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Tobias Schmidt authoredTobias Schmidt authored
init_context_menu.py 14.53 KiB
import platform
from PyQt4 import QtCore, QtGui
import sip
from ost import geom, gfx, gui, seq
from ost import settings
from ost import LogError, mol
from ost.bindings import tmtools
from ost.bindings import msms
from ost.seq import alg
import ost
from ost.gui.scene.query_editor import QueryEditorWidget,QueryDialog
class SelectRefDialog(QtGui.QDialog):
def __init__(self, ent_list, parent=None):
QtGui.QDialog.__init__(self, parent)
self.ent_list_ = ent_list
vb = QtGui.QVBoxLayout()
self.setLayout(vb)
self.setWindowTitle("Select Reference Object")
self.label = QtGui.QLabel("Please Select the Reference Object")
self.list = QtGui.QTableWidget(self)
self.list.horizontalHeader().setStretchLastSection(True)
self.list.setColumnCount(2)
self.list.verticalHeader().setVisible(False)
self.list.horizontalHeader().setVisible(False)
self.list.setSelectionBehavior(QtGui.QAbstractItemView.SelectRows)
self.list.setSelectionMode(QtGui.QAbstractItemView.SingleSelection)
vb.addWidget(self.label)
vb.addWidget(self.list)
self.show_scores = QtGui.QCheckBox(self)
self.show_scores.setText("Show Scores")
self.show_scores.setChecked(True)
vb.addWidget(self.show_scores)
self.show_alignment = QtGui.QCheckBox(self)
self.show_alignment.setText("Display Alignment")
self.show_alignment.setChecked(False)
vb.addWidget(self.show_alignment)
hb = QtGui.QHBoxLayout()
hb.setDirection(QtGui.QBoxLayout.LeftToRight)
cancel_btn = QtGui.QPushButton("Cancel", self)
load_btn = QtGui.QPushButton("Select", self)
hb.addStretch(1)
hb.addWidget(cancel_btn)
hb.addWidget(load_btn)
vb.addItem(hb)
load_btn.setDefault(True)
QtCore.QObject.connect(load_btn, QtCore.SIGNAL("clicked()"), self.Select)
QtCore.QObject.connect(cancel_btn, QtCore.SIGNAL("clicked()"), self.reject)
row = 0
for ent in self.ent_list_:
variant = QtCore.QVariant(ent)
self.list.insertRow(row)
new_item = QtGui.QTableWidgetItem("%i"%(row+1))
new_item.setFlags(QtCore.Qt.ItemIsSelectable|QtCore.Qt.ItemIsEnabled)
new_item.setData(QtCore.Qt.UserRole,variant)
self.list.setItem(row, 0, new_item)
new_item = QtGui.QTableWidgetItem(ent.GetName())
new_item.setFlags(QtCore.Qt.ItemIsSelectable|QtCore.Qt.ItemIsEnabled)
self.list.setItem(row, 1, new_item)
row += 1
self.list.resizeColumnsToContents()
def Select(self):
items = self.list.selectedItems()
for item in items:
if(item.column()==0):
ent = item.data(QtCore.Qt.UserRole).toPyObject()
self.ent_list_.remove(ent)
self.ent_list_.insert(0,ent)
self.accept()
def GetShowScores(self):
return self.show_scores.isChecked()
def GetDisplayAlignment(self):
return self.show_alignment.isChecked()
def GetEntities(self):
return self.ent_list_
class ShowResultDialog(QtGui.QDialog):
def __init__(self, ent_list, res_list, parent=None):
QtGui.QDialog.__init__(self, parent)
self.ent_list_ = ent_list
vb = QtGui.QVBoxLayout()
self.setLayout(vb)
self.setWindowTitle("Alignment result")
self.label = QtGui.QLabel("Alignment results with %s as reference"%ent_list[0].GetName())
self.list = QtGui.QTableWidget(self)
self.list.horizontalHeader().setStretchLastSection(True)
self.list.setColumnCount(4)
self.list.verticalHeader().setVisible(False)
self.list.setHorizontalHeaderLabels (["Name","RMSD","TMScore",""])
self.list.setSelectionBehavior(QtGui.QAbstractItemView.SelectRows)
vb.addWidget(self.label)
vb.addWidget(self.list)
hb = QtGui.QHBoxLayout()
hb.setDirection(QtGui.QBoxLayout.LeftToRight)
ok_btn = QtGui.QPushButton("OK", self)
hb.addStretch(1)
hb.addWidget(ok_btn)
vb.addItem(hb)
ok_btn.setDefault(True)
QtCore.QObject.connect(ok_btn, QtCore.SIGNAL("clicked()"), self.accept)
for i in range(0, len(res_list)):
self.list.insertRow(i)
new_item = QtGui.QTableWidgetItem(ent_list[i+1].GetName())
new_item.setFlags(QtCore.Qt.ItemIsEnabled)
self.list.setItem(i, 0, new_item)
new_item = QtGui.QTableWidgetItem("%.2f"%res_list[i].rmsd)
new_item.setFlags(QtCore.Qt.ItemIsEnabled)
self.list.setItem(i, 1, new_item)
new_item = QtGui.QTableWidgetItem("%i"%res_list[i].tm_score)
new_item.setFlags(QtCore.Qt.ItemIsEnabled)
self.list.setItem(i, 2, new_item)
new_item = QtGui.QTableWidgetItem()
new_item.setFlags(QtCore.Qt.ItemIsEnabled)
self.list.setItem(i, 3, new_item)
self.list.resizeColumnsToContents()
class CalculateSurfaceSettingsDialog(QtGui.QDialog):
def __init__(self, executable, parent=None):
QtGui.QDialog.__init__(self, parent)
vb = QtGui.QGridLayout()
self.setLayout(vb)
self.setWindowTitle("MSMS Surface Settings")
msmsexe_label=QtGui.QLabel("executable")
self.msmsexe_field=QtGui.QLineEdit()
self.msmsexe_field.setText(executable)
msmsexe_browsebutton=QtGui.QPushButton("Browse")
vb.addWidget(msmsexe_label, 0, 0)
vb.addWidget(self.msmsexe_field, 0, 1)
vb.addWidget(msmsexe_browsebutton, 0, 2)
surfname_label=QtGui.QLabel("surface name")
self.surfname_field=QtGui.QLineEdit()
self.surfname_field.setText("surface")
vb.addWidget(surfname_label, 1, 0)
vb.addWidget(self.surfname_field, 1, 1, 1, 2)
density_label=QtGui.QLabel("density")
self.density_spinbox=QtGui.QSpinBox()
self.density_spinbox.setRange(1, 10)
self.density_spinbox.setValue(4)
vb.addWidget(density_label, 2, 0)
vb.addWidget(self.density_spinbox, 2, 1, 1, 2)
probe_label=QtGui.QLabel("probe radius")
self.probe_spinbox=QtGui.QDoubleSpinBox()
self.probe_spinbox.setDecimals(1)
self.probe_spinbox.setSingleStep(0.1)
self.probe_spinbox.setRange(0.3, 5.0)
self.probe_spinbox.setValue(1.4)
vb.addWidget(probe_label, 3, 0)
vb.addWidget(self.probe_spinbox, 3, 1, 1, 2)
selection_label=QtGui.QLabel("selection")
self.selection_field=QtGui.QLineEdit()
self.selection_field.setText("")
vb.addWidget(selection_label, 4, 0)
vb.addWidget(self.selection_field, 4, 1, 1, 2)
self.noh_box=QtGui.QCheckBox("no hydrogens")
vb.addWidget(self.noh_box, 5, 0)
self.nohet_box=QtGui.QCheckBox("no hetatoms")
vb.addWidget(self.nohet_box, 5, 1)
self.nowat_box=QtGui.QCheckBox("no waters")
vb.addWidget(self.nowat_box, 5, 2)
cancel_btn = QtGui.QPushButton("Cancel", self)
ok_btn = QtGui.QPushButton("OK", self)
vb.addWidget(cancel_btn, 6, 1)
vb.addWidget(ok_btn, 6, 2)
QtCore.QObject.connect(msmsexe_browsebutton, QtCore.SIGNAL("clicked()"), self.GetPath)
QtCore.QObject.connect(ok_btn, QtCore.SIGNAL("clicked()"), self.accept)
QtCore.QObject.connect(cancel_btn, QtCore.SIGNAL("clicked()"), self.reject)
def GetPath(self):
path=QtGui.QFileDialog().getOpenFileName(self, "Choose MSMS Executable")
if path!='':
self.msmsexe_field.setText(path)
class SurfaceContextMenu(QtCore.QObject):
def __init__(self, context_menu):
try:
settings_name="msms"
self.executable=settings.Locate(settings_name)
except settings.FileNotFound:
self.executable=""
QtCore.QObject.__init__(self, context_menu.qobject)
self.action = QtGui.QAction("Calculate Surface", self)
QtCore.QObject.connect(self.action, QtCore.SIGNAL("triggered()"),
self.CalculateSurface)
context_menu.AddAction(self.action, gui.ContextActionType.ENTITY)
def CalculateSurface(self):
scene_selection = gui.SceneSelection.Instance()
ent_list = list()
for i in range(0,scene_selection.GetActiveNodeCount()):
ent_list.append(scene_selection.GetActiveNode(i))
cssd = CalculateSurfaceSettingsDialog(self.executable)
if(cssd.exec_()):
self.__CalculateSurface(ent_list,
str(cssd.surfname_field.text()),
str(cssd.msmsexe_field.text()),
cssd.density_spinbox.value(),
cssd.probe_spinbox.value(),
str(cssd.selection_field.text()),
cssd.noh_box.isChecked(),
cssd.nohet_box.isChecked(),
cssd.nowat_box.isChecked())
def __CalculateSurface(self,ent_list,name,msms_exe,density,
radius,selection,noh,nohet,nowat):
for entity in ent_list:
if isinstance(entity, gfx.Entity):
try:
s=msms.CalculateSurface(entity.view,
msms_exe=msms_exe,
density=density,
radius=radius,
selection=selection,
no_hydrogens=noh,
no_hetatoms=nohet,
no_waters=nowat)[0]
gfx.Scene().Add(gfx.Surface("%s_%s"%(entity.GetName(),name),s))
except (RuntimeError, msms.MsmsProcessError):
LogError("WARNING: Surface could not be calculated")
return
except UserWarning:
LogError("WARNING: Entry with the same name already present in scene")
return
class AlignmentContextMenu(QtCore.QObject):
def __init__(self, context_menu):
try:
try: # workaround for interrupted system call bug on OSX
if platform.system() == "Windows":
settings_name="tmalign.exe"
else:
settings_name="tmalign"
except IOError:
# if platform.system() fails with an IOError we are most likely on a buggy mac an therefore
# use "tmalign"
settings_name="tmalign"
settings.Locate(settings_name)
QtCore.QObject.__init__(self, context_menu.qobject)
self.action = QtGui.QAction("Align", self)
QtCore.QObject.connect(self.action,QtCore.SIGNAL("triggered()"), self.Align)
context_menu.AddAction(self.action, gui.ContextActionType.ENTITY | gui.ContextActionType.MULTI)
self.seq_viewer = None
except settings.FileNotFound:
return
def Align(self):
scene_selection = gui.SceneSelection.Instance()
ent_list = list()
for i in range(0,scene_selection.GetActiveNodeCount()):
ent_list.append(scene_selection.GetActiveNode(i))
sd = SelectRefDialog(ent_list)
if(sd.exec_()):
self.__Align(sd.GetEntities(),sd.GetShowScores(), sd.GetDisplayAlignment())
def __Align(self, ent_list,show_scores=True, display_alignment=False):
node = ent_list[0]
res_list = list()
if isinstance(node, gfx.Entity):
ref = node.view.handle
for i in range(1,len(ent_list)):
node = ent_list[i]
if isinstance(node, gfx.Entity):
res_list.append(tmtools.TMAlign(node.view.handle, ref))
node.UpdatePositions()
if show_scores:
self.__ShowScore(ent_list, res_list)
if display_alignment:
self.__DisplayAlignment(ent_list, res_list)
def __ShowScore(self, ent_list, res_list):
if(len(res_list)==1):
res = res_list[0]
string = "RMSD: %.2f, TMScore: %i"%(res.rmsd, res.tm_score)
gui.GostyApp.Instance().perspective.StatusMessage(string)
elif(len(res_list)>1):
ShowResultDialog(ent_list, res_list).exec_()
def __DisplayAlignment(self, ent_list, res_list):
if(len(res_list)>0):
ref_seq = seq.CreateSequence("%s (ref)"%ent_list[0].GetName(),res_list[0].ref_sequence.GetGaplessString())
aln_list = seq.AlignmentList()
if(ref_seq.IsValid()):
for i in range(0, len(res_list)):
res_list[i].alignment.SetSequenceName(1,ent_list[i+1].GetName())
aln_list.append(res_list[i].alignment)
alignment = alg.MergePairwiseAlignments(aln_list, ref_seq)
gosty = gui.GostyApp.Instance()
main_area = gosty.perspective.GetMainArea()
if self.seq_viewer:
self.seq_viewer.qobject.close()
self.seq_viewer = gui.SequenceViewer(True)
self.seq_viewer.AddAlignment(alignment)
self.seq_viewer.ChangeDisplayMode("Highlight conservation 1")
self.seq_viewer.Show()
class SelectMenuPoints(QtCore.QObject):
def __init__(self, context_menu):
QtCore.QObject.__init__(self, context_menu.qobject)
action=QtGui.QAction("Select...", self)
QtCore.QObject.connect(action, QtCore.SIGNAL('triggered()'),
self._Select)
context_menu.AddAction(action, gui.ENTITY)
action=QtGui.QAction("Copy Selection...", self)
QtCore.QObject.connect(action, QtCore.SIGNAL('triggered()'),
self._CopyViews)
context_menu.AddAction(action, gui.ENTITY)
action=QtGui.QAction('Select...', self)
QtCore.QObject.connect(action, QtCore.SIGNAL('triggered()'),
self._SelectViewsSameEntity)
context_menu.AddAction(action, gui.ENTITY_VIEW|gui.VIEWS_SAME_OBJECT)
def _Select(self):
scene_selection=gui.SceneSelection.Instance()
ent=scene_selection.GetActiveNode(0)
dialog=QueryDialog('Select...')
if dialog.exec_():
q=mol.Query(dialog.query)
if q.IsValid():
ent.selection=ent.view.Select(dialog.query, dialog.query_flags)
else:
ost.LogError("invalid query: %s" % q.error)
def _UniqueName(self, ent):
"""
Returns a name based on ent that is unique within the scene
"""
ent_name=ent.GetName()
num=2
while True:
candidate_name='%s-%d' % (ent_name, num)
if not gfx.Scene().HasNode(candidate_name):
return candidate_name
num+=1
def _SelectViewsSameEntity(self):
union=gui.SceneSelection.Instance().GetViewUnion()
dialog=QueryDialog('Select...')
if dialog.exec_():
q=mol.Query(dialog.query)
if q.IsValid():
ve=gui.SceneSelection.Instance().GetViewEntity()
ve.selection=union.Select(q, dialog.query_flags)
else:
ost.LogError("invalid query: %s" % q.error)
def _CopyViews(self):
views_to_add=[]
scene_selection=gui.SceneSelection.Instance()
ent=scene_selection.GetActiveNode(0)
dialog=QueryDialog('Select...')
if dialog.exec_():
q=mol.Query(dialog.query)
if q.IsValid():
for i in range(scene_selection.GetActiveNodeCount()):
ent=scene_selection.GetActiveNode(i)
selected=ent.view.Select(q, dialog.query_flags)
gfx_ent=gfx.Entity(self._UniqueName(ent),selected)
gfx.Scene().Add(gfx_ent)
else:
ost.LogError("invalid query: %s" % q.error)
def _InitContextMenu(app):
cm=app.scene_win.GetContextMenu()
AlignmentContextMenu(cm)
SurfaceContextMenu(cm)
SelectMenuPoints(cm)