From 74feb333987ec3f1a2fd9424740b52d5e1e9b1ba Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 16 Jun 2011 14:17:39 +0200
Subject: [PATCH] Added dialog superpositiondialog to scene menu (menu.py) of
dng
---
modules/gui/doc/dialogs.rst | 25 ++
modules/gui/doc/gui.rst | 2 +-
modules/gui/doc/images/100208_Dialogs.png | Bin 0 -> 3016 bytes
.../doc/images/100624_superpose_dialog.png | Bin 0 -> 15322 bytes
modules/gui/pymod/CMakeLists.txt | 1 +
modules/gui/pymod/__init__.py | 22 +-
modules/gui/pymod/dng/init.py | 1 +
modules/gui/pymod/dng/menu.py | 33 +-
modules/gui/pymod/dng/superpositiondialog.py | 282 ++++++++++++++++++
9 files changed, 362 insertions(+), 4 deletions(-)
create mode 100644 modules/gui/doc/dialogs.rst
create mode 100644 modules/gui/doc/images/100208_Dialogs.png
create mode 100644 modules/gui/doc/images/100624_superpose_dialog.png
create mode 100644 modules/gui/pymod/dng/superpositiondialog.py
diff --git a/modules/gui/doc/dialogs.rst b/modules/gui/doc/dialogs.rst
new file mode 100644
index 000000000..a2bc2a7f2
--- /dev/null
+++ b/modules/gui/doc/dialogs.rst
@@ -0,0 +1,25 @@
+Dialogs
+================================================================================
+.. currentmodule:: ost.gui
+
+OpenStructure provides several :class:`Dialogs` which can be called from its
+many menus in the top bar.
+
+
+.. image:: images/100208_Dialogs.png
+
+Scene Menu
+--------------------------------------------------------------------------------
+
+
+Superpose
+^^^^^^^^^
+
+ Structurally superpose two entities.
+
+ .. image:: images/100624_superpose_dialog.png
+
+ The ``Superpose`` entry in the ``Scene`` menu is only accessible if two
+ instances of the graphical :class:`~ost.gfx.Entity` are selected.
+
+ .. autoclass:: ost.gui.dng.superpositiondialog.SuperpositionDialog
diff --git a/modules/gui/doc/gui.rst b/modules/gui/doc/gui.rst
index 675bf6b13..19a407ac0 100644
--- a/modules/gui/doc/gui.rst
+++ b/modules/gui/doc/gui.rst
@@ -19,4 +19,4 @@ C++ Qt widgets as well as with PyQt widgets. Learn more about :doc:`python_cpp`.
tools
python_shell
sequence_viewer
-
+ dialogs
diff --git a/modules/gui/doc/images/100208_Dialogs.png b/modules/gui/doc/images/100208_Dialogs.png
new file mode 100644
index 0000000000000000000000000000000000000000..f42f8809a3848f01390db42a71dbcc96bba53a01
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diff --git a/modules/gui/pymod/CMakeLists.txt b/modules/gui/pymod/CMakeLists.txt
index dc6329131..9a623a9a1 100644
--- a/modules/gui/pymod/CMakeLists.txt
+++ b/modules/gui/pymod/CMakeLists.txt
@@ -90,6 +90,7 @@ set(OST_GUI_PYMOD_MODULES
set(OST_GUI_PYMOD_DNG_MODULES
__init__.py
termuse.py
+ superpositiondialog.py
init.py
menu.py
)
diff --git a/modules/gui/pymod/__init__.py b/modules/gui/pymod/__init__.py
index c54365524..a63b91820 100644
--- a/modules/gui/pymod/__init__.py
+++ b/modules/gui/pymod/__init__.py
@@ -184,7 +184,27 @@ class OneOf:
if isinstance(node, cl):
return True
return False
-
+
+class TwoOf:
+ def __init__(self, *classes):
+ self.classes=classes
+ def __call__(self):
+ sel=SceneSelection.Instance()
+ act_count=sel.GetActiveNodeCount()
+ if act_count<2:
+ return False
+ found=0
+ for i in range(0, act_count):
+ node=sel.GetActiveNode(i)
+ for cl in self.classes:
+ if isinstance(node, cl):
+ found += 1
+ if found > 2:
+ return False
+ if found == 2:
+ return True
+ return False
+
class ManyOf:
def __init__(self, *classes):
self.classes=classes
diff --git a/modules/gui/pymod/dng/init.py b/modules/gui/pymod/dng/init.py
index 661ddadc4..d46af73d8 100644
--- a/modules/gui/pymod/dng/init.py
+++ b/modules/gui/pymod/dng/init.py
@@ -21,6 +21,7 @@ from ost.gui.init_spacenav import _InitSpaceNav
from ost.gui.init_context_menu import _InitContextMenu
from ost.gui.init_splash import _InitSplash
from ost.gui.dng import termuse
+from ost.gui.dng import superpositiondialog
import ost.gui.dng.menu
from PyQt4.QtGui import *
def _my_exit(code):
diff --git a/modules/gui/pymod/dng/menu.py b/modules/gui/pymod/dng/menu.py
index c2b672c2b..de943d322 100644
--- a/modules/gui/pymod/dng/menu.py
+++ b/modules/gui/pymod/dng/menu.py
@@ -1,9 +1,12 @@
from PyQt4.QtCore import *
from PyQt4.QtGui import *
-from ost import gui, gfx, io
+from ost import *
+from ost import gui
from ost.gui.scene.loader_manager_widget import LoaderManagerWidget
from ost.gui.init_splash import _InitSplash
from ost.gui.dng import termuse
+from ost.gui.dng import superpositiondialog
+
import sys
class FileMenu(QMenu):
def __init__(self, parent=None):
@@ -134,6 +137,8 @@ class SceneMenu(QMenu):
enabled=gui.ManyOf(gfx.GfxObj))
gui.AddMenuAction(self, 'Fit To Screen', self._FitToScreen,
enabled=gui.OneOf(gfx.Entity))
+ gui.AddMenuAction(self, 'Superpose', self._SuperposeDialog,
+ enabled=gui.TwoOf(gfx.Entity))
gui.AddMenuAction(self, 'Save Snapshot', self._ExportScene)
gui.AddMenuAction(self, 'Scene Clipping', self._ClipScene, shortcut='Ctrl+Shift+C')
@@ -169,7 +174,31 @@ class SceneMenu(QMenu):
def _FitToScreen(self):
sel=gui.SceneSelection.Instance()
gfx.FitToScreen(sel.GetActiveNode(0))
-
+
+ def _SuperposeDialog(self):
+ sel=gui.SceneSelection.Instance()
+ act_count=sel.GetActiveNodeCount()
+ # we now that there have to be 2 gfx.Entities, because of using TwoOf to
+ # enable menu entry!
+ i = 0;
+ gfx_ent_1 = sel.GetActiveNode(i)
+ while not isinstance(gfx_ent_1, gfx.Entity):
+ i += 1
+ gfx_ent_1 = sel.GetActiveNode(i)
+ i += 1
+ gfx_ent_2 = sel.GetActiveNode(i)
+ while not isinstance(gfx_ent_2, gfx.Entity):
+ i += 1
+ gfx_ent_2 = sel.GetActiveNode(i)
+ sd = superpositiondialog.SuperpositionDialog(gfx_ent_1, gfx_ent_2)
+ if sd.reference == 0:
+ gfx_ent_1.UpdatePositions()
+ gfx.Scene().CenterOn(gfx_ent_1)
+ else:
+ gfx_ent_2.UpdatePositions()
+ gfx.Scene().CenterOn(gfx_ent_2)
+ LogScript('RMSD: %.3f'%sd.rmsd)
+
class WindowMenu(QMenu):
def __init__(self, parent=None):
QMenu.__init__(self, parent)
diff --git a/modules/gui/pymod/dng/superpositiondialog.py b/modules/gui/pymod/dng/superpositiondialog.py
new file mode 100644
index 000000000..f426bc330
--- /dev/null
+++ b/modules/gui/pymod/dng/superpositiondialog.py
@@ -0,0 +1,282 @@
+#------------------------------------------------------------------------------
+# This file is part of the OpenStructure project <www.openstructure.org>
+#
+# Copyright (C) 2008-2011 by the OpenStructure authors
+#
+# This library is free software; you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation; either version 3.0 of the License, or (at your option)
+# any later version.
+# This library is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this library; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+#------------------------------------------------------------------------------
+#
+# Authors: Stefan Bienert
+#
+from PyQt4.QtCore import *
+from PyQt4.QtGui import *
+from ost.mol.alg import Superpose
+from ost import mol
+
+class ChainComboBox(QComboBox):
+ def __init__(self, ent, parent=None):
+ # class variables
+ self.all_chains = 'All'
+ QComboBox.__init__(self, parent)
+ self.entity = ent
+ self.addItem(self.all_chains)
+ for chain in self.entity.chains:
+ self.addItem(chain.name)
+ if self.count()>0:
+ self.setCurrentIndex(0)
+
+ def SetItems(self, ent):
+ self.clear()
+ self.entity = ent
+ self.addItem(self.all_chains)
+ for chain in self.entity.chains:
+ self.addItem(chain.name)
+ if self.count()>0:
+ self.setCurrentIndex(0)
+ return
+
+ def _GetSelectedChain(self):
+ if self.currentIndex() == -1:
+ return mol.EntityHandle()
+ elif self.currentText() == self.all_chains:
+ return self.entity
+ return self.entity.Select('cname=' + str(self.currentText()))
+
+ def _SetSelectedChain(self, chain):
+ if hasattr(chain, 'name'):
+ name = chain.name
+ else:
+ name = str(chain)
+ for i in range(self.count()):
+ if self.itemText(i) == name:
+ self.setCurrentIndex(i)
+ break
+ selected_chain = property(_GetSelectedChain, _SetSelectedChain)
+
+class SuperpositionDialog(QDialog):
+ """
+ Provides a graphical user interface to structurally superpose two entities.
+ Uses function :func:`~ost.mol.alg.Superpose`. The RMSD of two superposed
+ molecules will be stored in attribute ``rmsd``. An index for the selected
+ reference molecule will be stored in attribute ``reference``.
+
+ :param ent_one: The first entity
+ :type ent_one: :class:`~ost.mol.EntityView`, :class:`~ost.mol.EntityHandle`
+ or :class:`~ost.gfx.Entity`
+ :param ent_two: The second entity
+ :type ent_two: :class:`~ost.mol.EntityView`, :class:`~ost.mol.EntityHandle`
+ or :class:`~ost.gfx.Entity`
+
+ **Example Usage:**
+
+ .. code-block:: python
+
+ e1=io.LoadPDB('examples/code_fragments/entity/pdb1ake.ent')
+ e2=io.LoadPDB('examples/code_fragments/entity/pdb4ake.ent')
+
+ sd = superpositiondialog.SuperpositionDialog(e1, e2)
+
+ g1=gfx.Entity('G1', e1)
+ g2=gfx.Entity('G2', e2)
+ scene.Add(g1)
+ scene.Add(g2)
+
+ if sd.reference == 0:
+ scene.CenterOn(g1)
+ else:
+ scene.CenterOn(g2)
+
+ LogScript('RMSD: %.3f'%sd.rmsd)
+ """
+
+ def __init__(self, ent_one, ent_two, parent=None):
+ # class variables
+ self.rmsd = 0.0
+ self._mmethod_dict = {'number': 'number',
+ 'index': 'index',
+ 'local alignment': 'local-aln',
+ 'global alignment': 'global-aln'}
+ QDialog.__init__(self, parent)
+ self.setWindowTitle('Superpose structures')
+ if not isinstance(ent_one, mol.EntityHandle) and \
+ not isinstance(ent_one, mol.EntityView):
+ n_one = ent_one.GetName()
+ self.ent_one = ent_one.GetView()
+ else:
+ if isinstance(ent_one, mol.EntityHandle):
+ n_one = ent_one.GetName()
+ elif isinstance(ent_one, mol.EntityView):
+ n_one = ent_one.GetHandle().GetName()
+ self.ent_one = ent_one
+ if len(n_one) == 0:
+ n_one = '1'
+ if not isinstance(ent_two, mol.EntityHandle) and \
+ not isinstance(ent_two, mol.EntityView):
+ n_two = ent_two.GetName()
+ self.ent_two = ent_two.GetView()
+ else:
+ if isinstance(ent_two, mol.EntityHandle):
+ n_two = ent_two.GetName()
+ elif isinstance(ent_two, mol.EntityView):
+ n_two = ent_two.GetHandle().GetName()
+ self.ent_two = ent_two
+ if len(n_two) == 0:
+ n_two = '2'
+ if n_one == n_two:
+ n_one = n_one + ' 1'
+ n_two = n_two + ' 2'
+ layout = 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(self._reference, grow, 1)
+ grow += 1
+ # chains
+ self._chain_one = ChainComboBox(self.ent_one, self)
+ self._chain_two = ChainComboBox(self.ent_two, self)
+ layout.addWidget(QLabel("reference chain"), grow, 0)
+ layout.addWidget(self._chain_one, grow, 1)
+ grow += 1
+ layout.addWidget(QLabel("chain"), grow, 0)
+ layout.addWidget(self._chain_two, grow, 1)
+ grow += 1
+ # link chain and reference selection
+ QObject.connect(self._reference,
+ SIGNAL('currentIndexChanged(int)'),
+ self._ChangeChainSelection)
+ # match methods
+ self._methods = self._MatchMethods()
+ layout.addWidget(QLabel('match residues by'), grow, 0)
+ grow += 1
+ layout.addWidget(self._methods)
+ # atoms
+ self._atoms = self._FetchAtoms(self._methods.size(),
+ self.ent_one,
+ self.ent_two)
+ self._atmselectbx, self._atmselectgrp = self._AtomSelectionBox()
+ layout.addWidget(self._atmselectbx, grow, 1)
+ grow += 1
+ # buttons
+ ok_button = QPushButton("Superpose")
+ QObject.connect(ok_button, SIGNAL('clicked()'), self.accept)
+ cancel_button = QPushButton("Cancel")
+ hbox_layout = QHBoxLayout()
+ hbox_layout.addStretch(1)
+ layout.addLayout(hbox_layout, grow, 0, 1, 2)
+ grow += 1
+ QObject.connect(cancel_button, SIGNAL('clicked()'), self.reject)
+ QObject.connect(self, SIGNAL('accepted()'), self._Superpose)
+ hbox_layout.addWidget(cancel_button, 0)
+ hbox_layout.addWidget(ok_button, 0)
+ ok_button.setDefault(True)
+ self.exec_()
+
+ def _Superpose(self):
+ view_one = self._chain_one.selected_chain
+ view_two = self._chain_two.selected_chain
+ atoms = self._GetAtomSelection()
+ sp = Superpose(view_one, view_two,
+ self._mmethod_dict[str(self._methods.currentText())],
+ atoms)
+ self.rmsd = sp.rmsd
+
+ def _toggle_atoms(self, checked):
+ if checked:
+ self._atoms.setEnabled(True)
+ else:
+ self._atoms.setEnabled(False)
+
+ def _AtomSelectionBox(self):
+ bt1 = QRadioButton('All')
+ bt2 = QRadioButton('Backbone')
+ bt3 = QRadioButton('CA')
+ self.cstmbtntxt = 'Custom'
+ custom_rbutton = QRadioButton(self.cstmbtntxt)
+ group = QButtonGroup()
+ group.addButton(bt1)
+ group.addButton(bt2)
+ group.addButton(bt3)
+ group.addButton(custom_rbutton)
+ bt1.setChecked(True)
+ vbox_layout = QVBoxLayout()
+ vbox_layout.addWidget(bt1)
+ vbox_layout.addWidget(bt2)
+ vbox_layout.addWidget(bt3)
+ vbox_layout.addWidget(custom_rbutton)
+ vbox_layout.addWidget(self._atoms)
+ QObject.connect(custom_rbutton, SIGNAL('toggled(bool)'), self._toggle_atoms)
+ box = QGroupBox("atom selection")
+ box.setLayout(vbox_layout)
+ return box, group
+
+ def _GetAtomSelection(self):
+ checkedbtn = self._atmselectgrp.checkedButton()
+ if str(checkedbtn.text()) != self.cstmbtntxt:
+ return str(checkedbtn.text())
+ slctn_model = self._atoms.selectionModel()
+ dt_model = slctn_model.model()
+ atms = list()
+ for idx in slctn_model.selectedRows():
+ slctn = dt_model.data(idx, Qt.DisplayRole).toString()
+ atms.append(str(slctn))
+ return atms
+
+ def _FetchAtoms(self, dim, ent_a, ent_b):
+ # fetch list of atoms: only those which are in both entities are considered
+ atm_dict = {}
+ for atm in ent_a.GetAtomList():
+ atm_dict[atm.name] = 0
+ for atm in ent_b.GetAtomList():
+ if atm.name in atm_dict:
+ atm_dict[atm.name] = 1
+ atmlst = QStringList()
+ for atm in sorted(atm_dict.keys()):
+ if atm_dict[atm]:
+ atmlst.append(atm)
+ elems = QStringListModel(atmlst)
+ atoms = QListView(self)
+ dim.setHeight(3*dim.height())
+ atoms.setFixedSize(dim)
+ atoms.setModel(elems)
+ atoms.setSelectionMode(QAbstractItemView.MultiSelection)
+ atoms.setEditTriggers(QAbstractItemView.NoEditTriggers)
+ atoms.setEnabled(False)
+ return atoms
+
+ def _ReferenceSelection(self, name_a, name_b):
+ cbox = QComboBox()
+ cbox.addItem(name_a)
+ cbox.addItem(name_b)
+ if cbox.count() > 0:
+ cbox.setCurrentIndex(0)
+ return cbox
+
+ def _ChangeChainSelection(self, index):
+ if index == 0:
+ self._chain_one.SetItems(self.ent_one)
+ self._chain_two.SetItems(self.ent_two)
+ self.reference = 0;
+ elif index == 1:
+ self._chain_one.SetItems(self.ent_two)
+ self._chain_two.SetItems(self.ent_one)
+ self.reference = 1;
+ return
+
+ def _MatchMethods(self):
+ methods=QComboBox(self)
+ for method in sorted(self._mmethod_dict):
+ methods.addItem(method)
+ return methods
--
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