox = PM_CheckBox(
pmGroupBox,
text="Between above segments only",
widgetColumn=0,
setAsDefault=True,
spanWidth=True,
)
#If this preferece value is True, the search algotithm will search for
#the potential crossover sites only *between* the segments in the
#segment list widget (thus ignoring other segments not in that list)
if env.prefs[
makeCrossoversCommand_crossoverSearch_bet_given_segments_only_prefs_key]:
self.crossoversBetGivenSegmentsOnly_checkBox.setCheckState(
Qt.Checked)
else:
self.crossoversBetGivenSegmentsOnly_checkBox.setCheckState(
Qt.Unchecked)
self.makeCrossoverPushButton = PM_PushButton(
pmGroupBox, label="", text="Make All Crossovers", spanWidth=True)
def _loadPM_CheckBox(self, inPmGroupBox):
"""
PM_CheckBox.
"""
self.checkBoxGroupBox = \
PM_GroupBox( inPmGroupBox,
title = "<b> PM_CheckBox examples</b>" )
self.checkBox1 = \
PM_CheckBox( self.checkBoxGroupBox,
text = "Label on left:",
widgetColumn = 1,
state = Qt.Checked,
setAsDefault = True,
)
self.checkBox2 = \
PM_CheckBox( self.checkBoxGroupBox,
text = ": Label on right",
widgetColumn = 1,
state = Qt.Checked,
setAsDefault = True,
)
self.checkBox3 = \
PM_CheckBox( self.checkBoxGroupBox,
text = "CheckBox (spanWidth = True):",
state = Qt.Unchecked,
setAsDefault = False,
)
def _loadJoinOptionsGroupbox(self, pmGroupBox):
"""
Load widgets in this group box.
"""
self.clickToJoinDnaStrandsCheckBox = \
PM_CheckBox(pmGroupBox ,
text = 'Click on strand to join',
widgetColumn = 0,
spanWidth = True)
connect_checkbox_with_boolean_pref(
self.clickToJoinDnaStrandsCheckBox,
joinStrandsCommand_clickToJoinDnaStrands_prefs_key )
self.recursive_clickToJoinDnaStrandsCheckBox = \
PM_CheckBox(pmGroupBox ,
text = 'Recursively join strands',
widgetColumn = 1,
spanWidth = True)
connect_checkbox_with_boolean_pref(
self.recursive_clickToJoinDnaStrandsCheckBox,
joinStrandsCommand_recursive_clickToJoinDnaStrands_prefs_key)
if not env.prefs[joinStrandsCommand_clickToJoinDnaStrands_prefs_key]:
self.recursive_clickToJoinDnaStrandsCheckBox.setEnabled(False)
def _loadMergeOptionsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Merge Options groupbox (which is a groupbox within
the B{Advanced Options group box}).
@param inPmGroupBox: The Merge Options groupbox
@type inPmGroupBox: L{PM_GroupBox}
@WARNING: This method initializes some instance varaiables for various
checkboxes. (Example: self.mergeCopiesCheckBox.default = False). This
won't be needed once extrudeMode.py is cleaned up.
"""
self.mergeCopiesCheckBox = \
PM_CheckBox(inPmGroupBox,
text = 'Merge copies' ,
widgetColumn = 1,
state = Qt.Unchecked
)
self.mergeCopiesCheckBox.default = False
self.mergeCopiesCheckBox.attr = 'whendone_all_one_part'
self.mergeCopiesCheckBox.repaintQ = False
self.extrudePrefMergeSelection = \
PM_CheckBox(inPmGroupBox,
text = 'Merge selection' ,
widgetColumn = 1,
state = Qt.Unchecked
)
self.extrudePrefMergeSelection.default = False
self.extrudePrefMergeSelection.attr = 'whendone_merge_selection'
self.extrudePrefMergeSelection.repaintQ = False
def _loadDisplayOptionsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Display Options groupbox.
@param inPmGroupBox: The Display Options groupbox
@type inPmGroupBox: L{PM_GroupBox}
"""
displayChoices = ['Tubes', 'Spheres']
self.dispModeComboBox = \
PM_ComboBox( inPmGroupBox,
label = 'Display style:',
choices = displayChoices,
index = 0,
setAsDefault = False,
spanWidth = False )
self.gridLineCheckBox = PM_CheckBox(inPmGroupBox,
text="Show grid lines",
widgetColumn=0,
state=Qt.Checked)
self.fullModelCheckBox = PM_CheckBox(inPmGroupBox,
text="Show model",
widgetColumn=0,
state=Qt.Unchecked)
def _loadDisplayOptionsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Display Options groupbox (which is a groupbox within
the B{Advanced Options group box} ) .
@param inPmGroupBox: The Display Options groupbox
@type inPmGroupBox: L{PM_GroupBox}
@WARNING: This method initializes some instance varaiables for various
checkboxes. (Example: self.mergeCopiesCheckBox.default = False). This
won't be needed once extrudeMode.py is cleaned up.
"""
self.showEntireModelCheckBox = \
PM_CheckBox(inPmGroupBox,
text = 'Show entire model' ,
widgetColumn = 1,
state = Qt.Unchecked
)
self.showEntireModelCheckBox.default = False
self.showEntireModelCheckBox.attr = 'show_entire_model'
self.showEntireModelCheckBox.repaintQ = True
self.showBondOffsetCheckBox = \
PM_CheckBox(inPmGroupBox,
text = 'Show bond-offset spheres' ,
widgetColumn = 1,
state = Qt.Unchecked
)
self.showBondOffsetCheckBox.default = False
self.showBondOffsetCheckBox.attr = 'show_bond_offsets'
self.showBondOffsetCheckBox.repaintQ = True
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.nameLineEdit = PM_LineEdit(pmGroupBox, label="Name:")
self.lengthLineEdit = PM_LineEdit(pmGroupBox, label="Length:")
self.lengthLineEdit.setEnabled(False)
self.currentResidueComboBox = PM_ComboBox(pmGroupBox,
label="Current residue:",
setAsDefault=False)
BUTTON_LIST = [
("QToolButton", 1, "Previous residue",
"ui/actions/Properties Manager/Previous.png", "",
"Previous residue", 0),
("QToolButton", 2, "Next residue",
"ui/actions/Properties Manager/Next.png", "", "Next residue", 1)
]
self.prevNextButtonRow = \
PM_ToolButtonRow( pmGroupBox,
title = "",
buttonList = BUTTON_LIST,
label = 'Previous / Next:',
isAutoRaise = True,
isCheckable = False
)
self.prevButton = self.prevNextButtonRow.getButtonById(1)
self.nextButton = self.prevNextButtonRow.getButtonById(2)
self.recenterViewCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Center view on current residue",
setAsDefault = True,
state = Qt.Unchecked,
widgetColumn = 0,
spanWidth = True)
self.lockEditedCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Lock edited rotamers",
setAsDefault = True,
state = Qt.Checked,
widgetColumn = 0,
spanWidth = True)
self.showAllResiduesCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Show all residues",
setAsDefault = False,
state = Qt.Unchecked,
widgetColumn = 0,
spanWidth = True)
return
def _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 the second group box.
"""
self.headerdata_seq = ['', 'ID', 'Set', 'BR', 'Descriptor']
self.recenterViewCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Re-center view on selected residue",
setAsDefault = True,
widgetColumn = 0,
state = Qt.Unchecked)
self.selectAllPushButton = PM_PushButton(pmGroupBox,
text="All",
setAsDefault=True)
self.selectAllPushButton.setFixedHeight(25)
self.selectNonePushButton = PM_PushButton(pmGroupBox,
text="None",
setAsDefault=True)
self.selectNonePushButton.setFixedHeight(25)
self.selectInvertPushButton = PM_PushButton(pmGroupBox,
text="Invert",
setAsDefault=True)
self.selectInvertPushButton.setFixedHeight(25)
buttonList = [('PM_PushButton', self.selectAllPushButton, 0, 0),
('PM_PushButton', self.selectNonePushButton, 1, 0),
('PM_PushButton', self.selectInvertPushButton, 2, 0)]
self.buttonGrid = PM_WidgetGrid(pmGroupBox, widgetList=buttonList)
self.sequenceTable = PM_TableWidget(pmGroupBox)
#self.sequenceTable.setModel(self.tableModel)
self.sequenceTable.resizeColumnsToContents()
self.sequenceTable.verticalHeader().setVisible(False)
#self.sequenceTable.setRowCount(0)
self.sequenceTable.setColumnCount(5)
self.checkbox = QCheckBox()
self.sequenceTable.setFixedHeight(345)
self.sequenceTable.setGridStyle(Qt.NoPen)
self.sequenceTable.setHorizontalHeaderLabels(self.headerdata_seq)
###self._fillSequenceTable()
self.showSequencePushButton = PM_PushButton(pmGroupBox,
text="Show Sequence",
setAsDefault=True,
spanWidth=True)
def _loadSelectionOptionsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Selection Options group box.
@param inPmGroupBox: The Selection Options box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
self.selectionFilterCheckBox = \
PM_CheckBox( inPmGroupBox,
text = "Enable atom selection filter",
widgetColumn = 0,
state = Qt.Unchecked )
self.selectionFilterCheckBox.setDefaultValue(False)
self.filterlistLE = PM_LineEdit( inPmGroupBox,
label = "",
text = "",
setAsDefault = False,
spanWidth = True )
self.filterlistLE.setReadOnly(True)
if self.selectionFilterCheckBox.isChecked():
self.filterlistLE.setEnabled(True)
else:
self.filterlistLE.setEnabled(False)
self.showSelectedAtomInfoCheckBox = \
PM_CheckBox(
inPmGroupBox,
text = "Show Selected Atom Info",
widgetColumn = 0,
state = Qt.Unchecked)
self.selectedAtomPosGroupBox = \
PM_GroupBox( inPmGroupBox, title = "")
self._loadSelectedAtomPosGroupBox(self.selectedAtomPosGroupBox)
self.toggle_selectedAtomPosGroupBox(show = 0)
self.enable_or_disable_selectedAtomPosGroupBox( bool_enable = False)
self.reshapeSelectionCheckBox = \
PM_CheckBox( inPmGroupBox,
text = 'Dragging reshapes selection',
widgetColumn = 0,
state = Qt.Unchecked )
connect_checkbox_with_boolean_pref( self.reshapeSelectionCheckBox,
reshapeAtomsSelection_prefs_key )
env.prefs[reshapeAtomsSelection_prefs_key] = False
self.waterCheckBox = \
PM_CheckBox( inPmGroupBox,
text = "Z depth filter (water surface)",
widgetColumn = 0,
state = Qt.Unchecked )
def _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 group box.
"""
#stereoSettingsGroupBox = PM_GroupBox( None )
self.stereoEnabledCheckBox = \
PM_CheckBox(pmGroupBox,
text = 'Enable Stereo View',
widgetColumn = 1
)
stereoModeChoices = [
'Relaxed view', 'Cross-eyed view', 'Red/blue anaglyphs',
'Red/cyan anaglyphs', 'Red/green anaglyphs'
]
self.stereoModeComboBox = \
PM_ComboBox( pmGroupBox,
label = "Stereo Mode:",
choices = stereoModeChoices,
setAsDefault = True)
self.stereoModeComboBox.setCurrentIndex(
env.prefs[stereoViewMode_prefs_key] - 1)
self.stereoSeparationSlider = \
PM_Slider( pmGroupBox,
currentValue = 50,
minimum = 0,
maximum = 300,
label = 'Separation'
)
self.stereoSeparationSlider.setValue(
env.prefs[stereoViewSeparation_prefs_key])
self.stereoAngleSlider = \
PM_Slider( pmGroupBox,
currentValue = 50,
minimum = 0,
maximum = 100,
label = 'Angle'
)
self.stereoAngleSlider.setValue(env.prefs[stereoViewAngle_prefs_key])
self._updateWidgets()
def _loadRotateGroupBox(self, inPmGroupBox):
"""
Load widgets in the Rotate group box,
@param inPmGroupBox: The Rotate GroupBox in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
rotateChoices = ["Free Drag", "By Specified Angle"]
self.rotateComboBox = \
PM_ComboBox( inPmGroupBox,
label = '',
choices = rotateChoices,
index = 0,
setAsDefault = False,
spanWidth = True )
self.rotateAsUnitCB = \
PM_CheckBox( inPmGroupBox,
text = 'Rotate as a unit' ,
widgetColumn = 0,
state = Qt.Checked )
self.freeDragRotateGroupBox = PM_GroupBox(inPmGroupBox)
self._loadFreeDragRotateGroupBox(self.freeDragRotateGroupBox)
self.bySpecifiedAngleGroupBox = PM_GroupBox(inPmGroupBox)
self._loadBySpecifiedAngleGroupBox(self.bySpecifiedAngleGroupBox)
self.updateRotateGroupBoxes(0)
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in the second group box.
"""
self.headerdata_seq = ['', 'ID', 'Set', 'BR', 'Descriptor']
self.recenterViewCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Re-center view on selected residue",
setAsDefault = True,
widgetColumn = 0,
state = Qt.Unchecked)
self.selectAllPushButton = PM_PushButton( pmGroupBox,
text = "All",
setAsDefault = True)
self.selectAllPushButton.setFixedHeight(25)
self.selectNonePushButton = PM_PushButton( pmGroupBox,
text = "None",
setAsDefault = True)
self.selectNonePushButton.setFixedHeight(25)
self.selectInvertPushButton = PM_PushButton( pmGroupBox,
text = "Invert",
setAsDefault = True)
self.selectInvertPushButton.setFixedHeight(25)
buttonList = [ ('PM_PushButton', self.selectAllPushButton, 0, 0),
('PM_PushButton', self.selectNonePushButton, 1, 0),
('PM_PushButton', self.selectInvertPushButton, 2, 0)]
self.buttonGrid = PM_WidgetGrid( pmGroupBox,
widgetList = buttonList)
self.sequenceTable = PM_TableWidget( pmGroupBox)
#self.sequenceTable.setModel(self.tableModel)
self.sequenceTable.resizeColumnsToContents()
self.sequenceTable.verticalHeader().setVisible(False)
#self.sequenceTable.setRowCount(0)
self.sequenceTable.setColumnCount(5)
self.checkbox = QCheckBox()
self.sequenceTable.setFixedHeight(345)
self.sequenceTable.setGridStyle(Qt.NoPen)
self.sequenceTable.setHorizontalHeaderLabels(self.headerdata_seq)
###self._fillSequenceTable()
self.showSequencePushButton = PM_PushButton( pmGroupBox,
text = "Show Sequence",
setAsDefault = True,
spanWidth = True)
def _loadJoinOptionsGroupbox(self, pmGroupBox):
"""
Load widgets in this group box.
"""
self.clickToJoinDnaStrandsCheckBox = \
PM_CheckBox(pmGroupBox ,
text = 'Click on strand to join',
widgetColumn = 0,
spanWidth = True)
connect_checkbox_with_boolean_pref(
self.clickToJoinDnaStrandsCheckBox,
joinStrandsCommand_clickToJoinDnaStrands_prefs_key )
self.recursive_clickToJoinDnaStrandsCheckBox = \
PM_CheckBox(pmGroupBox ,
text = 'Recursively join strands',
widgetColumn = 1,
spanWidth = True)
connect_checkbox_with_boolean_pref(
self.recursive_clickToJoinDnaStrandsCheckBox,
joinStrandsCommand_recursive_clickToJoinDnaStrands_prefs_key)
if not env.prefs[joinStrandsCommand_clickToJoinDnaStrands_prefs_key]:
self.recursive_clickToJoinDnaStrandsCheckBox.setEnabled(False)
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 _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box 1.
"""
self.nameLineEdit = PM_LineEdit(pmGroupBox,
label="Name:",
text="",
setAsDefault=False)
self.numberOfBasesSpinBox = \
PM_SpinBox( pmGroupBox,
label = "Number of bases:",
value = self._numberOfBases,
setAsDefault = False,
minimum = 2,
maximum = 10000 )
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.
self.numberOfBasesSpinBox.setEnabled(False)
return
def _loadProductSpecsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Product specifications group box.
@param inPmGroupBox: The roduct specifications box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
productChoices = ['Rod', 'Ring']
self.extrude_productTypeComboBox = \
PM_ComboBox( inPmGroupBox,
label = 'Final product:',
labelColumn = 0,
choices = productChoices,
index = 0,
setAsDefault = True,
spanWidth = False )
# names used in the code, same order
#if you comment out items from combobox, you also have to remove them
# from this list unless they are at the end!!!
self.extrude_productTypeComboBox_ptypes = ["straight rod", \
"closed ring", \
"corkscrew"]
self.extrudeSpinBox_n = \
PM_SpinBox( inPmGroupBox,
label = "Number of copies:",
labelColumn = 0,
value = 3,
minimum = 1,
maximum = 99
)
#@WARNING: This method initializes some instance varaiables for various
#checkboxes. (Example: self.mergeCopiesCheckBox.default = False).
#These values are needed in extrudemode.py. This
#won't be needed once extrudeMode.py is cleaned up. -- ninad 2007-09-10
self.extrudeBondCriterionSlider = \
PM_Slider( inPmGroupBox,
currentValue = 100,
minimum = 0,
maximum = 300,
label = 'Tolerence'
)
self.extrudeBondCriterionLabel = \
self.extrudeBondCriterionSlider.labelWidget
self.extrudeBondCriterionSlider_dflt = 100
self.extrudeBondCriterionSlider.setPageStep(5)
self.makeBondsCheckBox = \
PM_CheckBox(inPmGroupBox,
text = 'Make bonds' ,
widgetColumn = 0,
state = Qt.Checked
)
self.makeBondsCheckBox.default = True
self.makeBondsCheckBox.attr = 'whendone_make_bonds'
self.makeBondsCheckBox.repaintQ = False
def _loadDisplayOptionsGroupBox(self, pmGroupBox):
"""
Load widgets in the Display Options GroupBox
@see: DnaOrCnt_PropertyManager. _loadDisplayOptionsGroupBox
"""
#Call the superclass method that loads the cursor text checkboxes.
#Note, as of 2008-05-19, the superclass, DnaOrCnt_PropertyManager
#only loads the cursor text groupboxes. Subclasses like this can
#call custom methods like self._loadCursorTextCheckBoxes etc if they
#don't need all groupboxes that the superclass loads.
_superclass._loadDisplayOptionsGroupBox(self, pmGroupBox)
self._rubberbandLineGroupBox = PM_GroupBox(pmGroupBox,
title='Rubber band line:')
dnaLineChoices = ['Ribbons', 'Ladder']
self.dnaRubberBandLineDisplayComboBox = \
PM_ComboBox( self._rubberbandLineGroupBox ,
label = " Display as:",
choices = dnaLineChoices,
setAsDefault = True)
self.lineSnapCheckBox = \
PM_CheckBox(self._rubberbandLineGroupBox ,
text = 'Enable line snap' ,
widgetColumn = 1,
state = Qt.Checked
)
def _loadGroupBox1(self, pmGroupBox):
"""
load widgets in groupbox1
"""
self._loadSegmentListWidget(pmGroupBox)
self.crossoversBetGivenSegmentsOnly_checkBox = PM_CheckBox(
pmGroupBox,
text = "Between above segments only",
widgetColumn = 0,
setAsDefault = True,
spanWidth = True,
)
#If this preferece value is True, the search algotithm will search for
#the potential crossover sites only *between* the segments in the
#segment list widget (thus ignoring other segments not in that list)
if env.prefs[makeCrossoversCommand_crossoverSearch_bet_given_segments_only_prefs_key]:
self.crossoversBetGivenSegmentsOnly_checkBox.setCheckState(Qt.Checked)
else:
self.crossoversBetGivenSegmentsOnly_checkBox.setCheckState(Qt.Unchecked)
self.makeCrossoverPushButton = PM_PushButton(
pmGroupBox,
label = "",
text = "Make All Crossovers",
spanWidth = True )
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 _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 _loadAdvancedOptionsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Advanced Options group box.
@param inPmGroupBox: The Advanced Options box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
self.autoBondCheckBox = \
PM_CheckBox( inPmGroupBox,
text = 'Auto bond',
widgetColumn = 0,
state = Qt.Checked )
self.highlightingCheckBox = \
PM_CheckBox( inPmGroupBox,
text = "Hover highlighting",
widgetColumn = 0,
state = Qt.Checked )
def _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 _loadArrowOnBackBone(self, pmGroupBox):
"""
Loads Arrow on the backbone checkbox
"""
self.pmGroupBox4 = PM_GroupBox(pmGroupBox, title="Global preference:")
self.arrowsOnBackBones_checkBox = PM_CheckBox(
self.pmGroupBox4,
text="Show arrows on back bones",
widgetColumn=0,
setAsDefault=True,
spanWidth=True)
prefs_key = arrowsOnBackBones_prefs_key
if env.prefs[prefs_key] == True:
self.arrowsOnBackBones_checkBox.setCheckState(Qt.Checked)
else:
self.arrowsOnBackBones_checkBox.setCheckState(Qt.Unchecked)
return
def _loadAdvancedOptionsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Advanced Options group box.
@param inPmGroupBox: The Advanced Options box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
self.snapGridCheckBox = \
PM_CheckBox(inPmGroupBox,
text = "Snap to grid",
state = Qt.Checked
)
tooltip = "Snap selection point to a nearest cell grid point."
self.snapGridCheckBox.setToolTip(tooltip)
self.freeViewCheckBox = \
PM_CheckBox(inPmGroupBox,
text = "Enable free view",
state = Qt.Unchecked
)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
aa_list = []
for mol in self.win.assy.molecules:
if mol.isProteinChunk():
aa_list = mol.protein.get_amino_acid_id_list()
break
self.aminoAcidsComboBox = PM_ComboBox(pmGroupBox,
label="Residue:",
choices=aa_list,
setAsDefault=False)
self.previousAAPushButton = \
PM_PushButton( pmGroupBox,
text = "Previous AA",
setAsDefault = True)
self.nextAAPushButton = \
PM_PushButton( pmGroupBox,
text = "Next AA",
setAsDefault = True)
self.recenterViewCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Re-center view",
setAsDefault = True,
state = Qt.Checked)
self.expandAllPushButton = \
PM_PushButton( pmGroupBox,
text = "Expand All",
setAsDefault = True)
self.collapseAllPushButton = \
PM_PushButton( pmGroupBox,
text = "Collapse All",
setAsDefault = True)
def _load5PrimeEndArrowAndCustomColor(self, pmGroupBox):
"""
Loads 5' end custom color checkbox and color chooser dialog
"""
self.pmGroupBox2 = PM_GroupBox(pmGroupBox, title="5' end:")
self.arrowsOnFivePrimeEnds_checkBox = PM_CheckBox(
self.pmGroupBox2,
text="Show arrowhead",
widgetColumn=0,
setAsDefault=True,
spanWidth=True)
prefs_key = self._prefs_key_arrowsOnFivePrimeEnds()
if env.prefs[prefs_key]:
self.arrowsOnFivePrimeEnds_checkBox.setCheckState(Qt.Checked)
else:
self.arrowsOnFivePrimeEnds_checkBox.setCheckState(Qt.Unchecked)
self.strandFivePrimeArrowheadsCustomColorCheckBox = PM_CheckBox(
self.pmGroupBox2,
text="Display custom color",
widgetColumn=0,
setAsDefault=True,
spanWidth=True)
prefs_key = self._prefs_key_dnaStrandFivePrimeArrowheadsCustomColor()
self.fivePrimeEndColorChooser = \
PM_ColorComboBox(self.pmGroupBox2,
color = env.prefs[prefs_key]
)
prefs_key = self._prefs_key_useCustomColorForFivePrimeArrowheads()
if env.prefs[prefs_key]:
self.strandFivePrimeArrowheadsCustomColorCheckBox.setCheckState(
Qt.Checked)
self.fivePrimeEndColorChooser.show()
else:
self.strandFivePrimeArrowheadsCustomColorCheckBox.setCheckState(
Qt.Unchecked)
self.fivePrimeEndColorChooser.hide()
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 _loadArrowOnBackBone(self, pmGroupBox):
"""
Loads Arrow on the backbone checkbox
"""
self.pmGroupBox4 = PM_GroupBox(pmGroupBox, title="Global preference:")
self.arrowsOnBackBones_checkBox = PM_CheckBox(
self.pmGroupBox4,
text="Show arrows on back bones",
widgetColumn=0,
setAsDefault=True,
spanWidth=True)
return
def _loadBreakOptionsGroupbox(self, pmGroupBox):
"""
Load widgets in this group box.
"""
self.assignColorToBrokenDnaStrandsCheckBox = \
PM_CheckBox(pmGroupBox ,
text = 'Assign new color to broken strands',
widgetColumn = 1 )
connect_checkbox_with_boolean_pref(
self.assignColorToBrokenDnaStrandsCheckBox,
assignColorToBrokenDnaStrands_prefs_key )
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 _addCheckBoxes(self, paramsForCheckBoxes):
"""
Creates PM_CheckBoxes within the groupbox and also connects each one
with its individual prefs key.
"""
for checkBoxText, prefs_key in paramsForCheckBoxes:
checkBox = \
PM_CheckBox( self,
text = checkBoxText,
widgetColumn = self._checkBoxColumn,
state = Qt.Checked)
connect_checkbox_with_boolean_pref(checkBox, prefs_key)
self.checkBoxes.append(checkBox)
def _loadSelectionOptionsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Selection Options group box.
@param inPmGroupBox: The Selection Options box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
self.selectionFilterCheckBox = \
PM_CheckBox( inPmGroupBox,
text = "Enable atom selection filter",
widgetColumn = 0,
state = Qt.Unchecked )
self.selectionFilterCheckBox.setDefaultValue(False)
self.filterlistLE = PM_LineEdit(inPmGroupBox,
label="",
text="",
setAsDefault=False,
spanWidth=True)
self.filterlistLE.setReadOnly(True)
if self.selectionFilterCheckBox.isChecked():
self.filterlistLE.setEnabled(True)
else:
self.filterlistLE.setEnabled(False)
self.showSelectedAtomInfoCheckBox = \
PM_CheckBox(
inPmGroupBox,
text = "Show Selected Atom Info",
widgetColumn = 0,
state = Qt.Unchecked)
self.selectedAtomPosGroupBox = \
PM_GroupBox( inPmGroupBox, title = "")
self._loadSelectedAtomPosGroupBox(self.selectedAtomPosGroupBox)
self.toggle_selectedAtomPosGroupBox(show=0)
self.enable_or_disable_selectedAtomPosGroupBox(bool_enable=False)
self.reshapeSelectionCheckBox = \
PM_CheckBox( inPmGroupBox,
text = 'Dragging reshapes selection',
widgetColumn = 0,
state = Qt.Unchecked )
connect_checkbox_with_boolean_pref(self.reshapeSelectionCheckBox,
reshapeAtomsSelection_prefs_key)
env.prefs[reshapeAtomsSelection_prefs_key] = False
self.waterCheckBox = \
PM_CheckBox( inPmGroupBox,
text = "Z depth filter (water surface)",
widgetColumn = 0,
state = Qt.Unchecked )
def _loadArrowOnBackBone(self, pmGroupBox):
"""
Loads Arrow on the backbone checkbox
"""
self.pmGroupBox4 = PM_GroupBox(pmGroupBox, title="Global preference:")
self.arrowsOnBackBones_checkBox = PM_CheckBox(
self.pmGroupBox4, text="Show arrows on back bones", widgetColumn=0, setAsDefault=True, spanWidth=True
)
prefs_key = arrowsOnBackBones_prefs_key
if env.prefs[prefs_key] == True:
self.arrowsOnBackBones_checkBox.setCheckState(Qt.Checked)
else:
self.arrowsOnBackBones_checkBox.setCheckState(Qt.Unchecked)
return
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
#stereoSettingsGroupBox = PM_GroupBox( None )
self.stereoEnabledCheckBox = \
PM_CheckBox(pmGroupBox,
text = 'Enable Stereo View',
widgetColumn = 1
)
stereoModeChoices = ['Relaxed view',
'Cross-eyed view',
'Red/blue anaglyphs',
'Red/cyan anaglyphs',
'Red/green anaglyphs']
self.stereoModeComboBox = \
PM_ComboBox( pmGroupBox,
label = "Stereo Mode:",
choices = stereoModeChoices,
setAsDefault = True)
self.stereoModeComboBox.setCurrentIndex(env.prefs[stereoViewMode_prefs_key]-1)
self.stereoSeparationSlider = \
PM_Slider( pmGroupBox,
currentValue = 50,
minimum = 0,
maximum = 300,
label = 'Separation'
)
self.stereoSeparationSlider.setValue(env.prefs[stereoViewSeparation_prefs_key])
self.stereoAngleSlider = \
PM_Slider( pmGroupBox,
currentValue = 50,
minimum = 0,
maximum = 100,
label = 'Angle'
)
self.stereoAngleSlider.setValue(env.prefs[stereoViewAngle_prefs_key])
self._updateWidgets()
def _loadFuseOptionsGroupBox(self, inPmGroupBox):
"""
Load the widgets inside the Fuse Options groupbox.
"""
#@ Warning: If you change fuseChoices, you must also change the
# constants MAKEBONDS and FUSEATOMS in FuseChunks_Command.py.
# This implementation is fragile and should be fixed. Mark 2008-07-16
fuseChoices = ['Make bonds between chunks',
'Fuse overlapping atoms']
self.fuseComboBox = \
PM_ComboBox( inPmGroupBox,
label = '',
choices = fuseChoices,
index = 0,
setAsDefault = False,
spanWidth = True)
self.connect(self.fuseComboBox,
SIGNAL("activated(const QString&)"),
self.parentMode.change_fuse_mode)
self.fusePushButton = PM_PushButton( inPmGroupBox,
label = "",
text = "Make Bonds",
spanWidth = True )
self.connect( self.fusePushButton,
SIGNAL("clicked()"),
self.parentMode.fuse_something)
self.toleranceSlider = PM_Slider( inPmGroupBox,
currentValue = 100,
minimum = 0,
maximum = 300,
label = \
'Tolerance:100% => 0 bondable pairs'
)
self.connect(self.toleranceSlider,
SIGNAL("valueChanged(int)"),
self.parentMode.tolerance_changed)
self.mergeChunksCheckBox = PM_CheckBox( inPmGroupBox,
text = 'Merge chunks',
widgetColumn = 0,
state = Qt.Checked )
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in MotorParamsGroupBox.
"""
if self.command and self.command.struct:
force = self.command.struct.force
stiffness = self.command.struct.stiffness
enable_minimize = self.command.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 _loadMovieControlsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Movie Controls group box.
@param inPmGroupBox: The Movie Controls groupbox in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
#Movie Slider
self.frameNumberSlider = \
PM_Slider( inPmGroupBox,
currentValue = 0,
minimum = 0,
maximum = 999999,
label = 'Current Frame: 0/900'
)
self.movieFrameUpdateLabel = self.frameNumberSlider.labelWidget
#Movie Controls
self.movieButtonsToolBar = NE1ToolBar(inPmGroupBox)
_movieActionList = [self.movieResetAction,
self.moviePlayRevActiveAction,
self.moviePlayRevAction,
self.moviePauseAction,
self.moviePlayAction,
self.moviePlayActiveAction,
self.movieMoveToEndAction
]
for _action in _movieActionList:
self.movieButtonsToolBar.addAction(_action)
self.moviePlayActiveAction.setVisible(0)
self.moviePlayRevActiveAction.setVisible(0)
WIDGET_LIST = [("PM_", self.movieButtonsToolBar, 0)]
self.moviecontrolsWidgetRow = PM_WidgetRow(inPmGroupBox,
widgetList = WIDGET_LIST,
spanWidth = True)
self.movieLoop_checkbox = PM_CheckBox(inPmGroupBox,
text = "Loop",
widgetColumn = 0,
state = Qt.Unchecked)
def _loadAdvancedOptionsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Advanced Options group box.
@param inPmGroupBox: The Advanced Options box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
self.snapGridCheckBox = \
PM_CheckBox(inPmGroupBox,
text = "Snap to grid",
state = Qt.Checked
)
tooltip = "Snap selection point to a nearest cell grid point."
self.snapGridCheckBox.setToolTip(tooltip)
self.freeViewCheckBox = \
PM_CheckBox(inPmGroupBox,
text = "Enable free view",
state = Qt.Unchecked
)
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
aa_list = []
for mol in self.win.assy.molecules:
if mol.isProteinChunk():
aa_list = mol.protein.get_amino_acid_id_list()
break
self.aminoAcidsComboBox = PM_ComboBox( pmGroupBox,
label = "Residue:",
choices = aa_list,
setAsDefault = False)
self.previousAAPushButton = \
PM_PushButton( pmGroupBox,
text = "Previous AA",
setAsDefault = True)
self.nextAAPushButton = \
PM_PushButton( pmGroupBox,
text = "Next AA",
setAsDefault = True)
self.recenterViewCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Re-center view",
setAsDefault = True,
state = Qt.Checked)
self.expandAllPushButton = \
PM_PushButton( pmGroupBox,
text = "Expand All",
setAsDefault = True)
self.collapseAllPushButton = \
PM_PushButton( pmGroupBox,
text = "Collapse All",
setAsDefault = True)
def _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)
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 MakeCrossovers_PropertyManager( Command_PropertyManager,
ListWidgetItems_PM_Mixin ):
"""
The MakeCrossovers_PropertyManager class provides a Property Manager
for the B{Make Crossovers} 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 = "Make Crossovers"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildDna/MakeCrossovers.png"
def __init__( self, command):
"""
Constructor for the property manager.
"""
self.isAlreadyConnected = False
self.isAlreadyDisconnected = False
self._previous_model_changed_params = None
_superclass.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
self.defaultLogMessage = """Pairs of white cylinders (if any) in the
3D workspace indicate potential crossover sites. Clicking on such a
cylinder pair will make that crossover."""
self.updateMessage(self.defaultLogMessage)
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
self.segmentListWidget.connect_or_disconnect_signals(isConnect)
change_connect(self.addSegmentsToolButton,
SIGNAL("toggled(bool)"),
self.activateAddSegmentsTool)
change_connect(self.removeSegmentsToolButton,
SIGNAL("toggled(bool)"),
self.activateRemoveSegmentsTool)
change_connect(self.makeCrossoverPushButton,
SIGNAL("clicked()"),
self._makeAllCrossovers)
connect_checkbox_with_boolean_pref(
self.crossoversBetGivenSegmentsOnly_checkBox,
makeCrossoversCommand_crossoverSearch_bet_given_segments_only_prefs_key)
def show(self):
"""
Overrides the superclass method
@see: self._deactivateAddRemoveSegmentsTool
"""
_superclass.show(self)
self._deactivateAddRemoveSegmentsTool()
def _makeAllCrossovers(self):
self.command.makeAllCrossovers()
def _addGroupBoxes( self ):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self, title = "Segments for Crossover Search" )
self._loadGroupBox1( self._pmGroupBox1 )
def _loadGroupBox1(self, pmGroupBox):
"""
load widgets in groupbox1
"""
self._loadSegmentListWidget(pmGroupBox)
self.crossoversBetGivenSegmentsOnly_checkBox = PM_CheckBox(
pmGroupBox,
text = "Between above segments only",
widgetColumn = 0,
setAsDefault = True,
spanWidth = True,
)
#If this preferece value is True, the search algotithm will search for
#the potential crossover sites only *between* the segments in the
#segment list widget (thus ignoring other segments not in that list)
if env.prefs[makeCrossoversCommand_crossoverSearch_bet_given_segments_only_prefs_key]:
self.crossoversBetGivenSegmentsOnly_checkBox.setCheckState(Qt.Checked)
else:
self.crossoversBetGivenSegmentsOnly_checkBox.setCheckState(Qt.Unchecked)
self.makeCrossoverPushButton = PM_PushButton(
pmGroupBox,
label = "",
text = "Make All Crossovers",
spanWidth = True )
def _update_UI_do_updates(self):
"""
@see: Command_PropertyManager._update_UI_do_updates()
@see: DnaSegment_EditCommand.command_update_UI()
@see: DnaSegment_EditCommand.hasResizableStructure()
@see: self._current_model_changed_params()
"""
currentParams = self._current_model_changed_params()
#Optimization. Return from the model_changed method if the
#params are the same.
if same_vals(currentParams, self._previous_model_changed_params):
return
number_of_segments, \
crossover_search_pref_junk,\
bool_valid_segmentList_junk = currentParams
#update the self._previous_model_changed_params with this new param set.
self._previous_model_changed_params = currentParams
#Ensures that there are only PAM3 DNA segments in the commad's tructure
#list (command._structList. Call this before updating the list widgets!
self.command.ensureValidSegmentList()
self.updateListWidgets()
self.command.updateCrossoverSites()
def _current_model_changed_params(self):
"""
Returns a tuple containing the parameters that will be compared
against the previously stored parameters. This provides a quick test
to determine whether to do more things in self.model_changed()
@see: self.model_changed() which calls this
@see: self._previous_model_changed_params attr.
"""
params = None
if self.command:
#update the list first.
self.command.updateSegmentList()
bool_valid_segmentList = self.command.ensureValidSegmentList()
number_of_segments = len(self.command.getSegmentList())
crossover_search_pref = \
env.prefs[makeCrossoversCommand_crossoverSearch_bet_given_segments_only_prefs_key]
params = (number_of_segments,
crossover_search_pref,
bool_valid_segmentList
)
return params
def _addWhatsThisText( self ):
"""
What's This text for widgets in the DNA Property Manager.
"""
whatsThis_MakeCrossoversPropertyManager(self)
def _addToolTipText(self):
"""
Tool Tip text for widgets in the DNA Property Manager.
"""
pass
class BreakOrJoinStrands_PropertyManager(Command_PropertyManager):
_baseNumberLabelGroupBox = None
def __init__( self, command ):
"""
Constructor for the property manager.
"""
_superclass.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
return
def connect_or_disconnect_signals(self, isConnect):
"""
Connect or disconnect widget signals sent to their slot methods.
This can be overridden in subclasses. By default it does nothing.
@param isConnect: If True the widget will send the signals to the slot
method.
@type isConnect: boolean
"""
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
# DNA Strand arrowhead display options signal-slot connections.
self._connect_checkboxes_to_global_prefs_keys(isConnect)
change_connect(self.fivePrimeEndColorChooser,
SIGNAL("editingFinished()"),
self.chooseCustomColorOnFivePrimeEnds)
change_connect(self.threePrimeEndColorChooser,
SIGNAL("editingFinished()"),
self.chooseCustomColorOnThreePrimeEnds)
change_connect(self.strandFivePrimeArrowheadsCustomColorCheckBox,
SIGNAL("toggled(bool)"),
self.allowChoosingColorsOnFivePrimeEnd)
change_connect(self.strandThreePrimeArrowheadsCustomColorCheckBox,
SIGNAL("toggled(bool)"),
self.allowChoosingColorsOnThreePrimeEnd)
self._baseNumberLabelGroupBox.connect_or_disconnect_signals(isConnect)
return
def show(self):
"""
Shows the Property Manager. Extends superclass method.
@see: Command_PropertyManager.show()
"""
_superclass.show(self)
#Required to update the color combobox for Dna base number labels.
self._baseNumberLabelGroupBox.updateWidgets()
def _connect_checkboxes_to_global_prefs_keys(self, isConnect = True):
"""
#doc
"""
if not isConnect:
return
#ORDER of items in tuples checkboxes and prefs_keys is IMPORTANT!
checkboxes = (
self.arrowsOnThreePrimeEnds_checkBox,
self.arrowsOnFivePrimeEnds_checkBox,
self.strandThreePrimeArrowheadsCustomColorCheckBox,
self.strandFivePrimeArrowheadsCustomColorCheckBox,
self.arrowsOnBackBones_checkBox)
prefs_keys = (
self._prefs_key_arrowsOnThreePrimeEnds(),
self._prefs_key_arrowsOnFivePrimeEnds(),
self._prefs_key_useCustomColorForThreePrimeArrowheads(),
self._prefs_key_useCustomColorForFivePrimeArrowheads(),
arrowsOnBackBones_prefs_key)
for checkbox, prefs_key in zip(checkboxes, prefs_keys):
connect_checkbox_with_boolean_pref(checkbox, prefs_key)
return
#Load various widgets ====================
def _loadBaseNumberLabelGroupBox(self, pmGroupBox):
self._baseNumberLabelGroupBox = PM_DnaBaseNumberLabelsGroupBox(pmGroupBox,
self.command)
def _loadDisplayOptionsGroupBox(self, pmGroupBox):
"""
Load widgets in the display options groupbox
"""
title = "Arrowhead prefs in %s:"%self.command.featurename
self._arrowheadPrefsGroupBox = PM_GroupBox(
pmGroupBox,
title = title)
#load all the options
self._load3PrimeEndArrowAndCustomColor(self._arrowheadPrefsGroupBox)
self._load5PrimeEndArrowAndCustomColor(self._arrowheadPrefsGroupBox)
self._loadArrowOnBackBone(pmGroupBox)
return
def _load3PrimeEndArrowAndCustomColor(self, pmGroupBox):
"""
Loads 3' end arrow head and custom color checkbox and color chooser dialog
"""
self.pmGroupBox3 = PM_GroupBox(pmGroupBox, title = "3' end:")
self.arrowsOnThreePrimeEnds_checkBox = PM_CheckBox( self.pmGroupBox3,
text = "Show arrowhead",
widgetColumn = 0,
setAsDefault = True,
spanWidth = True )
self.strandThreePrimeArrowheadsCustomColorCheckBox = PM_CheckBox( self.pmGroupBox3,
text = "Display custom color",
widgetColumn = 0,
setAsDefault = True,
spanWidth = True)
prefs_key = self._prefs_key_dnaStrandThreePrimeArrowheadsCustomColor()
self.threePrimeEndColorChooser = \
PM_ColorComboBox(self.pmGroupBox3,
color = env.prefs[prefs_key])
prefs_key = self._prefs_key_useCustomColorForThreePrimeArrowheads()
if env.prefs[prefs_key]:
self.strandThreePrimeArrowheadsCustomColorCheckBox.setCheckState(Qt.Checked)
self.threePrimeEndColorChooser.show()
else:
self.strandThreePrimeArrowheadsCustomColorCheckBox.setCheckState(Qt.Unchecked)
self.threePrimeEndColorChooser.hide()
return
def _load5PrimeEndArrowAndCustomColor(self, pmGroupBox):
"""
Loads 5' end custom color checkbox and color chooser dialog
"""
self.pmGroupBox2 = PM_GroupBox(pmGroupBox, title = "5' end:")
self.arrowsOnFivePrimeEnds_checkBox = PM_CheckBox( self.pmGroupBox2,
text = "Show arrowhead",
widgetColumn = 0,
setAsDefault = True,
spanWidth = True
)
self.strandFivePrimeArrowheadsCustomColorCheckBox = PM_CheckBox( self.pmGroupBox2,
text = "Display custom color",
widgetColumn = 0,
setAsDefault = True,
spanWidth = True )
prefs_key = self._prefs_key_dnaStrandFivePrimeArrowheadsCustomColor()
self.fivePrimeEndColorChooser = \
PM_ColorComboBox(self.pmGroupBox2,
color = env.prefs[prefs_key]
)
prefs_key = self._prefs_key_useCustomColorForFivePrimeArrowheads()
if env.prefs[prefs_key]:
self.strandFivePrimeArrowheadsCustomColorCheckBox.setCheckState(Qt.Checked)
self.fivePrimeEndColorChooser.show()
else:
self.strandFivePrimeArrowheadsCustomColorCheckBox.setCheckState(Qt.Unchecked)
self.fivePrimeEndColorChooser.hide()
return
def _loadArrowOnBackBone(self, pmGroupBox):
"""
Loads Arrow on the backbone checkbox
"""
self.pmGroupBox4 = PM_GroupBox(pmGroupBox, title = "Global preference:")
self.arrowsOnBackBones_checkBox = PM_CheckBox( self.pmGroupBox4,
text = "Show arrows on back bones",
widgetColumn = 0,
setAsDefault = True,
spanWidth = True
)
return
def allowChoosingColorsOnFivePrimeEnd(self, state):
"""
Show or hide color chooser based on the
strandFivePrimeArrowheadsCustomColorCheckBox's state
"""
if self.strandFivePrimeArrowheadsCustomColorCheckBox.isChecked():
self.fivePrimeEndColorChooser.show()
else:
self.fivePrimeEndColorChooser.hide()
return
def allowChoosingColorsOnThreePrimeEnd(self, state):
"""
Show or hide color chooser based on the
strandThreePrimeArrowheadsCustomColorCheckBox's state
"""
if self.strandThreePrimeArrowheadsCustomColorCheckBox.isChecked():
self.threePrimeEndColorChooser.show()
else:
self.threePrimeEndColorChooser.hide()
return
def chooseCustomColorOnThreePrimeEnds(self):
"""
Choose custom color for 3' ends
"""
color = self.threePrimeEndColorChooser.getColor()
prefs_key = self._prefs_key_dnaStrandThreePrimeArrowheadsCustomColor()
env.prefs[prefs_key] = color
self.win.glpane.gl_update()
return
def chooseCustomColorOnFivePrimeEnds(self):
"""
Choose custom color for 5' ends
"""
color = self.fivePrimeEndColorChooser.getColor()
prefs_key = self._prefs_key_dnaStrandFivePrimeArrowheadsCustomColor()
env.prefs[prefs_key] = color
self.win.glpane.gl_update()
return
#Return varius prefs_keys for arrowhead display options ui elements =======
def _prefs_key_arrowsOnThreePrimeEnds(self):
"""
Return the appropriate KEY of the preference for whether to
draw arrows on 3' strand ends of PAM DNA.
"""
return arrowsOnThreePrimeEnds_prefs_key
def _prefs_key_arrowsOnFivePrimeEnds(self):
"""
Return the appropriate KEY of the preference for whether to
draw arrows on 5' strand ends of PAM DNA.
"""
return arrowsOnFivePrimeEnds_prefs_key
def _prefs_key_useCustomColorForThreePrimeArrowheads(self):
"""
Return the appropriate KEY of the preference for whether to use a
custom color for 3' arrowheads (if they are drawn)
or for 3' strand end atoms (if arrowheads are not drawn)
"""
return useCustomColorForThreePrimeArrowheads_prefs_key
def _prefs_key_useCustomColorForFivePrimeArrowheads(self):
"""
Return the appropriate KEY of the preference for whether to use a
custom color for 5' arrowheads (if they are drawn)
or for 5' strand end atoms (if arrowheads are not drawn).
"""
return useCustomColorForFivePrimeArrowheads_prefs_key
def _prefs_key_dnaStrandThreePrimeArrowheadsCustomColor(self):
"""
Return the appropriate KEY of the preference for what custom color
to use when drawing 3' arrowheads (if they are drawn)
or 3' strand end atoms (if arrowheads are not drawn).
"""
return dnaStrandThreePrimeArrowheadsCustomColor_prefs_key
def _prefs_key_dnaStrandFivePrimeArrowheadsCustomColor(self):
"""
Return the appropriate KEY of the preference for what custom color
to use when drawing 5' arrowheads (if they are drawn)
or 5' strand end atoms (if arrowheads are not drawn).
"""
return dnaStrandFivePrimeArrowheadsCustomColor_prefs_key
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in MotorParamsGroupBox.
"""
if self.editCommand and self.editCommand.struct:
torque = self.editCommand.struct.torque
initial_speed = self.editCommand.struct.initial_speed
final_speed = self.editCommand.struct.speed
dampers_enabled = self.editCommand.struct.dampers_enabled
enable_minimize = self.editCommand.struct.enable_minimize
else:
torque = 0.0
initial_speed = 0.0
final_speed = 0.0
dampers_enabled = False
enable_minimize = False
self.torqueDblSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
label = "Torque :",
value = torque,
setAsDefault = True,
minimum = 0.0,
maximum = 1000.0,
singleStep = 1.0,
decimals = 1,
suffix =' nN-nm')
self.initialSpeedDblSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
label = "Initial speed :",
value = initial_speed,
setAsDefault = True,
minimum = 0.0,
maximum = 100.0,
singleStep = 1.0,
decimals = 1,
suffix = ' GHz')
self.finalSpeedDblSpinBox = \
PM_DoubleSpinBox(pmGroupBox,
label = "Final speed :",
value = final_speed,
setAsDefault = True,
minimum = 0.0,
maximum = 100.0,
singleStep = 1.0,
decimals = 1,
suffix = ' GHz')
self.dampersCheckBox = \
PM_CheckBox(pmGroupBox,
text = "Dampers",
widgetColumn = 0
)
self.dampersCheckBox.setChecked(dampers_enabled)
self.enableMinimizeCheckBox = \
PM_CheckBox(pmGroupBox,
text = "Enable in minimize",
widgetColumn = 0
)
self.enableMinimizeCheckBox.setChecked(enable_minimize)
self.directionPushButton = \
PM_PushButton(pmGroupBox,
label = "Direction :",
text = "Reverse",
spanWidth = False)
return
class EditResidues_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 Residues"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildProtein/Residues.png"
rosetta_all_set = "PGAVILMFWYCSTNQDEHKR"
rosetta_polar_set = "___________STNQDEHKR"
rosetta_apolar_set = "PGAVILMFWYC_________"
def __init__( self, command ):
"""
Constructor for the property manager.
"""
self.currentWorkingDirectory = env.prefs[workingDirectory_prefs_key]
_superclass.__init__(self, command)
self.sequenceEditor = self.win.createProteinSequenceEditorIfNeeded()
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
self.editingItem = False
return
def connect_or_disconnect_signals(self, isConnect = True):
if isConnect:
change_connect = self.win.connect
else:
change_connect = self.win.disconnect
change_connect(self.applyAnyPushButton,
SIGNAL("clicked()"),
self._applyAny)
change_connect(self.applySamePushButton,
SIGNAL("clicked()"),
self._applySame)
change_connect(self.applyLockedPushButton,
SIGNAL("clicked()"),
self._applyLocked)
change_connect(self.applyPolarPushButton,
SIGNAL("clicked()"),
self._applyPolar)
change_connect(self.applyApolarPushButton,
SIGNAL("clicked()"),
self._applyApolar)
change_connect(self.selectAllPushButton,
SIGNAL("clicked()"),
self._selectAll)
change_connect(self.selectNonePushButton,
SIGNAL("clicked()"),
self._selectNone)
change_connect(self.selectInvertPushButton,
SIGNAL("clicked()"),
self._invertSelection)
change_connect(self.applyDescriptorPushButton,
SIGNAL("clicked()"),
self._applyDescriptor)
change_connect(self.removeDescriptorPushButton,
SIGNAL("clicked()"),
self._removeDescriptor)
change_connect(self.sequenceTable,
SIGNAL("cellClicked(int, int)"),
self._sequenceTableCellChanged)
change_connect(self.sequenceTable,
SIGNAL("itemChanged(QTableWidgetItem*)"),
self._sequenceTableItemChanged)
change_connect(self.descriptorsTable,
SIGNAL("itemChanged(QTableWidgetItem*)"),
self._descriptorsTableItemChanged)
change_connect(self.newDescriptorPushButton,
SIGNAL("clicked()"),
self._addNewDescriptor)
change_connect(self.showSequencePushButton,
SIGNAL("clicked()"),
self._showSeqEditor)
return
def _showSeqEditor(self):
"""
Shows sequence editor
"""
if self.showSequencePushButton.isEnabled():
self.sequenceEditor.show()
return
def show(self):
"""
Shows the Property Manager. Extends superclass method.
"""
env.history.statusbar_msg("")
#Urmi 20080728: Set the current protein and this will be used for accessing
#various properties of this protein
self.set_current_protein()
if self.current_protein:
msg = "Editing structure <b>%s</b>." % self.current_protein.name
self.showSequencePushButton.setEnabled(True)
else:
msg = "Select a single structure to edit."
self.showSequencePushButton.setEnabled(False)
self.sequenceEditor.hide()
_superclass.show(self)
self._fillSequenceTable()
self.updateMessage(msg)
return
def set_current_protein(self):
"""
Set the current protein for which all the properties are displayed to the
one chosen in the build protein combo box
"""
self.current_protein = self.win.assy.getSelectedProteinChunk()
return
def _addGroupBoxes( self ):
"""
Add the Property Manager group boxes.
"""
if sys.platform == "darwin":
# Workaround for table font size difference between Mac/Win
self.labelfont = QFont("Helvetica", 12)
self.descriptorfont = QFont("Courier New", 12)
else:
self.labelfont = QFont("Helvetica", 9)
self.descriptorfont = QFont("Courier New", 9)
self._pmGroupBox1 = PM_GroupBox( self,
title = "Descriptors")
self._loadGroupBox1( self._pmGroupBox1 )
self._pmGroupBox2 = PM_GroupBox( self,
title = "Sequence")
self._loadGroupBox2( self._pmGroupBox2 )
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in the first group box.
"""
self.headerdata_desc = ['Name', 'Descriptor']
self.set_names = ["Any", "Same", "Locked", "Apolar", "Polar"]
self.rosetta_set_names = ["ALLAA", "NATAA", "NATRO", "APOLA", "POLAR"]
self.descriptor_list = ["PGAVILMFWYCSTNQDEHKR",
"____________________",
"____________________",
"PGAVILMFWYC_________",
"___________STNQDEHKR"]
self.applyAnyPushButton = PM_PushButton( pmGroupBox,
text = "ALLAA",
setAsDefault = True)
self.applySamePushButton = PM_PushButton( pmGroupBox,
text = "NATAA",
setAsDefault = True)
self.applyLockedPushButton = PM_PushButton( pmGroupBox,
text = "NATRO",
setAsDefault = True)
self.applyPolarPushButton = PM_PushButton( pmGroupBox,
text = "APOLA",
setAsDefault = True)
self.applyApolarPushButton = PM_PushButton( pmGroupBox,
text = "POLAR",
setAsDefault = True)
#self.applyBackrubPushButton = PM_PushButton( pmGroupBox,
# text = "BACKRUB",
# setAsDefault = True)
self.applyAnyPushButton.setFixedHeight(25)
self.applyAnyPushButton.setFixedWidth(60)
self.applySamePushButton.setFixedHeight(25)
self.applySamePushButton.setFixedWidth(60)
self.applyLockedPushButton.setFixedHeight(25)
self.applyLockedPushButton.setFixedWidth(60)
self.applyPolarPushButton.setFixedHeight(25)
self.applyPolarPushButton.setFixedWidth(60)
self.applyApolarPushButton.setFixedHeight(25)
self.applyApolarPushButton.setFixedWidth(60)
applyButtonList = [
('PM_PushButton', self.applyAnyPushButton, 0, 0),
('PM_PushButton', self.applySamePushButton, 1, 0),
('PM_PushButton', self.applyLockedPushButton, 2, 0),
('PM_PushButton', self.applyPolarPushButton, 3, 0),
('PM_PushButton', self.applyApolarPushButton, 4, 0) ]
self.applyButtonGrid = PM_WidgetGrid( pmGroupBox,
label = "Apply standard set",
widgetList = applyButtonList)
self.descriptorsTable = PM_TableWidget( pmGroupBox,
label = "Custom descriptors")
self.descriptorsTable.setFixedHeight(100)
self.descriptorsTable.setRowCount(0)
self.descriptorsTable.setColumnCount(2)
self.descriptorsTable.verticalHeader().setVisible(False)
self.descriptorsTable.horizontalHeader().setVisible(True)
self.descriptorsTable.setGridStyle(Qt.NoPen)
self.descriptorsTable.setHorizontalHeaderLabels(self.headerdata_desc)
self._updateSetLists()
self._fillDescriptorsTable()
self.descriptorsTable.resizeColumnsToContents()
self.newDescriptorPushButton = PM_PushButton( pmGroupBox,
text = "New",
setAsDefault = True)
self.newDescriptorPushButton.setFixedHeight(25)
self.removeDescriptorPushButton = PM_PushButton( pmGroupBox,
text = "Remove",
setAsDefault = True)
self.removeDescriptorPushButton.setFixedHeight(25)
self.applyDescriptorPushButton = PM_PushButton( pmGroupBox,
text = "Apply",
setAsDefault = True)
self.applyDescriptorPushButton.setFixedHeight(25)
addDescriptorButtonList = [('PM_PushButton', self.newDescriptorPushButton, 0, 0),
('PM_PushButton', self.removeDescriptorPushButton, 1, 0),
('PM_PushButton', self.applyDescriptorPushButton, 2, 0) ]
self.addDescriptorGrid = PM_WidgetGrid( pmGroupBox,
alignment = "Center",
widgetList = addDescriptorButtonList)
def _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in the second group box.
"""
self.headerdata_seq = ['', 'ID', 'Set', 'BR', 'Descriptor']
self.recenterViewCheckBox = \
PM_CheckBox( pmGroupBox,
text = "Re-center view on selected residue",
setAsDefault = True,
widgetColumn = 0,
state = Qt.Unchecked)
self.selectAllPushButton = PM_PushButton( pmGroupBox,
text = "All",
setAsDefault = True)
self.selectAllPushButton.setFixedHeight(25)
self.selectNonePushButton = PM_PushButton( pmGroupBox,
text = "None",
setAsDefault = True)
self.selectNonePushButton.setFixedHeight(25)
self.selectInvertPushButton = PM_PushButton( pmGroupBox,
text = "Invert",
setAsDefault = True)
self.selectInvertPushButton.setFixedHeight(25)
buttonList = [ ('PM_PushButton', self.selectAllPushButton, 0, 0),
('PM_PushButton', self.selectNonePushButton, 1, 0),
('PM_PushButton', self.selectInvertPushButton, 2, 0)]
self.buttonGrid = PM_WidgetGrid( pmGroupBox,
widgetList = buttonList)
self.sequenceTable = PM_TableWidget( pmGroupBox)
#self.sequenceTable.setModel(self.tableModel)
self.sequenceTable.resizeColumnsToContents()
self.sequenceTable.verticalHeader().setVisible(False)
#self.sequenceTable.setRowCount(0)
self.sequenceTable.setColumnCount(5)
self.checkbox = QCheckBox()
self.sequenceTable.setFixedHeight(345)
self.sequenceTable.setGridStyle(Qt.NoPen)
self.sequenceTable.setHorizontalHeaderLabels(self.headerdata_seq)
###self._fillSequenceTable()
self.showSequencePushButton = PM_PushButton( pmGroupBox,
text = "Show Sequence",
setAsDefault = True,
spanWidth = True)
def _addWhatsThisText( self ):
#from ne1_ui.WhatsThisText_for_PropertyManagers import WhatsThis_EditResidues_PropertyManager
#WhatsThis_EditResidues_PropertyManager(self)
pass
def _addToolTipText(self):
#from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_EditProteinDisplayStyle_PropertyManager
#ToolTip_EditProteinDisplayStyle_PropertyManager(self)
pass
def _fillSequenceTable(self):
"""
Fills in the sequence table.
"""
if not self.current_protein:
return
else:
currentProteinChunk = self.current_protein
self.editingItem = True
aa_list = currentProteinChunk.protein.get_amino_acids()
aa_list_len = len(aa_list)
self.sequenceTable.setRowCount(aa_list_len)
for index in range(aa_list_len):
# Selection checkbox column
item_widget = QTableWidgetItem("")
item_widget.setFont(self.labelfont)
item_widget.setCheckState(Qt.Checked)
item_widget.setTextAlignment(Qt.AlignLeft)
item_widget.setSizeHint(QSize(20,12))
item_widget.setFlags(Qt.ItemIsSelectable |
Qt.ItemIsEnabled |
Qt.ItemIsUserCheckable)
self.sequenceTable.setItem(index, 0, item_widget)
# Amino acid index column
item_widget = QTableWidgetItem(str(index+1))
item_widget.setFont(self.labelfont)
item_widget.setFlags(
Qt.ItemIsSelectable |
Qt.ItemIsEnabled)
item_widget.setTextAlignment(Qt.AlignCenter)
self.sequenceTable.setItem(index, 1, item_widget)
# Mutation descriptor name column
aa = self._get_aa_for_index(index)
item_widget = QTableWidgetItem(self._get_descriptor_name(aa))
item_widget.setFont(self.labelfont)
item_widget.setFlags(Qt.ItemIsSelectable |
Qt.ItemIsEnabled)
item_widget.setTextAlignment(Qt.AlignCenter)
self.sequenceTable.setItem(index, 2, item_widget)
# Backrub checkbox column
item_widget = QTableWidgetItem("")
item_widget.setFont(self.labelfont)
if aa.get_backrub_mode():
item_widget.setCheckState(Qt.Checked)
else:
item_widget.setCheckState(Qt.Unchecked)
item_widget.setTextAlignment(Qt.AlignLeft)
item_widget.setSizeHint(QSize(20,12))
item_widget.setFlags(Qt.ItemIsSelectable |
Qt.ItemIsEnabled |
Qt.ItemIsUserCheckable)
self.sequenceTable.setItem(index, 3, item_widget)
# Mutation descriptor column
aa_string = self._get_mutation_descriptor(aa)
item_widget = QTableWidgetItem(aa_string)
item_widget.setFont(self.descriptorfont)
self.sequenceTable.setItem(index, 4, item_widget)
self.sequenceTable.setRowHeight(index, 16)
self.editingItem = False
self.sequenceTable.resizeColumnsToContents()
self.sequenceTable.setColumnWidth(0, 35)
self.sequenceTable.setColumnWidth(2, 80)
self.sequenceTable.setColumnWidth(3, 35)
return
def _fillDescriptorsTable(self):
"""
Fills in the descriptors table from descriptors user pref.
"""
dstr = env.prefs[proteinCustomDescriptors_prefs_key].split(":")
for i in range(len(dstr) / 2):
self._addNewDescriptorTableRow(dstr[2*i], dstr[2*i+1])
def _selectAll(self):
"""
Select all rows in the sequence table.
"""
for row in range(self.sequenceTable.rowCount()):
self.sequenceTable.item(row, 0).setCheckState(Qt.Checked)
def _selectNone(self):
"""
Unselect all rows in the sequence table.
"""
for row in range(self.sequenceTable.rowCount()):
self.sequenceTable.item(row, 0).setCheckState(Qt.Unchecked)
def _invertSelection(self):
"""
Inverto row selection range in the sequence table.
"""
for row in range(self.sequenceTable.rowCount()):
item_widget = self.sequenceTable.item(row, 0)
if item_widget.checkState() == Qt.Checked:
item_widget.setCheckState(Qt.Unchecked)
else:
item_widget.setCheckState(Qt.Checked)
def _get_mutation_descriptor(self, aa):
"""
Get mutation descriptor string for a given amino acid.
"""
aa_string = self.rosetta_all_set
range = aa.get_mutation_range()
aa_string = self.rosetta_all_set
if range == "NATRO" or \
range == "NATAA":
code = aa.get_one_letter_code()
aa_string = re.sub("[^"+code+"]",'_', aa_string)
elif range == "POLAR":
aa_string = self.rosetta_polar_set
elif range == "APOLA":
aa_string = self.rosetta_apolar_set
elif range == "PIKAA":
aa_string = aa.get_mutation_descriptor()
return aa_string
def _get_descriptor_name(self, aa):
"""
Returns a mutation descriptor name for an amino acid.
"""
range_name = aa.get_mutation_range()
for i in range(len(self.rosetta_set_names)):
if range_name == self.rosetta_set_names[i]:
if range_name == "PIKAA":
# Find a descriptor with a list of
# custom descriptors.
dstr = self._makeProperAAString(aa.get_mutation_descriptor())
for i in range(5, len(self.descriptor_list)):
if dstr == self.descriptor_list[i]:
return self.set_names[i]
else:
return self.set_names[i]
return "Custom"
def _get_aa_for_index(self, index, expand = False):
"""
Get amino acid by index.
@return: amino acid (Residue)
"""
if not self.current_protein:
return None
else:
currentProteinChunk = self.current_protein
currentProteinChunk.protein.set_current_amino_acid_index(index)
current_aa = currentProteinChunk.protein.get_current_amino_acid()
if expand:
currentProteinChunk.protein.collapse_all_rotamers()
currentProteinChunk.protein.expand_rotamer(current_aa)
return current_aa
def _sequenceTableCellChanged(self, crow, ccol):
"""
Slot for sequence table CellChanged event.
"""
item = self.sequenceTable.item(crow, ccol)
for row in range(self.sequenceTable.rowCount()):
self.sequenceTable.removeCellWidget(row, 2)
self.sequenceTable.setRowHeight(row, 16)
if ccol == 2:
# Make the row a little bit wider.
self.sequenceTable.setRowHeight(crow, 22)
# Create and insert a Combo Box into a current cell.
self.setComboBox = QComboBox()
self.setComboBox.addItems(self.set_names)
self.win.connect(self.setComboBox,
SIGNAL("activated(int)"),
self._setComboBoxIndexChanged)
self.sequenceTable.setCellWidget(crow, 2, self.setComboBox)
current_aa = self._get_aa_for_index(crow, expand=True)
if current_aa:
# Center on the selected amino acid.
if self.recenterViewCheckBox.isChecked():
ca_atom = current_aa.get_c_alpha_atom()
if ca_atom:
self.win.glpane.pov = -ca_atom.posn()
self.win.glpane.gl_update()
# Update backrub status for selected amino acid.
if ccol == 3:
cbox = self.sequenceTable.item(crow, 3)
if cbox.checkState() == Qt.Checked:
current_aa.set_backrub_mode(True)
else:
current_aa.set_backrub_mode(False)
from PyQt4.Qt import QTextCursor
cursor = self.sequenceEditor.sequenceTextEdit.textCursor()
#boundary condition
if crow == -1:
crow = 0
cursor.setPosition(crow, QTextCursor.MoveAnchor)
cursor.setPosition(crow + 1, QTextCursor.KeepAnchor)
self.sequenceEditor.sequenceTextEdit.setTextCursor( cursor )
def _applyDescriptor(self):
"""
Apply mutation descriptor to the selected amino acids.
"""
cdes = self.descriptorsTable.currentRow()
for row in range(self.sequenceTable.rowCount()):
self._setComboBoxIndexChanged(cdes + 5, tablerow = row, selectedOnly = True)
def _setComboBoxIndexChanged( self, index, tablerow = None, selectedOnly = False):
"""
Slot for mutation descriptor combo box (in third column of the sequence
table.)
"""
if tablerow is None:
crow = self.sequenceTable.currentRow()
else:
crow = tablerow
item = self.sequenceTable.item(crow, 2)
if item:
self.editingItem = True
cbox = self.sequenceTable.item(crow, 0)
if not selectedOnly or \
cbox.checkState() == Qt.Checked:
item.setText(self.set_names[index])
item = self.sequenceTable.item(crow, 4)
aa = self._get_aa_for_index(crow)
set_name = self.rosetta_set_names[index]
aa.set_mutation_range(set_name)
if set_name == "PIKAA":
aa.set_mutation_descriptor(self.descriptor_list[index])
item.setText(self._get_mutation_descriptor(aa))
for row in range(self.sequenceTable.rowCount()):
self.sequenceTable.removeCellWidget(row, 2)
self.sequenceTable.setRowHeight(row, 16)
self.editingItem = False
def scrollToPosition(self, index):
"""
Scrolls the Sequence Table to a given sequence position.
"""
item = self.sequenceTable.item(index, 0)
if item:
self.sequenceTable.scrollToItem(item)
def _applyAny(self):
"""
Apply "ALLAA" descriptor.
"""
for row in range(self.sequenceTable.rowCount()):
self._setComboBoxIndexChanged(0, tablerow = row, selectedOnly = True)
def _applySame(self):
"""
Apply "NATAA" descriptor.
"""
for row in range(self.sequenceTable.rowCount()):
self._setComboBoxIndexChanged(1, tablerow = row, selectedOnly = True)
def _applyLocked(self):
"""
Apply "NATRO" descriptor.
"""
for row in range(self.sequenceTable.rowCount()):
self._setComboBoxIndexChanged(2, tablerow = row, selectedOnly = True)
def _applyPolar(self):
"""
Apply "POLAR" descriptor.
"""
for row in range(self.sequenceTable.rowCount()):
self._setComboBoxIndexChanged(3, tablerow = row, selectedOnly = True)
def _applyApolar(self):
"""
Apply "APOLA" descriptor.
"""
for row in range(self.sequenceTable.rowCount()):
self._setComboBoxIndexChanged(4, tablerow = row, selectedOnly = True)
def resizeEvent(self, event):
"""
Called whenever PM width has changed. Sets correct width of the
rows in descriptor and sequence tables.
"""
self.descriptorsTable.setColumnWidth(1,
self.descriptorsTable.width()-self.descriptorsTable.columnWidth(0)-20)
self.sequenceTable.setColumnWidth(4,
self.sequenceTable.width()-
(self.sequenceTable.columnWidth(0) +
self.sequenceTable.columnWidth(1) +
self.sequenceTable.columnWidth(2) +
self.sequenceTable.columnWidth(3))-20)
def _addNewDescriptorTableRow(self, name, descriptor):
"""
Adds a new row to the descriptor table.
"""
row = self.descriptorsTable.rowCount()
self.descriptorsTable.insertRow(row)
item_widget = QTableWidgetItem(name)
item_widget.setFont(self.labelfont)
item_widget.setFlags(Qt.ItemIsSelectable |
Qt.ItemIsEnabled |
Qt.ItemIsEditable)
item_widget.setTextAlignment(Qt.AlignLeft)
self.descriptorsTable.setItem(row, 0, item_widget)
self.descriptorsTable.resizeColumnToContents(0)
s = self._makeProperAAString(descriptor)
item_widget = QTableWidgetItem(s)
item_widget.setFont(self.descriptorfont)
item_widget.setFlags(Qt.ItemIsSelectable |
Qt.ItemIsEnabled |
Qt.ItemIsEditable)
item_widget.setTextAlignment(Qt.AlignLeft)
self.descriptorsTable.setItem(row, 1, item_widget)
self.descriptorsTable.setColumnWidth(1,
self.descriptorsTable.width()-self.descriptorsTable.columnWidth(0)-20)
self.descriptorsTable.setRowHeight(row, 16)
def _addNewDescriptor(self):
"""
Adds a new descriptor to the descriptor table.
"""
self._addNewDescriptorTableRow("New Set", "PGAVILMFWYCSTNQDEHKR")
self._makeDescriptorUserPref()
self._updateSetLists()
def _removeDescriptor(self):
"""
Removes a highlighted descriptor from the descriptors table.
"""
crow = self.descriptorsTable.currentRow()
if crow >= 0:
self.descriptorsTable.removeRow(crow)
self._makeDescriptorUserPref()
self._updateSetLists()
def _makeDescriptorUserPref(self):
"""
Constructs a custom descriptors string.
"""
dstr = ""
for row in range(self.descriptorsTable.rowCount()):
item0 = self.descriptorsTable.item(row, 0)
item1 = self.descriptorsTable.item(row, 1)
if item0 and \
item1:
dstr += item0.text() + \
":" + \
item1.text() + \
":"
env.prefs[proteinCustomDescriptors_prefs_key] = dstr
def _makeProperAAString(self, string):
"""
Creates a proper amino acid string from an arbitrary string.
"""
aa_string = str(string).upper()
new_aa_string = ""
for i in range(len(self.rosetta_all_set)):
if aa_string.find(self.rosetta_all_set[i]) == -1:
new_aa_string += "_"
else:
new_aa_string += self.rosetta_all_set[i]
return new_aa_string
def _sequenceTableItemChanged(self, item):
"""
Called when an item in the sequence table has changed.
"""
if self.editingItem:
return
if self.sequenceTable.column(item) == 4:
self.editingItem = True
crow = self.sequenceTable.currentRow()
dstr = self._makeProperAAString(str(item.text()).upper())
item.setText(dstr)
aa = self._get_aa_for_index(crow)
if aa:
aa.set_mutation_range("PIKAA")
aa.set_mutation_descriptor(dstr.replace("_",""))
item = self.sequenceTable.item(crow, 2)
if item:
item.setText("Custom")
self.editingItem = False
def _descriptorsTableItemChanged(self, item):
"""
Called when an item in the descriptors table has changed.
"""
if self.editingItem:
return
if self.descriptorsTable.column(item) == 1:
self.editingItem = True
item.setText(self._makeProperAAString(str(item.text()).upper()))
self.editingItem = False
self._makeDescriptorUserPref()
self._updateSetLists()
def _updateSetLists(self):
"""
Updates lists of descriptor sets and descriptor set names.
"""
self.set_names = self.set_names[:5]
self.descriptor_list = self.descriptor_list[:5]
self.rosetta_set_names = self.rosetta_set_names[:5]
dstr = env.prefs[proteinCustomDescriptors_prefs_key].split(":")
for i in range(len(dstr) / 2):
self.set_names.append(dstr[2*i])
self.descriptor_list.append(dstr[2*i+1])
self.rosetta_set_names.append("PIKAA")
#self._addNewDescriptorTableRow(dstr[2*i], dstr[2*i+1])
return
def _update_UI_do_updates_TEMP(self):
"""
Overrides superclass method.
@see: Command_PropertyManager._update_UI_do_updates()
"""
self.current_protein = self.win.assy.getSelectedProteinChunk()
if self.current_protein is self.previous_protein:
print "_update_UI_do_updates(): DO NOTHING."
return
# NOTE: Changing the display styles of the protein chunks can take some
# time. We should put up the wait (hourglass) cursor here and restore
# before returning.
# Update all PM widgets that need to be since something has changed.
print "_update_UI_do_updates(): UPDATING the PMGR."
self.update_name_field()
self.sequenceEditor.update()
self.update_residue_combobox()
if self.previous_protein:
self.previous_protein.setDisplayStyle(self.previous_protein_display_style)
self.previous_protein = self.current_protein
if self.current_protein:
self.previous_protein_display_style = self.current_protein.getDisplayStyle()
self.current_protein.setDisplayStyle(diPROTEIN)
return
class LinearMotorPropertyManager(MotorPropertyManager):
"""
The LinearMotorProperty manager class provides UI and propMgr object for the
LinearMotor_EditCommand.
"""
# The title that appears in the Property Manager header.
title = "Linear Motor"
# 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/Simulation/LinearMotor.png"
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
MotorPropertyManager.connect_or_disconnect_signals(self, isConnect)
change_connect(self.directionPushButton,
SIGNAL("clicked()"),
self.reverse_direction)
change_connect(self.motorLengthDblSpinBox,
SIGNAL("valueChanged(double)"),
self.change_motor_size)
change_connect(self.motorWidthDblSpinBox,
SIGNAL("valueChanged(double)"),
self.change_motor_size)
change_connect(self.spokeRadiusDblSpinBox,
SIGNAL("valueChanged(double)"),
self.change_motor_size)
change_connect(self.motorColorComboBox,
SIGNAL("editingFinished()"),
self.change_jig_color)
return
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.
"""
if self.command and self.command.struct:
force = self.command.struct.force
stiffness = self.command.struct.stiffness
enable_minimize = self.command.struct.enable_minimize
length = self.command.struct.length
width = self.command.struct.width
spoke_radius = self.command.struct.sradius
normcolor = self.command.struct.normcolor
else:
force = 0.0
stiffness = 0.0
enable_minimize = False
length = 10
width = 1
spoke_radius = 0.2
normcolor = gray
self.forceDblSpinBox.setValue(force)
self.stiffnessDblSpinBox.setValue(stiffness)
self.enableMinimizeCheckBox.setChecked(enable_minimize)
self.motorLengthDblSpinBox.setValue(length)
self.motorWidthDblSpinBox.setValue(width)
self.spokeRadiusDblSpinBox.setValue(spoke_radius)
return
def change_motor_size(self, gl_update=True):
"""
Slot method to change the jig's length, width and/or spoke radius.
"""
self.command.struct.length = self.motorLengthDblSpinBox.value()
self.command.struct.width = self.motorWidthDblSpinBox.value()
# spoke radius --
self.command.struct.sradius = self.spokeRadiusDblSpinBox.value()
if gl_update:
self.glpane.gl_update()
return
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in MotorParamsGroupBox.
"""
if self.command and self.command.struct:
force = self.command.struct.force
stiffness = self.command.struct.stiffness
enable_minimize = self.command.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 _loadGroupBox2(self, pmGroupBox):
"""
Load widgets in groubox 2.
"""
if self.command and self.command.struct:
length = self.command.struct.length
width = self.command.struct.width
spoke_radius = self.command.struct.sradius
normcolor = self.command.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 _addWhatsThisText(self):
"""
What's This text for widgets in this Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_LinearMotorPropertyManager
whatsThis_LinearMotorPropertyManager(self)
return
def _addToolTipText(self):
"""
What's Tool Tip text for widgets in this Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_LinearMotorPropertyManager
ToolTip_LinearMotorPropertyManager(self)
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)
class Ui_BuildCrystal_PropertyManager(Command_PropertyManager):
"""
The Ui_BuildCrystal_PropertyManager class defines UI elements for the Property
Manager of the B{Crystal 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> - the title that appears in the property manager header.
title = "Build Crystal"
# <iconPath> - full path to PNG file that appears in the header.
# The name of this Property Manager. This will be set to
# the name of the PM_Dialog object via setObjectName().
pmName = title
iconPath = "ui/actions/Tools/Build Structures/Build Crystal.png"
def __init__(self, command):
"""
Constructor for the B{Crystal} property manager class that defines
its UI.
@param command: The parent mode where this Property Manager is used
@type command: L{BuildCrystal_Command}
"""
_superclass.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_CANCEL_BUTTON | \
PM_WHATS_THIS_BUTTON)
def _addGroupBoxes(self):
"""
Add various group boxes to the Property manager.
"""
self._addCrystalSpecsGroupbox()
self._addLayerPropertiesGroupBox()
self._addDisplayOptionsGroupBox()
self._addAdvancedOptionsGroupBox()
def _addCrystalSpecsGroupbox(self):
"""
Add 'Crystal groupbox' to the PM
"""
self.crystalSpecsGroupBox = \
PM_GroupBox(self, title = "Crystal Specifications")
self._loadCrystalSpecsGroupBox(self.crystalSpecsGroupBox)
def _addLayerPropertiesGroupBox(self):
"""
Add 'Layer Properties' groupbox to the PM
"""
self.layerPropertiesGroupBox = \
PM_GroupBox(self, title = "Layer Properties")
self._loadLayerPropertiesGroupBox(self.layerPropertiesGroupBox)
def _addAdvancedOptionsGroupBox(self):
"""
Add 'Advanced Options' groupbox
"""
self.advancedOptionsGroupBox = \
PM_GroupBox( self, title = "Advanced Options" )
self._loadAdvancedOptionsGroupBox(self.advancedOptionsGroupBox)
def _addDisplayOptionsGroupBox(self):
"""
Add 'Display Options' groupbox
"""
self.displayOptionsGroupBox = PM_GroupBox(self,
title = 'Display Options')
self._loadDisplayOptionsGroupBox(self.displayOptionsGroupBox)
def _loadCrystalSpecsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Crystal Specifications group box.
@param inPmGroupBox: The Crystal Specifications groupbox in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
latticeChoices = ["Diamond", "Lonsdaleite"]
self.latticeCBox = \
PM_ComboBox( inPmGroupBox,
label = 'Lattice:',
labelColumn = 0,
choices = latticeChoices,
index = 0,
setAsDefault = True,
spanWidth = False )
# Button list to create a toolbutton row.
# Format:
# - buttonType,
# - buttonId,
# - buttonText ,
# - iconPath
# - tooltip
# - shortcut
# - column
BUTTON_LIST = [
( "QToolButton", 0, "Surface 100",
"ui/actions/Properties Manager/Surface100.png",
"Surface 100", "", 0),
( "QToolButton", 1, "Surface 110",
"ui/actions/Properties Manager/Surface110.png",
"Surface 110", "", 1),
( "QToolButton", 2, "Surface 111",
"ui/actions/Properties Manager/Surface111.png",
"Surface 110", "", 2)
]
self.gridOrientationButtonRow = \
PM_ToolButtonRow(inPmGroupBox,
title = "",
label = "Orientation:",
buttonList = BUTTON_LIST,
checkedId = 0,
setAsDefault = True,
spanWidth = False
)
self.orientButtonGroup = self.gridOrientationButtonRow.buttonGroup
self.surface100_btn = self.gridOrientationButtonRow.getButtonById(0)
self.surface110_btn = self.gridOrientationButtonRow.getButtonById(1)
self.surface111_btn = self.gridOrientationButtonRow.getButtonById(2)
self.rotateGridByAngleSpinBox = \
PM_SpinBox( inPmGroupBox,
label = "Rotate by: ",
labelColumn = 0,
value = 45,
minimum = 0,
maximum = 360,
singleStep = 5,
suffix = " degrees")
GRID_ANGLE_BUTTONS = [
("QToolButton", 0, "Anticlockwise",
"ui/actions/Properties Manager/rotate_minus.png",
"", "+", 0 ),
( "QToolButton", 1, "Clockwise",
"ui/actions/Properties Manager/rotate_plus.png",
"", "-", 1 )
]
self.gridRotateButtonRow = \
PM_ToolButtonRow( inPmGroupBox,
title = "",
buttonList = GRID_ANGLE_BUTTONS,
label = 'Rotate grid:',
isAutoRaise = False,
isCheckable = False
)
self.rotGridAntiClockwiseButton = \
self.gridRotateButtonRow.getButtonById(0)
self.rotGridClockwiseButton = \
self.gridRotateButtonRow.getButtonById(1)
def _loadLayerPropertiesGroupBox(self, inPmGroupBox):
"""
Load widgets in the Layer Properties group box.
@param inPmGroupBox: The Layer Properties groupbox in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
self.currentLayerComboBox = \
PM_ComboBox( inPmGroupBox,
index = 0,
spanWidth = True
)
self.addLayerButton = PM_PushButton(inPmGroupBox)
self.addLayerButton.setIcon(
geticon('ui/actions/Properties Manager/addlayer.png'))
self.addLayerButton.setFixedSize(QSize(26, 26))
self.addLayerButton.setIconSize(QSize(22, 22))
# A widget list to create a widget row.
# Format:
# - Widget type,
# - widget object,
# - column
firstRowWidgetList = [('PM_ComboBox', self.currentLayerComboBox, 1),
('PM_PushButton', self.addLayerButton, 2)
]
widgetRow = PM_WidgetRow(inPmGroupBox,
title = '',
widgetList = firstRowWidgetList,
label = "Layer:",
labelColumn = 0,
)
self.layerCellsSpinBox = \
PM_SpinBox( inPmGroupBox,
label = "Lattice cells:",
labelColumn = 0,
value = 2,
minimum = 1,
maximum = 25
)
self.layerThicknessLineEdit = PM_LineEdit(inPmGroupBox,
label = "Thickness:",
text = "",
setAsDefault = False,
spanWidth = False )
#self.layerThicknessLineEdit.setReadOnly(True)
self.layerThicknessLineEdit.setDisabled(True)
tooltip = "Thickness of layer in Angstroms"
self.layerThicknessLineEdit.setToolTip(tooltip)
def _loadAdvancedOptionsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Advanced Options group box.
@param inPmGroupBox: The Advanced Options box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
self.snapGridCheckBox = \
PM_CheckBox(inPmGroupBox,
text = "Snap to grid",
state = Qt.Checked
)
tooltip = "Snap selection point to a nearest cell grid point."
self.snapGridCheckBox.setToolTip(tooltip)
self.freeViewCheckBox = \
PM_CheckBox(inPmGroupBox,
text = "Enable free view",
state = Qt.Unchecked
)
def _loadDisplayOptionsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Display Options groupbox.
@param inPmGroupBox: The Display Options groupbox
@type inPmGroupBox: L{PM_GroupBox}
"""
displayChoices = ['Tubes', 'Spheres']
self.dispModeComboBox = \
PM_ComboBox( inPmGroupBox,
label = 'Display style:',
choices = displayChoices,
index = 0,
setAsDefault = False,
spanWidth = False )
self.gridLineCheckBox = PM_CheckBox(inPmGroupBox,
text = "Show grid lines",
widgetColumn = 0,
state = Qt.Checked)
self.fullModelCheckBox = PM_CheckBox(inPmGroupBox,
text = "Show model",
widgetColumn = 0,
state = Qt.Unchecked)
def _addWhatsThisText(self):
"""
What's This text for 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_CookiePropertyManager
whatsThis_CookiePropertyManager(self)
def _addToolTipText(self):
"""
What's Tool Tip text for widgets in this Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_CookiePropertyManager
ToolTip_CookiePropertyManager(self)
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 TestGraphics_PropertyManager(Command_PropertyManager):
"""
The TestGraphics_PropertyManager class provides a Property Manager
for the Test Graphics 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 = "Test Graphics"
pmName = title
iconPath = None ###k "ui/actions/View/Stereo_View.png" ### FIX - use some generic or default icon
def __init__( self, command ):
"""
Constructor for the property manager.
"""
_superclass.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON |
PM_WHATS_THIS_BUTTON)
msg = "Test the performance effect of graphics settings below. " \
"(To avoid bugs, choose testCase before bypassing paintGL.)"
self.updateMessage(msg)
def _addGroupBoxes( self ):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self,
title = "Settings") ### fix title
self._loadGroupBox1( self._pmGroupBox1 )
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
from widgets.prefs_widgets import ObjAttr_StateRef ### toplevel
self._cb2 = \
PM_CheckBox(pmGroupBox,
text = "redraw continuously",
)
self._cb2.connectWithState( ObjAttr_StateRef( self.command, 'redraw_continuously' ))
self._cb3 = \
PM_CheckBox(pmGroupBox,
text = "spin model",
)
self._cb3.connectWithState( ObjAttr_StateRef( self.command, 'spin_model' ))
self._cb4 = \
PM_CheckBox(pmGroupBox,
text = "print fps to console",
)
self._cb4.connectWithState( ObjAttr_StateRef( self.command, 'print_fps' ))
self._cb1 = \
PM_CheckBox(pmGroupBox,
text = "replace paintGL with testCase",
)
self._cb1.connectWithState( ObjAttr_StateRef( self.command, 'bypass_paintgl' ))
# note: this state (unlike the highest-quality staterefs)
# is not change-tracked [as of 081003], so nothing aside from
# user clicks on this checkbox should modify it after this runs,
# or our UI state will become out of sync with the state.
self.testCase_ComboBox = PM_ComboBox(pmGroupBox,
label = "testCase:", labelColumn = 0,
choices = self.command.testCaseChoicesText,
setAsDefault = False )
self.testCase_ComboBox.setCurrentIndex(self.command.testCaseIndex)
self.nSpheres_ComboBox = PM_ComboBox(pmGroupBox,
label = "n x n spheres:", labelColumn = 0,
choices = self.command._NSPHERES_CHOICES,
setAsDefault = False )
nSpheres_index = self.command._NSPHERES_CHOICES.index( str( self.command.nSpheres) )
self.nSpheres_ComboBox.setCurrentIndex( nSpheres_index)
self._set_nSpheresIndex( nSpheres_index)
self.detail_level_ComboBox = PM_ComboBox(pmGroupBox,
label = "Level of detail:", labelColumn = 0,
choices = ["Low", "Medium", "High", "Variable"],
setAsDefault = False )
lod = env.prefs[levelOfDetail_prefs_key]
if lod > 2:
lod = 2
if lod < 0: # only lod == -1 is legal here
lod = 3
self.detail_level_ComboBox.setCurrentIndex(lod)
self.set_level_of_detail_index(lod)
self._updateWidgets()
## def updateUI(self): # BUG: this is not being called -- I guess the bypassed paintGL doesn't call it.
## self._updateWidgets() ### will this be too slow?
def _addWhatsThisText( self ):
"""
What's This text for widgets in the Stereo Property Manager.
"""
pass
def _addToolTipText(self):
"""
Tool Tip text for widgets in the Stereo Property Manager.
"""
pass
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.testCase_ComboBox,
SIGNAL("currentIndexChanged(int)"),
self.command._set_testCaseIndex )
change_connect(self.nSpheres_ComboBox,
SIGNAL("currentIndexChanged(int)"),
self._set_nSpheresIndex )
change_connect(self.detail_level_ComboBox,
SIGNAL("currentIndexChanged(int)"),
# in current code, SIGNAL("activated(int)")
self.set_level_of_detail_index )
return
# ==
def _set_nSpheresIndex(self, index):
self.command.nSpheres = int( self.command._NSPHERES_CHOICES[index] )
def set_level_of_detail_index(self, level_of_detail_index): # copied from other code, renamed, revised
"""
Change the level of detail, where <level_of_detail_index> is a value
between 0 and 3 where:
- 0 = low
- 1 = medium
- 2 = high
- 3 = variable (based on number of atoms in the part)
@note: the prefs db value for 'variable' is -1, to allow for higher LOD
levels in the future.
"""
lod = level_of_detail_index
if lod == 3:
lod = -1
self.command.detailLevel = lod
def _updateWidgets(self):
"""
Update widget configuration based on state of prior widgets.
"""
## # presently, the LOD is not noticed by the test cases... oops, not true!
## self.detail_level_ComboBox.setEnabled( not self.command.bypass_paintgl )
return
pass
class FixedBBProteinSim_PropertyManager(Command_PropertyManager):
"""
The FixedBBProteinSim_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 = "Fixed Backbone Design"
pmName = title
iconPath = "ui/actions/Command Toolbar/BuildProtein/FixedBackbone.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 from the various options below to design "\
"an optimized <b>fixed backbone protein sequence</b> with Rosetta."
self.updateMessage(msg)
return
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.runRosettaFixedBBSim)
return
#Protein Display methods
def show(self):
"""
Shows the Property Manager.
"""
#@REVIEW: Why does it create sequence editor here? Also, is it
#required to be done before the superclass.show call? Similar code
#found in CompareProteins_PM and some other files --Ninad 2008-10-02
self.sequenceEditor = self.win.createProteinSequenceEditorIfNeeded()
self.sequenceEditor.hide()
_superclass.show(self)
return
def _addGroupBoxes( self ):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self,
title = "Rosetta Fixed backbone sequence design")
self._loadGroupBox1( self._pmGroupBox1 )
return
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.numSimSpinBox = PM_SpinBox( pmGroupBox,
labelColumn = 0,
label = "Number of simulations:",
minimum = 1,
maximum = 999,
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 = "Launch Rosetta",
setAsDefault = True,
spanWidth = True)
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 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 runRosettaFixedBBSim(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>Fixed Backbone</i> simulation."
self.updateMessage(msg)
return
otherOptionsText = str(self.otherCommandLineOptions.toPlainText())
numSim = self.numSimSpinBox.value()
argList = [numSim, otherOptionsText, proteinChunk.name]
from simulation.ROSETTA.rosetta_commandruns import rosettaSetup_CommandRun
if argList[0] > 0:
cmdrun = rosettaSetup_CommandRun(self.win, argList, "ROSETTA_FIXED_BACKBONE_SEQUENCE_DESIGN")
cmdrun.run()
return
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
self.numSimSpinBox = PM_SpinBox( pmGroupBox,
labelColumn = 0,
label = "Number of simulations:",
minimum = 1,
maximum = 999,
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 = "Launch Rosetta",
setAsDefault = True,
spanWidth = True)
return
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 Ui_BuildAtomsPropertyManager(Command_PropertyManager):
"""
The Ui_BuildAtomsPropertyManager class defines UI elements for the Property
Manager of the B{Build Atoms mode}.
@ivar title: The title that appears in the property manager header.
@type title: str
@ivar pmName: The name of this property manager. This is used to set
the name of the PM_Dialog object via setObjectName().
@type name: str
@ivar iconPath: The relative path to the PNG file that contains a
22 x 22 icon image that appears in the PM header.
@type iconPath: str
"""
# The title that appears in the Property Manager header
title = "Build Atoms"
# The name of this Property Manager. This will be set to
# the name of the PM_Dialog object via setObjectName().
pmName = title
# The relative path to the PNG file that appears in the header
iconPath = "ui/actions/Tools/Build Structures/BuildAtoms.png"
def __init__(self, command):
"""
Constructor for the B{Build Atoms} property manager class that defines
its UI.
@param command: The parent mode where this Property Manager is used
@type command: L{depositMode}
"""
self.previewGroupBox = None
self.regularElementChooser = None
self.PAM5Chooser = None
self.PAM3Chooser = None
self.elementChooser = None
self.advancedOptionsGroupBox = None
self.bondToolsGroupBox = None
self.selectionFilterCheckBox = None
self.filterlistLE = None
self.selectedAtomInfoLabel = None
#Initialize the following to None. (subclasses may not define this)
#Make sure you initialize it before adding groupboxes!
self.selectedAtomPosGroupBox = None
self.showSelectedAtomInfoCheckBox = None
_superclass.__init__(self, command)
self.showTopRowButtons(PM_DONE_BUTTON | PM_WHATS_THIS_BUTTON)
msg = ''
self.MessageGroupBox.insertHtmlMessage(msg, setAsDefault=False)
def _addGroupBoxes(self):
"""
Add various group boxes to the Build Atoms Property manager.
"""
self._addPreviewGroupBox()
self._addAtomChooserGroupBox()
self._addBondToolsGroupBox()
#@@@TODO HIDE the bonds tool groupbox initially as the
#by default, the atoms tool is active when BuildAtoms command is
#finist invoked.
self.bondToolsGroupBox.hide()
self._addSelectionOptionsGroupBox()
self._addAdvancedOptionsGroupBox()
def _addPreviewGroupBox(self):
"""
Adde the preview groupbox that shows the element selected in the
element chooser.
"""
self.previewGroupBox = PM_PreviewGroupBox( self, glpane = self.o )
def _addAtomChooserGroupBox(self):
"""
Add the Atom Chooser groupbox. This groupbox displays one of the
following three groupboxes depending on the choice selected in the
combobox:
a) Periodic Table Elements L{self.regularElementChooser}
b) PAM5 Atoms L{self.PAM5Chooser}
c) PAM3 Atoms L{self.PAM3Chooser}
@see: L{self.__updateAtomChooserGroupBoxes}
"""
self.atomChooserGroupBox = \
PM_GroupBox(self, title = "Atom Chooser")
self._loadAtomChooserGroupBox(self.atomChooserGroupBox)
self._updateAtomChooserGroupBoxes(currentIndex = 0)
def _addElementChooserGroupBox(self, inPmGroupBox):
"""
Add the 'Element Chooser' groupbox. (present within the
Atom Chooser Groupbox)
"""
if not self.previewGroupBox:
return
elementViewer = self.previewGroupBox.elementViewer
self.regularElementChooser = \
PM_ElementChooser( inPmGroupBox,
parentPropMgr = self,
elementViewer = elementViewer)
def _add_PAM5_AtomChooserGroupBox(self, inPmGroupBox):
"""
Add the 'PAM5 Atom Chooser' groupbox (present within the
Atom Chooser Groupbox)
"""
if not self.previewGroupBox:
return
elementViewer = self.previewGroupBox.elementViewer
self.PAM5Chooser = \
PM_PAM5_AtomChooser( inPmGroupBox,
parentPropMgr = self,
elementViewer = elementViewer)
def _add_PAM3_AtomChooserGroupBox(self, inPmGroupBox):
"""
Add the 'PAM3 Atom Chooser' groupbox (present within the
Atom Chooser Groupbox)
"""
if not self.previewGroupBox:
return
elementViewer = self.previewGroupBox.elementViewer
self.PAM3Chooser = \
PM_PAM3_AtomChooser( inPmGroupBox,
parentPropMgr = self,
elementViewer = elementViewer)
def _hideAllAtomChooserGroupBoxes(self):
"""
Hides all Atom Chooser group boxes.
"""
if self.regularElementChooser:
self.regularElementChooser.hide()
if self.PAM5Chooser:
self.PAM5Chooser.hide()
if self.PAM3Chooser:
self.PAM3Chooser.hide()
def _addBondToolsGroupBox(self):
"""
Add the 'Bond Tools' groupbox.
"""
self.bondToolsGroupBox = \
PM_GroupBox( self, title = "Bond Tools")
self._loadBondToolsGroupBox(self.bondToolsGroupBox)
def _addSelectionOptionsGroupBox(self):
"""
Add 'Selection Options' groupbox
"""
self.selectionOptionsGroupBox = \
PM_GroupBox( self, title = "Selection Options" )
self._loadSelectionOptionsGroupBox(self.selectionOptionsGroupBox)
def _loadAtomChooserGroupBox(self, inPmGroupBox):
"""
Load the widgets inside the Atom Chooser groupbox.
@param inPmGroupBox: The Atom Chooser box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
atomChooserChoices = [ "Periodic Table Elements",
"PAM5 Atoms",
"PAM3 Atoms" ]
self.atomChooserComboBox = \
PM_ComboBox( inPmGroupBox,
label = '',
choices = atomChooserChoices,
index = 0,
setAsDefault = False,
spanWidth = True )
#Following fixes bug 2550
self.atomChooserComboBox.setFocusPolicy(Qt.NoFocus)
self._addElementChooserGroupBox(inPmGroupBox)
self._add_PAM5_AtomChooserGroupBox(inPmGroupBox)
self._add_PAM3_AtomChooserGroupBox(inPmGroupBox)
def _loadSelectionOptionsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Selection Options group box.
@param inPmGroupBox: The Selection Options box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
self.selectionFilterCheckBox = \
PM_CheckBox( inPmGroupBox,
text = "Enable atom selection filter",
widgetColumn = 0,
state = Qt.Unchecked )
self.selectionFilterCheckBox.setDefaultValue(False)
self.filterlistLE = PM_LineEdit( inPmGroupBox,
label = "",
text = "",
setAsDefault = False,
spanWidth = True )
self.filterlistLE.setReadOnly(True)
if self.selectionFilterCheckBox.isChecked():
self.filterlistLE.setEnabled(True)
else:
self.filterlistLE.setEnabled(False)
self.showSelectedAtomInfoCheckBox = \
PM_CheckBox(
inPmGroupBox,
text = "Show Selected Atom Info",
widgetColumn = 0,
state = Qt.Unchecked)
self.selectedAtomPosGroupBox = \
PM_GroupBox( inPmGroupBox, title = "")
self._loadSelectedAtomPosGroupBox(self.selectedAtomPosGroupBox)
self.toggle_selectedAtomPosGroupBox(show = 0)
self.enable_or_disable_selectedAtomPosGroupBox( bool_enable = False)
self.reshapeSelectionCheckBox = \
PM_CheckBox( inPmGroupBox,
text = 'Dragging reshapes selection',
widgetColumn = 0,
state = Qt.Unchecked )
connect_checkbox_with_boolean_pref( self.reshapeSelectionCheckBox,
reshapeAtomsSelection_prefs_key )
env.prefs[reshapeAtomsSelection_prefs_key] = False
self.waterCheckBox = \
PM_CheckBox( inPmGroupBox,
text = "Z depth filter (water surface)",
widgetColumn = 0,
state = Qt.Unchecked )
def _loadSelectedAtomPosGroupBox(self, inPmGroupBox):
"""
Load the selected Atoms position groupbox It is a sub-gropbox of
L{self.selectionOptionsGroupBox)
@param inPmGroupBox: 'The Selected Atom Position Groupbox'
@type inPmGroupBox: L{PM_GroupBox}
"""
self.selectedAtomLineEdit = PM_LineEdit( inPmGroupBox,
label = "Selected Atom:",
text = "",
setAsDefault = False,
spanWidth = False )
self.selectedAtomLineEdit.setReadOnly(True)
self.selectedAtomLineEdit.setEnabled(False)
self.coordinateSpinboxes = PM_CoordinateSpinBoxes(inPmGroupBox)
# User input to specify x-coordinate
self.xCoordOfSelectedAtom = self.coordinateSpinboxes.xSpinBox
# User input to specify y-coordinate
self.yCoordOfSelectedAtom = self.coordinateSpinboxes.ySpinBox
# User input to specify z-coordinate
self.zCoordOfSelectedAtom = self.coordinateSpinboxes.zSpinBox
def _addAdvancedOptionsGroupBox(self):
"""
Add 'Advanced Options' groupbox
"""
self.advancedOptionsGroupBox = \
PM_GroupBox( self, title = "Advanced Options" )
self._loadAdvancedOptionsGroupBox(self.advancedOptionsGroupBox)
def _loadAdvancedOptionsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Advanced Options group box.
@param inPmGroupBox: The Advanced Options box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
self.autoBondCheckBox = \
PM_CheckBox( inPmGroupBox,
text = 'Auto bond',
widgetColumn = 0,
state = Qt.Checked )
self.highlightingCheckBox = \
PM_CheckBox( inPmGroupBox,
text = "Hover highlighting",
widgetColumn = 0,
state = Qt.Checked )
def _loadBondToolsGroupBox(self, inPmGroupBox):
"""
Load widgets in the Bond Tools group box.
@param inPmGroupBox: The Bond Tools box in the PM
@type inPmGroupBox: L{PM_GroupBox}
"""
# Button list to create a toolbutton row.
# Format:
# - buttonId,
# - buttonText ,
# - iconPath
# - tooltip
# - shortcut
# - column
BOND_TOOL_BUTTONS = \
[ ( "QToolButton", 0, "SINGLE", "", "", None, 0),
( "QToolButton", 1, "DOUBLE", "", "", None, 1),
( "QToolButton", 2, "TRIPLE", "", "", None, 2),
( "QToolButton", 3, "AROMATIC", "", "", None, 3),
( "QToolButton", 4, "GRAPHITIC", "", "", None, 4),
( "QToolButton", 5, "CUTBONDS", "", "", None, 5)
]
self.bondToolButtonRow = \
PM_ToolButtonRow(
inPmGroupBox,
title = "",
buttonList = BOND_TOOL_BUTTONS,
checkedId = None,
setAsDefault = True )
def _addWhatsThisText(self):
"""
"What's This" text for widgets in this Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_BuildAtomsPropertyManager
whatsThis_BuildAtomsPropertyManager(self)
def _addToolTipText(self):
"""
Tool Tip text for widgets in this Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_BuildAtomsPropertyManager
ToolTip_BuildAtomsPropertyManager(self)
def toggle_selectedAtomPosGroupBox(self, show = 0):
"""
Show or hide L{self.selectedAtomPosGroupBox} depending on the state of
the checkbox (L{self.showSelectedAtomInfoCheckBox})
@param show: Flag that shows or hides the groupbox (can have values
0 or 1
@type show: int
"""
if show:
self.selectedAtomPosGroupBox.show()
else:
self.selectedAtomPosGroupBox.hide()
def enable_or_disable_selectedAtomPosGroupBox(self, bool_enable = False):
"""
Enable or disable Selected AtomPosGroupBox present within
'selection options' and also the checkbox that shows or hide this
groupbox. These two widgets are enabled when only a single atom is
selected from the 3D workspace.
@param bool_enable: Flag that enables or disables widgets
@type bool_enable: boolean
"""
if self.showSelectedAtomInfoCheckBox:
self.showSelectedAtomInfoCheckBox.setEnabled(bool_enable)
if self.selectedAtomPosGroupBox:
self.selectedAtomPosGroupBox.setEnabled(bool_enable)
def _updateAtomChooserGroupBoxes(self, currentIndex):
"""
Updates the Atom Chooser Groupbox. It displays one of the
following three groupboxes depending on the choice selected in the
combobox:
a) Periodic Table Elements L{self.regularElementChooser}
b) PAM5 Atoms L{self.PAM5Chooser}
c) PAM3 Atoms L{self.PAM3Chooser}
It also sets self.elementChooser to the current active Atom chooser
and updates the display accordingly in the Preview groupbox.
"""
self._hideAllAtomChooserGroupBoxes()
if currentIndex is 0:
self.elementChooser = self.regularElementChooser
self.regularElementChooser.show()
if currentIndex is 1:
self.elementChooser = self.PAM5Chooser
self.PAM5Chooser.show()
if currentIndex is 2:
self.elementChooser = self.PAM3Chooser
self.PAM3Chooser.show()
if self.elementChooser:
self.elementChooser.updateElementViewer()
self.updateMessage()
def updateMessage(self):
"""
Update the Message groupbox with informative message.
Subclasses should override this.
"""
pass
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
from widgets.prefs_widgets import ObjAttr_StateRef ### toplevel
self._cb2 = \
PM_CheckBox(pmGroupBox,
text = "redraw continuously",
)
self._cb2.connectWithState( ObjAttr_StateRef( self.command, 'redraw_continuously' ))
self._cb3 = \
PM_CheckBox(pmGroupBox,
text = "spin model",
)
self._cb3.connectWithState( ObjAttr_StateRef( self.command, 'spin_model' ))
self._cb4 = \
PM_CheckBox(pmGroupBox,
text = "print fps to console",
)
self._cb4.connectWithState( ObjAttr_StateRef( self.command, 'print_fps' ))
self._cb1 = \
PM_CheckBox(pmGroupBox,
text = "replace paintGL with testCase",
)
self._cb1.connectWithState( ObjAttr_StateRef( self.command, 'bypass_paintgl' ))
# note: this state (unlike the highest-quality staterefs)
# is not change-tracked [as of 081003], so nothing aside from
# user clicks on this checkbox should modify it after this runs,
# or our UI state will become out of sync with the state.
self.testCase_ComboBox = PM_ComboBox(pmGroupBox,
label = "testCase:", labelColumn = 0,
choices = self.command.testCaseChoicesText,
setAsDefault = False )
self.testCase_ComboBox.setCurrentIndex(self.command.testCaseIndex)
self.nSpheres_ComboBox = PM_ComboBox(pmGroupBox,
label = "n x n spheres:", labelColumn = 0,
choices = self.command._NSPHERES_CHOICES,
setAsDefault = False )
nSpheres_index = self.command._NSPHERES_CHOICES.index( str( self.command.nSpheres) )
self.nSpheres_ComboBox.setCurrentIndex( nSpheres_index)
self._set_nSpheresIndex( nSpheres_index)
self.detail_level_ComboBox = PM_ComboBox(pmGroupBox,
label = "Level of detail:", labelColumn = 0,
choices = ["Low", "Medium", "High", "Variable"],
setAsDefault = False )
lod = env.prefs[levelOfDetail_prefs_key]
if lod > 2:
lod = 2
if lod < 0: # only lod == -1 is legal here
lod = 3
self.detail_level_ComboBox.setCurrentIndex(lod)
self.set_level_of_detail_index(lod)
self._updateWidgets()
class StereoProperties_PropertyManager(Command_PropertyManager):
"""
The StereoProperties_PropertyManager class provides a Property Manager
for the Stereo View 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 = "Stereo View"
pmName = title
iconPath = "ui/actions/View/Stereo_View.png"
def __init__( self, command ):
"""
Constructor for the property manager.
"""
_superclass.__init__(self, command)
self.showTopRowButtons( PM_DONE_BUTTON | \
PM_WHATS_THIS_BUTTON)
msg = "Modify the Stereo View 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
change_connect(self.stereoEnabledCheckBox,
SIGNAL("toggled(bool)"),
self._enableStereo )
change_connect( self.stereoModeComboBox,
SIGNAL("currentIndexChanged(int)"),
self._stereoModeComboBoxChanged )
change_connect(self.stereoSeparationSlider,
SIGNAL("valueChanged(int)"),
self._stereoModeSeparationSliderChanged )
change_connect(self.stereoAngleSlider,
SIGNAL("valueChanged(int)"),
self._stereoModeAngleSliderChanged )
def _addGroupBoxes( self ):
"""
Add the Property Manager group boxes.
"""
self._pmGroupBox1 = PM_GroupBox( self,
title = "Settings")
self._loadGroupBox1( self._pmGroupBox1 )
#@ self._pmGroupBox1.hide()
def _loadGroupBox1(self, pmGroupBox):
"""
Load widgets in group box.
"""
#stereoSettingsGroupBox = PM_GroupBox( None )
self.stereoEnabledCheckBox = \
PM_CheckBox(pmGroupBox,
text = 'Enable Stereo View',
widgetColumn = 1
)
stereoModeChoices = ['Relaxed view',
'Cross-eyed view',
'Red/blue anaglyphs',
'Red/cyan anaglyphs',
'Red/green anaglyphs']
self.stereoModeComboBox = \
PM_ComboBox( pmGroupBox,
label = "Stereo Mode:",
choices = stereoModeChoices,
setAsDefault = True)
self.stereoModeComboBox.setCurrentIndex(env.prefs[stereoViewMode_prefs_key]-1)
self.stereoSeparationSlider = \
PM_Slider( pmGroupBox,
currentValue = 50,
minimum = 0,
maximum = 300,
label = 'Separation'
)
self.stereoSeparationSlider.setValue(env.prefs[stereoViewSeparation_prefs_key])
self.stereoAngleSlider = \
PM_Slider( pmGroupBox,
currentValue = 50,
minimum = 0,
maximum = 100,
label = 'Angle'
)
self.stereoAngleSlider.setValue(env.prefs[stereoViewAngle_prefs_key])
self._updateWidgets()
def _addWhatsThisText( self ):
"""
What's This text for widgets in the Stereo Property Manager.
"""
pass
def _addToolTipText(self):
"""
Tool Tip text for widgets in the Stereo Property Manager.
"""
pass
def _enableStereo(self, enabled):
"""
Enable stereo view.
"""
glpane = self.o
if glpane:
glpane.set_stereo_enabled( enabled)
# switch to perspective mode
if enabled:
# store current projection mode
glpane.__StereoProperties_last_ortho = glpane.ortho
if glpane.ortho:
# dont use glpane.setViewProjection
# because we don't want to modify
# default projection setting
glpane.ortho = 0
else:
# restore default mode
if hasattr(glpane, "__StereoProperties_last_ortho"):
projection = glpane.__StereoProperties_last_ortho
if glpane.ortho != projection:
glpane.ortho = projection
self._updateWidgets()
glpane.gl_update()
def _stereoModeComboBoxChanged(self, mode):
"""
Change stereo mode.
@param mode: stereo mode (0=relaxed, 1=cross-eyed, 2=red/blue,
3=red/cyan, 4=red/green)
@type value: int
"""
env.prefs[stereoViewMode_prefs_key] = mode + 1
self._updateSeparationSlider()
def _stereoModeSeparationSliderChanged(self, value):
"""
Change stereo view separation.
@param value: separation (0..300)
@type value: int
"""
env.prefs[stereoViewSeparation_prefs_key] = value
def _stereoModeAngleSliderChanged(self, value):
"""
Change stereo view angle.
@param value: stereo angle (0..100)
@type value: int
"""
env.prefs[stereoViewAngle_prefs_key] = value
def _updateSeparationSlider(self):
"""
Update the separation slider widget.
"""
if self.stereoModeComboBox.currentIndex() >= 2:
# for anaglyphs disable the separation slider
self.stereoSeparationSlider.setEnabled(False)
else:
# otherwise, enable the separation slider
self.stereoSeparationSlider.setEnabled(True)
def _updateWidgets(self):
"""
Update stereo PM widgets.
"""
if self.stereoEnabledCheckBox.isChecked():
self.stereoModeComboBox.setEnabled(True)
self.stereoSeparationSlider.setEnabled(True)
self.stereoAngleSlider.setEnabled(True)
self._updateSeparationSlider()
else:
self.stereoModeComboBox.setEnabled(False)
self.stereoSeparationSlider.setEnabled(False)
self.stereoAngleSlider.setEnabled(False)
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)