From 43bafdb8ce37fd09e0c5c09595179bab0d94fcbd Mon Sep 17 00:00:00 2001
From: tobias <tobias@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Fri, 3 Sep 2010 12:38:39 +0000
Subject: [PATCH] additional selection options for right click menu
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2688 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/gui/src/scene_menu.cc | 34 +++++++++++++++++-
modules/gui/src/scene_menu.hh | 3 ++
modules/mol/base/pymod/export_entity_view.cc | 2 ++
modules/mol/base/src/entity_view.cc | 36 ++++++++++++++++++++
modules/mol/base/src/entity_view.hh | 10 ++++++
5 files changed, 84 insertions(+), 1 deletion(-)
diff --git a/modules/gui/src/scene_menu.cc b/modules/gui/src/scene_menu.cc
index 597064469..7952b8c47 100644
--- a/modules/gui/src/scene_menu.cc
+++ b/modules/gui/src/scene_menu.cc
@@ -29,8 +29,14 @@ namespace ost { namespace gui {
SceneMenu::SceneMenu() {
context_menu_=new QMenu();
select_menu_=context_menu_->addMenu("Select");
- QAction* a=select_menu_->addAction("Around Atom");
+ QAction* a=select_menu_->addAction("Atom");
+ connect(a, SIGNAL(triggered()), this, SLOT(SelectAtom()));
+ a=select_menu_->addAction("Residue");
+ connect(a, SIGNAL(triggered()), this, SLOT(SelectResidue()));
+ a=select_menu_->addAction("Around Atom");
connect(a, SIGNAL(triggered()), this, SLOT(SelectAroundAtom()));
+ a=select_menu_->addAction("Around Residue");
+ connect(a, SIGNAL(triggered()), this, SLOT(SelectAroundResidue()));
a=select_menu_->addAction("Backbone");
connect(a, SIGNAL(triggered()), this, SLOT(SelectBackbone()));
a=select_menu_->addAction("Sidechains");
@@ -76,6 +82,32 @@ void SceneMenu::SelectAroundAtom()
e->SetSelection(v);
}
+void SceneMenu::SelectAroundResidue()
+{
+ gfx::EntityP e=dyn_cast<gfx::Entity>(picked_.first);
+ mol::EntityView v=e->GetView().CreateEmptyView();
+ v.AddAtom(picked_.second);
+ v=v.ExtendViewToResidues();
+ v=v.ExtendViewToSurrounding(0.5);
+ e->SetSelection(v.ExtendViewToResidues());
+}
+
+void SceneMenu::SelectAtom()
+{
+ gfx::EntityP e=dyn_cast<gfx::Entity>(picked_.first);
+ mol::EntityView v=e->GetView().CreateEmptyView();
+ v.AddAtom(picked_.second);
+ e->SetSelection(v);
+}
+
+void SceneMenu::SelectResidue()
+{
+ gfx::EntityP e=dyn_cast<gfx::Entity>(picked_.first);
+ mol::EntityView v=e->GetView().CreateEmptyView();
+ v.AddAtom(picked_.second);
+ e->SetSelection(v.ExtendViewToResidues());
+}
+
void SceneMenu::Select(const String& str)
{
gfx::EntityP e=dyn_cast<gfx::Entity>(picked_.first);
diff --git a/modules/gui/src/scene_menu.hh b/modules/gui/src/scene_menu.hh
index 0b212bad9..8b8d1f402 100644
--- a/modules/gui/src/scene_menu.hh
+++ b/modules/gui/src/scene_menu.hh
@@ -43,6 +43,9 @@ public slots:
void SelectSidechains();
void SelectLigands();
void SelectAroundAtom();
+ void SelectAroundResidue();
+ void SelectAtom();
+ void SelectResidue();
void Select(const String& str);
void UnSelect();
void CenterOnAtom();
diff --git a/modules/mol/base/pymod/export_entity_view.cc b/modules/mol/base/pymod/export_entity_view.cc
index 3b3eadab2..4eadd54cd 100644
--- a/modules/mol/base/pymod/export_entity_view.cc
+++ b/modules/mol/base/pymod/export_entity_view.cc
@@ -86,6 +86,8 @@ void export_EntityView()
class_<EntityView, bases<EntityBase> >("EntityView", init<>())
.def("Copy", &EntityView::Copy)
+ .def("ExtendViewToResidues", &EntityView::ExtendViewToResidues)
+ .def("ExtendViewToSurrounding", &EntityView::ExtendViewToSurrounding)
.def("FindChain", find_chain_str)
.def("FindResidue", &EntityView::FindResidue)
.def("FindAtom", find_atom_a)
diff --git a/modules/mol/base/src/entity_view.cc b/modules/mol/base/src/entity_view.cc
index d81d02d98..945230d2f 100644
--- a/modules/mol/base/src/entity_view.cc
+++ b/modules/mol/base/src/entity_view.cc
@@ -773,6 +773,42 @@ void EntityView::RemoveAtomInternal(const AtomView& av)
data_->handle_to_view.erase(av.GetHandle().GetHashCode());
}
+EntityView EntityView::ExtendViewToResidues() const
+{
+ this->CheckValidity();
+ EntityView view=this->CreateEmptyView();
+ ResidueViewList residues=this->GetResidueList();
+ ResidueViewList::const_iterator res_it;
+ for (res_it=residues.begin(); res_it!=residues.end(); ++res_it) {
+ view.AddResidue((*res_it).GetHandle(),
+ mol::ViewAddFlag::INCLUDE_ALL|mol::ViewAddFlag::CHECK_DUPLICATES);
+ }
+ view.AddAllInclusiveBonds();
+ return view;
+}
+
+EntityView EntityView::ExtendViewToSurrounding(Real gap) const
+{
+ this->CheckValidity();
+ EntityView view=this->CreateEmptyView();
+ AtomViewList atoms=this->GetAtomList();
+ AtomViewList::const_iterator atm_it;
+ Real max_dist=5+gap;
+ for (atm_it=atoms.begin(); atm_it!=atoms.end(); ++atm_it) {
+ view.AddAtom((*atm_it),mol::ViewAddFlag::INCLUDE_ALL|mol::ViewAddFlag::CHECK_DUPLICATES);
+ AtomHandleList prot_atoms=this->GetHandle().FindWithin((*atm_it).GetPos(),max_dist);
+ AtomHandleList::const_iterator protatm_it;
+ for (protatm_it=prot_atoms.begin(); protatm_it!=prot_atoms.end(); ++protatm_it){
+ Real dist=geom::Distance((*atm_it).GetPos(), (*protatm_it).GetPos());
+ if (dist <= (*atm_it).GetRadius() + (*protatm_it).GetRadius() + gap) {
+ view.AddAtom((*protatm_it),mol::ViewAddFlag::INCLUDE_ALL|mol::ViewAddFlag::CHECK_DUPLICATES);
+ }
+ }
+ }
+ view.AddAllInclusiveBonds();
+ return view;
+}
+
namespace {
class EntityViewDumper : public EntityVisitor {
diff --git a/modules/mol/base/src/entity_view.hh b/modules/mol/base/src/entity_view.hh
index 6e3aa7bf8..e9566a1c2 100644
--- a/modules/mol/base/src/entity_view.hh
+++ b/modules/mol/base/src/entity_view.hh
@@ -286,6 +286,16 @@ public:
Real GetAngle(const AtomView& a1, const AtomView& a2,
const AtomView& a3) const;
+ /// \brief Extend current view to include all atoms of each residue where
+ /// at least one atom is selected currently
+ EntityView ExtendViewToResidues() const;
+
+ /// \brief Extend current view to include all atoms that are within the sum
+ /// of their vdw radii + gap
+ ///
+ /// Include all atoms within: at1.GetRadius() + at2.GetRadius() + gap
+ EntityView ExtendViewToSurrounding(Real gap) const;
+
/// \brief returns a string containing a human-readable summary of the
/// entity view
String Dump() const;
--
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