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Commit c8df74cd authored by Studer Gabriel's avatar Studer Gabriel
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fix superposition dialog

parent a9fb5aaa
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modules/gui/pymod/dng/superpositiondialog.py
+ 37
− 33
View file @ c8df74cd
......@@ -55,8 +55,9 @@ class ChainComboBox(QtWidgets.QComboBox):
if gfx:
self.gfx = gfx
def _HighlightChain(self, chain):
if str(chain) != 'All':
def _HighlightChain(self, chain_idx):
chain = self.itemText(chain_idx)
if chain != 'All':
self.gfx.SetSelection(self.entity.Select('cname="%s"' % str(chain)))
else:
self.gfx.SetSelection(self.entity.Select(''))
......@@ -130,7 +131,7 @@ class SuperpositionDialog(QtWidgets.QDialog):
self.gfx_select_one = None
self.gfx_select_two = None
QtWidgets.QDialog.__init__(self, parent)
self.setWindowTitle('Superpose structures')
self.setWindowTitle('Superpose Structures')
if not isinstance(ent_one, mol.EntityHandle) and \
not isinstance(ent_one, mol.EntityView):
n_one = ent_one.GetName()
......@@ -162,28 +163,28 @@ class SuperpositionDialog(QtWidgets.QDialog):
if n_one == n_two:
n_one = n_one + ' 1'
n_two = n_two + ' 2'
layout = QGridLayout(self)
layout = QtWidgets.QGridLayout(self)
# select reference molecule
self.reference = 0;
self._reference = self._ReferenceSelection(n_one, n_two)
grow = 0
layout.addWidget(QLabel("reference"), grow, 0)
layout.addWidget(QtWidgets.QLabel("reference"), grow, 0)
layout.addWidget(self._reference, grow, 1)
grow += 1
# chains
self._chain_one = ChainComboBox(self.ent_one, self.gfx_one, self)
self._chain_two = ChainComboBox(self.ent_two, self.gfx_two, self)
layout.addWidget(QLabel("reference chain"), grow, 0)
layout.addWidget(QtWidgets.QLabel("reference chain"), grow, 0)
layout.addWidget(self._chain_one, grow, 1)
grow += 1
layout.addWidget(QLabel("chain"), grow, 0)
layout.addWidget(QtWidgets.QLabel("chain"), grow, 0)
layout.addWidget(self._chain_two, grow, 1)
grow += 1
# link chain and reference selection
self._reference.currentIndexChanged.connect(self._ChangeChainSelection)
# match methods
self._methods = self._MatchMethods()
layout.addWidget(QLabel('match residues by'), grow, 0)
layout.addWidget(QtWidgets.QLabel('match residues by'), grow, 0)
grow += 1
layout.addWidget(self._methods)
......@@ -199,10 +200,10 @@ class SuperpositionDialog(QtWidgets.QDialog):
layout.addWidget(self._atmselectbx, grow, 1)
grow += 1
# buttons
ok_button = QPushButton("Superpose")
ok_button = QtWidgets.QPushButton("Superpose")
ok_button.clicked.connect(self.accept)
cancel_button = QPushButton("Cancel")
hbox_layout = QHBoxLayout()
cancel_button = QtWidgets.QPushButton("Cancel")
hbox_layout = QtWidgets.QHBoxLayout()
hbox_layout.addStretch(1)
layout.addLayout(hbox_layout, grow, 0, 1, 2)
grow += 1
......@@ -222,10 +223,13 @@ class SuperpositionDialog(QtWidgets.QDialog):
view_one = self._chain_one.selected_chain
view_two = self._chain_two.selected_chain
atoms = self._GetAtomSelection()
print "atoms:", atoms
print "view lengths:", len(view_one.atoms), len(view_two.atoms)
sp = Superpose(view_two, view_one,
self._mmethod_dict[str(self._methods.currentText())],
atoms, iterative=self._iterative,
max_iterations=self._it_in.value(), distance_threshold=self._dist_in.value())
max_iterations=self._it_in.value(),
distance_threshold=self._dist_in.value())
self.rmsd = sp.rmsd
if self._iterative:
self.rmsd_superposed_atoms = sp.rmsd_superposed_atoms
......@@ -238,25 +242,25 @@ class SuperpositionDialog(QtWidgets.QDialog):
self._atoms.setEnabled(False)
def _AtomSelectionBox(self):
bt1 = QRadioButton('All')
bt2 = QRadioButton('Backbone')
bt3 = QRadioButton('CA')
bt1 = QtWidgets.QRadioButton('All')
bt2 = QtWidgets.QRadioButton('Backbone')
bt3 = QtWidgets.QRadioButton('CA')
self.cstmbtntxt = 'Custom'
custom_rbutton = QRadioButton(self.cstmbtntxt)
group = QButtonGroup()
custom_rbutton = QtWidgets.QRadioButton(self.cstmbtntxt)
group = QtWidgets.QButtonGroup()
group.addButton(bt1)
group.addButton(bt2)
group.addButton(bt3)
group.addButton(custom_rbutton)
bt1.setChecked(True)
vbox_layout = QVBoxLayout()
vbox_layout = QtWidgets.QVBoxLayout()
vbox_layout.addWidget(bt1)
vbox_layout.addWidget(bt2)
vbox_layout.addWidget(bt3)
vbox_layout.addWidget(custom_rbutton)
vbox_layout.addWidget(self._atoms)
custom_rbutton.toggled.connect(self._toggle_atoms)
box = QGroupBox("atom selection")
box = QtWidgets.QGroupBox("atom selection")
box.setLayout(vbox_layout)
return box, group
......@@ -280,22 +284,22 @@ class SuperpositionDialog(QtWidgets.QDialog):
for atm in ent_b.GetAtomList():
if atm.name in atm_dict:
atm_dict[atm.name] = 1
atmlst = QStringList()
atmlst = list()
for atm in sorted(atm_dict.keys()):
if atm_dict[atm]:
atmlst.append(atm)
elems = QStringListModel(atmlst)
atoms = QListView(self)
elems = QtCore.QStringListModel(atmlst)
atoms = QtWidgets.QListView(self)
dim.setHeight(3*dim.height())
atoms.setFixedSize(dim)
atoms.setModel(elems)
atoms.setSelectionMode(QAbstractItemView.MultiSelection)
atoms.setEditTriggers(QAbstractItemView.NoEditTriggers)
atoms.setSelectionMode(QtWidgets.QAbstractItemView.MultiSelection)
atoms.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers)
atoms.setEnabled(False)
return atoms
def _ReferenceSelection(self, name_a, name_b):
cbox = QComboBox()
cbox = QtWidgets.QComboBox()
cbox.addItem(name_a)
cbox.addItem(name_b)
if cbox.count() > 0:
......@@ -313,13 +317,13 @@ class SuperpositionDialog(QtWidgets.QDialog):
self._iterative=False
def _ItBox(self):
bt1 = QRadioButton("On")
iteration_label=QLabel("Max Iterations: ")
distance_label=QLabel("Dist Thresh: ")
iteration_in=QSpinBox()
bt1 = QtWidgets.QRadioButton("On")
iteration_label=QtWidgets.QLabel("Max Iterations: ")
distance_label=QtWidgets.QLabel("Dist Thresh: ")
iteration_in=QtWidgets.QSpinBox()
iteration_in.setRange(1,30)
iteration_in.setValue(8)
distance_in=QDoubleSpinBox()
distance_in=QtWidgets.QDoubleSpinBox()
distance_in.setRange(1.0,10.0)
distance_in.setValue(3.0)
distance_in.setDecimals(1)
......@@ -328,7 +332,7 @@ class SuperpositionDialog(QtWidgets.QDialog):
distance_in.setEnabled(False)
bt1.setChecked(False)
self._iterative=False
vbox_layout = QVBoxLayout()
vbox_layout = QtWidgets.QVBoxLayout()
vbox_layout.addWidget(bt1)
vbox_layout.addWidget(iteration_label)
vbox_layout.addWidget(iteration_in)
......@@ -336,7 +340,7 @@ class SuperpositionDialog(QtWidgets.QDialog):
vbox_layout.addWidget(distance_in)
vbox_layout.addSpacing(50)
bt1.toggled.connect(self._toggle_iterative)
box = QGroupBox("Iterative")
box = QtWidgets.QGroupBox("Iterative")
box.setLayout(vbox_layout)
return box,iteration_in, distance_in
......@@ -351,7 +355,7 @@ class SuperpositionDialog(QtWidgets.QDialog):
self.reference = 1;
def _MatchMethods(self):
methods=QComboBox(self)
methods=QtWidgets.QComboBox(self)
for method in sorted(self._mmethod_dict):
methods.addItem(method)
return methods
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