class PeptideGeneratorPropertyManager(PM_Dialog):
"""
The PeptideGeneratorPropertyManager class provides a Property Manager
for the "Build > Peptide" command.
"""
# The title that appears in the property manager header.
title = "Peptide Generator"
# The name of this property manager. This will be set to
# the name of the PropMgr (this) object via setObjectName().
pmName = title
# The relative path to PNG file that appears in the header.
iconPath = "ui/actions/Tools/Build Structures/Peptide.png"
def __init__(self):
"""Construct the Peptide Property Manager.
"""
PM_Dialog.__init__(self, self.pmName, self.iconPath, self.title)
# phi psi angles will define the secondary structure of the peptide chain
self.phi = -57.0
self.psi = -47.0
self.chirality = 1
self.ss_idx = 1
self.peptide_cache = []
self.updateMessageGroupBox()
def updateMessageGroupBox(self):
msg = ""
msg = msg + "Click on the Amino Acid buttons to add a new residuum to\
the polypeptide chain. Click <b>Done</b> to insert it into the project."
# This causes the "Message" box to be displayed as well.
# setAsDefault=True causes this message to be reset whenever
# this PropMgr is (re)displayed via show(). Mark 2007-06-01.
self.MessageGroupBox.insertHtmlMessage(msg, setAsDefault=True)
def _addGroupBoxes(self):
"""
Add the group boxe to the Peptide Property Manager dialog.
"""
self.pmGroupBox1 = \
PM_GroupBox( self,
title = "Peptide Parameters" )
# Add group box widgets.
self._loadGroupBox1(self.pmGroupBox1)
def _loadGroupBox1(self, inPmGroupBox):
"""
Load widgets in the group box.
"""
memberChoices = ["Custom",
"Alpha helix",
"Beta strand",
"Pi helix",
"3_10 helix",
"Polyproline-II helix",
"Fully extended"]
self.aaTypeComboBox= \
PM_ComboBox( inPmGroupBox,
label = "Conformation :",
choices = memberChoices,
index = 1,
setAsDefault = True,
spanWidth = False )
self.connect( self.aaTypeComboBox,
SIGNAL("currentIndexChanged(int)"),
self._aaTypeChanged)
self.phiAngleField = \
PM_DoubleSpinBox( inPmGroupBox,
label = "Phi angle :",
value = -57.0,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
singleStep = 1.0,
decimals = 1,
suffix = " degrees")
self.connect( self.phiAngleField,
SIGNAL("valueChanged(double)"),
self._aaPhiAngleChanged)
self.phiAngleField.setEnabled(False)
self.psiAngleField = \
PM_DoubleSpinBox( inPmGroupBox,
label = "Psi angle :",
value = -47.0,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
singleStep = 1.0,
decimals = 1,
suffix = " degrees" )
self.connect( self.psiAngleField,
SIGNAL("valueChanged(double)"),
self._aaPsiAngleChanged)
self.psiAngleField.setEnabled(False)
self.invertChiralityPushButton = \
PM_PushButton( inPmGroupBox,
text = 'Invert chirality' ,
spanWidth = False
)
self.connect(self.invertChiralityPushButton,
SIGNAL("clicked()"),
self._aaChiralityChanged)
self.aaTypesButtonGroup = \
PM_ToolButtonGrid( inPmGroupBox,
buttonList = AA_BUTTON_LIST,
label = "Amino acids :",
checkedId = 0,
setAsDefault = True )
self.connect( self.aaTypesButtonGroup.buttonGroup,
SIGNAL("buttonClicked(int)"),
self._setAminoAcidType)
self.sequenceEditor = \
PM_TextEdit( inPmGroupBox,
label = "Sequence",
spanWidth = True )
self.sequenceEditor.insertHtml("", False, 4, 10, True)
self.sequenceEditor.setReadOnly(True)
self.startOverButton = \
PM_PushButton( inPmGroupBox,
label = "",
text = "Start Over",
spanWidth = True,
setAsDefault = True )
self.connect( self.startOverButton,
SIGNAL("clicked()"),
self._startOverClicked)
def _addWhatsThisText(self):
"""
What's This text for widgets in this Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_PeptideGeneratorPropertyManager
whatsThis_PeptideGeneratorPropertyManager(self)
def _addToolTipText(self):
"""
Tool Tip text for widgets in this Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_PeptideGeneratorPropertyManager
ToolTip_PeptideGeneratorPropertyManager(self)
def _aaChiralityChanged(self):
"""
Set chirality of the peptide chain.
"""
self.psi *= -1
self.phi *= -1
self.phiAngleField.setValue(self.phi)
self.psiAngleField.setValue(self.psi)
def _aaTypeChanged(self, idx):
"""
Slot for Peptide Structure Type combobox.
Changes phi/psi angles for secondary structure.
"""
self.ss_idx = idx
if idx == 0:
self.phiAngleField.setEnabled(True)
self.psiAngleField.setEnabled(True)
else:
self.phiAngleField.setEnabled(False)
self.psiAngleField.setEnabled(False)
if idx == 1: # alpha helix
self.phi = -57.0
self.psi = -47.0
elif idx == 2: # beta strand
self.phi = -135.0
self.psi = 135.0
elif idx == 3: # 3-10 helix
self.phi = -55.0
self.psi = -70.0
elif idx == 4: # pi helix
self.phi = -49.0
self.psi = -26.0
elif idx == 5: # polyprolin-II
self.phi = -75.0
self.psi = 150.0
elif idx == 6: # fully extended
self.phi = -180.0
self.psi = 180.0
else:
self.phi = self.phiAngleField.value()
self.psi = self.psiAngleField.value()
self.phi *= self.chirality
self.psi *= self.chirality
self.phiAngleField.setValue(self.phi)
self.psiAngleField.setValue(self.psi)
pass
def _aaPhiAngleChanged(self, phi):
self.phi = self.phiAngleField.value()
pass
def _aaPsiAngleChanged(self, psi):
self.psi = self.psiAngleField.value()
pass
def _setAminoAcidType(self, aaTypeIndex):
"""
Adds a new amino acid to the peptide molecule.
"""
button, idx, short_name, dum, name, symbol, x, y = AA_BUTTON_LIST[aaTypeIndex]
if self.ss_idx==1:
aa_txt = "<font color=red>"
elif self.ss_idx==2:
aa_txt = "<font color=blue>"
elif self.ss_idx==3:
aa_txt = "<font color=green>"
elif self.ss_idx==4:
aa_txt = "<font color=orange>"
elif self.ss_idx==5:
aa_txt = "<font color=magenta>"
elif self.ss_idx==6:
aa_txt = "<font color=darkblue>"
else:
aa_txt = "<font color=black>"
aa_txt += symbol+"</font>"
self.sequenceEditor.insertHtml(aa_txt, False, 4, 10, False)
self.addAminoAcid(aaTypeIndex)
pass
def _startOverClicked(self):
"""
Resets a sequence in the sequence editor window.
"""
self.sequenceEditor.clear()
self.peptide_cache = []
pass
class PeptideGeneratorPropertyManager(PM_Dialog):
"""
The PeptideGeneratorPropertyManager class provides a Property Manager
for the "Build > Peptide" command.
"""
# The title that appears in the property manager header.
title = "Peptide Generator"
# The name of this property manager. This will be set to
# the name of the PropMgr (this) object via setObjectName().
pmName = title
# The relative path to PNG file that appears in the header.
iconPath = "ui/actions/Tools/Build Structures/Peptide.png"
def __init__(self):
"""Construct the Peptide Property Manager.
"""
PM_Dialog.__init__(self, self.pmName, self.iconPath, self.title)
# phi psi angles will define the secondary structure of the peptide chain
self.phi = -57.0
self.psi = -47.0
self.chirality = 1
self.ss_idx = 1
self.peptide_cache = []
self.updateMessageGroupBox()
def updateMessageGroupBox(self):
msg = ""
msg = msg + "Click on the Amino Acid buttons to add a new residuum to\
the polypeptide chain. Click <b>Done</b> to insert it into the project."
# This causes the "Message" box to be displayed as well.
# setAsDefault=True causes this message to be reset whenever
# this PropMgr is (re)displayed via show(). Mark 2007-06-01.
self.MessageGroupBox.insertHtmlMessage(msg, setAsDefault=True)
def _addGroupBoxes(self):
"""
Add the group boxe to the Peptide Property Manager dialog.
"""
self.pmGroupBox1 = \
PM_GroupBox( self,
title = "Peptide Parameters" )
# Add group box widgets.
self._loadGroupBox1(self.pmGroupBox1)
def _loadGroupBox1(self, inPmGroupBox):
"""
Load widgets in the group box.
"""
memberChoices = [
"Custom", "Alpha helix", "Beta strand", "Pi helix", "3_10 helix",
"Polyproline-II helix", "Fully extended"
]
self.aaTypeComboBox= \
PM_ComboBox( inPmGroupBox,
label = "Conformation :",
choices = memberChoices,
index = 1,
setAsDefault = True,
spanWidth = False )
self.connect(self.aaTypeComboBox, SIGNAL("currentIndexChanged(int)"),
self._aaTypeChanged)
self.phiAngleField = \
PM_DoubleSpinBox( inPmGroupBox,
label = "Phi angle :",
value = -57.0,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
singleStep = 1.0,
decimals = 1,
suffix = " degrees")
self.connect(self.phiAngleField, SIGNAL("valueChanged(double)"),
self._aaPhiAngleChanged)
self.phiAngleField.setEnabled(False)
self.psiAngleField = \
PM_DoubleSpinBox( inPmGroupBox,
label = "Psi angle :",
value = -47.0,
setAsDefault = True,
minimum = -180.0,
maximum = 180.0,
singleStep = 1.0,
decimals = 1,
suffix = " degrees" )
self.connect(self.psiAngleField, SIGNAL("valueChanged(double)"),
self._aaPsiAngleChanged)
self.psiAngleField.setEnabled(False)
self.invertChiralityPushButton = \
PM_PushButton( inPmGroupBox,
text = 'Invert chirality' ,
spanWidth = False
)
self.connect(self.invertChiralityPushButton, SIGNAL("clicked()"),
self._aaChiralityChanged)
self.aaTypesButtonGroup = \
PM_ToolButtonGrid( inPmGroupBox,
buttonList = AA_BUTTON_LIST,
label = "Amino acids :",
checkedId = 0,
setAsDefault = True )
self.connect(self.aaTypesButtonGroup.buttonGroup,
SIGNAL("buttonClicked(int)"), self._setAminoAcidType)
self.sequenceEditor = \
PM_TextEdit( inPmGroupBox,
label = "Sequence",
spanWidth = True )
self.sequenceEditor.insertHtml("", False, 4, 10, True)
self.sequenceEditor.setReadOnly(True)
self.startOverButton = \
PM_PushButton( inPmGroupBox,
label = "",
text = "Start Over",
spanWidth = True,
setAsDefault = True )
self.connect(self.startOverButton, SIGNAL("clicked()"),
self._startOverClicked)
def _addWhatsThisText(self):
"""
What's This text for widgets in this Property Manager.
"""
from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_PeptideGeneratorPropertyManager
whatsThis_PeptideGeneratorPropertyManager(self)
def _addToolTipText(self):
"""
Tool Tip text for widgets in this Property Manager.
"""
from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_PeptideGeneratorPropertyManager
ToolTip_PeptideGeneratorPropertyManager(self)
def _aaChiralityChanged(self):
"""
Set chirality of the peptide chain.
"""
self.psi *= -1
self.phi *= -1
self.phiAngleField.setValue(self.phi)
self.psiAngleField.setValue(self.psi)
def _aaTypeChanged(self, idx):
"""
Slot for Peptide Structure Type combobox.
Changes phi/psi angles for secondary structure.
"""
self.ss_idx = idx
if idx == 0:
self.phiAngleField.setEnabled(True)
self.psiAngleField.setEnabled(True)
else:
self.phiAngleField.setEnabled(False)
self.psiAngleField.setEnabled(False)
if idx == 1: # alpha helix
self.phi = -57.0
self.psi = -47.0
elif idx == 2: # beta strand
self.phi = -135.0
self.psi = 135.0
elif idx == 3: # 3-10 helix
self.phi = -55.0
self.psi = -70.0
elif idx == 4: # pi helix
self.phi = -49.0
self.psi = -26.0
elif idx == 5: # polyprolin-II
self.phi = -75.0
self.psi = 150.0
elif idx == 6: # fully extended
self.phi = -180.0
self.psi = 180.0
else:
self.phi = self.phiAngleField.value()
self.psi = self.psiAngleField.value()
self.phi *= self.chirality
self.psi *= self.chirality
self.phiAngleField.setValue(self.phi)
self.psiAngleField.setValue(self.psi)
pass
def _aaPhiAngleChanged(self, phi):
self.phi = self.phiAngleField.value()
pass
def _aaPsiAngleChanged(self, psi):
self.psi = self.psiAngleField.value()
pass
def _setAminoAcidType(self, aaTypeIndex):
"""
Adds a new amino acid to the peptide molecule.
"""
button, idx, short_name, dum, name, symbol, x, y = AA_BUTTON_LIST[
aaTypeIndex]
if self.ss_idx == 1:
aa_txt = "<font color=red>"
elif self.ss_idx == 2:
aa_txt = "<font color=blue>"
elif self.ss_idx == 3:
aa_txt = "<font color=green>"
elif self.ss_idx == 4:
aa_txt = "<font color=orange>"
elif self.ss_idx == 5:
aa_txt = "<font color=magenta>"
elif self.ss_idx == 6:
aa_txt = "<font color=darkblue>"
else:
aa_txt = "<font color=black>"
aa_txt += symbol + "</font>"
self.sequenceEditor.insertHtml(aa_txt, False, 4, 10, False)
self.addAminoAcid(aaTypeIndex)
pass
def _startOverClicked(self):
"""
Resets a sequence in the sequence editor window.
"""
self.sequenceEditor.clear()
self.peptide_cache = []
pass
