From 1e8bd1fb8fb784b1791935e8b52bb7e65c9caea3 Mon Sep 17 00:00:00 2001
From: marco <marco@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Mon, 5 Jul 2010 06:58:30 +0000
Subject: [PATCH] introduce GetBounds() method for entity, chains and residues
GetGeometricStart()/GetGeometricEnd() has been deprecated and
will be removed sooner or later.
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2501 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
code_fragments/entity/gfx_symmetry.py | 2 +-
demos/bbox.py | 2 -
modules/geom/pymod/export_composite3.cc | 6 ++
modules/geom/src/vec3.cc | 6 ++
modules/geom/src/vec3.hh | 2 +
modules/gui/src/scene_menu.cc | 6 +-
modules/mol/base/pymod/bounds.hh | 36 ++++++++++++
modules/mol/base/pymod/export_chain.cc | 11 ++--
modules/mol/base/pymod/export_chain_view.cc | 11 ++--
modules/mol/base/pymod/export_entity.cc | 17 ++++--
modules/mol/base/pymod/export_entity_view.cc | 11 ++--
modules/mol/base/pymod/export_residue.cc | 12 ++--
modules/mol/base/pymod/export_residue_view.cc | 11 ++--
modules/mol/base/src/bounding_box.cc | 4 +-
modules/mol/base/src/chain_handle.cc | 16 +-----
modules/mol/base/src/chain_handle.hh | 13 +----
modules/mol/base/src/chain_view.cc | 45 +++++----------
modules/mol/base/src/chain_view.hh | 10 +---
modules/mol/base/src/entity_handle.cc | 19 +------
modules/mol/base/src/entity_handle.hh | 14 +----
modules/mol/base/src/entity_view.cc | 36 ++++--------
modules/mol/base/src/entity_view.hh | 10 +---
modules/mol/base/src/impl/chain_impl.cc | 34 ++++--------
modules/mol/base/src/impl/chain_impl.hh | 7 ++-
modules/mol/base/src/impl/entity_impl.cc | 55 ++++---------------
modules/mol/base/src/impl/entity_impl.hh | 9 +--
modules/mol/base/src/impl/residue_impl.cc | 40 ++++++--------
modules/mol/base/src/impl/residue_impl.hh | 6 +-
modules/mol/base/src/residue_handle.cc | 16 +-----
modules/mol/base/src/residue_handle.hh | 17 ++----
modules/mol/base/src/residue_view.cc | 31 ++---------
modules/mol/base/src/residue_view.hh | 9 +--
32 files changed, 204 insertions(+), 320 deletions(-)
create mode 100644 modules/mol/base/pymod/bounds.hh
diff --git a/code_fragments/entity/gfx_symmetry.py b/code_fragments/entity/gfx_symmetry.py
index a0d795ece..bfef9fb1b 100644
--- a/code_fragments/entity/gfx_symmetry.py
+++ b/code_fragments/entity/gfx_symmetry.py
@@ -8,7 +8,7 @@ ent=io.LoadEntity(filename)
edi=ent.RequestXCSEditor()
m=geom.Mat4()
-m.PasteTranslation(-ent.GetGeometricStart())
+m.PasteTranslation(-ent.bounds.min)
edi.ApplyTransform(m)
edi.UpdateICS()
frag=gfx.Entity('frag', ent)
diff --git a/demos/bbox.py b/demos/bbox.py
index 1e4215f45..242ba49b1 100644
--- a/demos/bbox.py
+++ b/demos/bbox.py
@@ -10,8 +10,6 @@ def RenderBBox(bbox):
bb.SetFillColor(gfx.Color(0.5, 0.8, 0.5, 0.2))
scene.Add(bb)
-print 'Center:',(helix.GetGeometricStart()+helix.GetGeometricEnd())*.5
-
RenderBBox(bbox)
scene.center=go.center
print 'Demo2: Translucent bounding box around an OpenStructure entity'
diff --git a/modules/geom/pymod/export_composite3.cc b/modules/geom/pymod/export_composite3.cc
index bf269d552..ed69d1ae4 100644
--- a/modules/geom/pymod/export_composite3.cc
+++ b/modules/geom/pymod/export_composite3.cc
@@ -161,6 +161,12 @@ scope PlaneScope =
return_value_policy<copy_const_reference>())
.def("GetMax", &AlignedCuboid::GetMax,
return_value_policy<copy_const_reference>())
+ .def("GetCenter", &AlignedCuboid::GetCenter)
+ .add_property("max", make_function(&AlignedCuboid::GetMax,
+ return_value_policy<copy_const_reference>()))
+ .add_property("min", make_function(&AlignedCuboid::GetMin,
+ return_value_policy<copy_const_reference>()))
+ .add_property("center", &AlignedCuboid::GetCenter)
;
}
diff --git a/modules/geom/src/vec3.cc b/modules/geom/src/vec3.cc
index 1e48f270c..e84c2b64a 100644
--- a/modules/geom/src/vec3.cc
+++ b/modules/geom/src/vec3.cc
@@ -34,6 +34,12 @@ Vec3::Vec3(Real x, Real y, Real z)
this->set(x,y,z);
}
+Vec3::Vec3(Real v)
+{
+ this->set(v, v, v);
+}
+
+
//#if OST_DOUBLE_PRECISION
//Vec3::Vec3(float x, float y, float z)
//{
diff --git a/modules/geom/src/vec3.hh b/modules/geom/src/vec3.hh
index fecac3370..1e534f1d1 100644
--- a/modules/geom/src/vec3.hh
+++ b/modules/geom/src/vec3.hh
@@ -64,6 +64,8 @@ public:
//! explicit initialization with an array of doubles
explicit Vec3(const Real[3]);
+ explicit Vec3(Real v);
+
#if OST_DOUBLE_PRECISION
//! explicit initialization with an array of floats
explicit Vec3(const float[3]);
diff --git a/modules/gui/src/scene_menu.cc b/modules/gui/src/scene_menu.cc
index ceba5546a..597064469 100644
--- a/modules/gui/src/scene_menu.cc
+++ b/modules/gui/src/scene_menu.cc
@@ -102,20 +102,20 @@ void SceneMenu::CenterOnResidue()
void SceneMenu::CenterOnChain()
{
mol::ChainHandle chain=picked_.second.GetResidue().GetChain();
- gfx::Scene::Instance().SetCenter(chain.GetGeometricCenter());
+ gfx::Scene::Instance().SetCenter(chain.GetBounds().GetCenter());
}
void SceneMenu::CenterOnView()
{
mol::ResidueHandle res=picked_.second.GetResidue();
- gfx::Scene::Instance().SetCenter(res.GetGeometricCenter());
+ gfx::Scene::Instance().SetCenter(res.GetBounds().GetCenter());
}
void SceneMenu::CenterOnSelection()
{
gfx::EntityP e=dyn_cast<gfx::Entity>(picked_.first);
if (e->GetSelection() && e->GetSelection().GetAtomCount()>0) {
- geom::Vec3 center=e->GetSelection().GetGeometricCenter();
+ geom::Vec3 center=e->GetSelection().GetBounds().GetCenter();
gfx::Scene::Instance().SetCenter(center);
}
}
diff --git a/modules/mol/base/pymod/bounds.hh b/modules/mol/base/pymod/bounds.hh
new file mode 100644
index 000000000..9182f67ee
--- /dev/null
+++ b/modules/mol/base/pymod/bounds.hh
@@ -0,0 +1,36 @@
+#ifndef OST_MOL_EXPORT_BOUNDS_HH
+#define OST_MOL_EXPORT_BOUNDS_HH
+
+#include <ost/log.hh>
+
+template <typename H>
+geom::Vec3 geom_center(const H& h)
+{
+ return h.GetBounds().GetCenter();
+}
+
+template <typename H>
+geom::Vec3 geom_size(const H& h)
+{
+ LOGN_MESSAGE("GetBoundarySize()/boundary_size is deprecated. Use bounds.size"
+ " instead")
+ return h.GetBounds().GetSize();
+}
+
+template <typename H>
+geom::Vec3 geom_start(const H& h)
+{
+ LOGN_MESSAGE("GetGeometricStart()/geometric_start is deprecated. Use "
+ "bounds.min instead")
+ return h.GetBounds().GetMin();
+}
+
+template <typename H>
+geom::Vec3 geom_end(const H& h)
+{
+ LOGN_MESSAGE("GetGeometricEnd()/geometric_end is deprecated. Use "
+ "bounds.max instead")
+ return h.GetBounds().GetMax();
+}
+
+#endif
diff --git a/modules/mol/base/pymod/export_chain.cc b/modules/mol/base/pymod/export_chain.cc
index a0c603fd7..1e2e59285 100644
--- a/modules/mol/base/pymod/export_chain.cc
+++ b/modules/mol/base/pymod/export_chain.cc
@@ -25,6 +25,7 @@ using namespace boost::python;
using namespace ost;
using namespace ost::mol;
#include <ost/export_helper/generic_property_def.hh>
+#include "bounds.hh"
namespace {
typedef void (ChainHandle::*RnumMethod)(const ResNum&);
@@ -83,15 +84,17 @@ void export_Chain()
.def("GetMass", &ChainHandle::GetMass)
.def("GetCenterOfMass", &ChainHandle::GetCenterOfMass)
.def("GetCenterOfAtoms", &ChainHandle::GetCenterOfAtoms)
- .def("GetGeometricCenter", &ChainHandle::GetGeometricCenter)
- .add_property("geometric_center", &ChainHandle::GetGeometricCenter)
+ .def("GetGeometricCenter", geom_center<ChainHandle>)
+ .add_property("geometric_center", geom_center<ChainHandle>)
.add_property("mass", &ChainHandle::GetMass)
.add_property("center_of_mass", &ChainHandle::GetCenterOfMass)
.add_property("center_of_atoms", &ChainHandle::GetCenterOfAtoms)
.add_property("in_sequence", &ChainHandle::InSequence)
.add_property("valid", &ChainHandle::IsValid)
- .def("GetGeometricStart", &ChainHandle::GetGeometricStart)
- .def("GetGeometricEnd", &ChainHandle::GetGeometricEnd)
+ .def("GetBounds", &ChainHandle::GetBounds)
+ .add_property("bounds", &ChainHandle::GetBounds)
+ .def("GetGeometricStart", geom_start<ChainHandle>)
+ .def("GetGeometricEnd", geom_end<ChainHandle>)
;
class_<ChainHandleList>("ChainHandleList", no_init)
diff --git a/modules/mol/base/pymod/export_chain_view.cc b/modules/mol/base/pymod/export_chain_view.cc
index ee6753b52..471b592a1 100644
--- a/modules/mol/base/pymod/export_chain_view.cc
+++ b/modules/mol/base/pymod/export_chain_view.cc
@@ -27,6 +27,7 @@ using namespace boost::python;
#include <ost/export_helper/vector.hh>
using namespace ost;
using namespace ost::mol;
+#include "bounds.hh"
namespace {
typedef ResidueView (ChainView::*RnumMethod)(const ResNum&) const;
@@ -92,15 +93,17 @@ void export_ChainView()
.def("GetMass", &ChainView::GetMass)
.def("GetCenterOfMass", &ChainView::GetCenterOfMass)
.def("GetCenterOfAtoms", &ChainView::GetCenterOfAtoms)
- .def("GetGeometricCenter", &ChainView::GetGeometricCenter)
- .add_property("geometric_center", &ChainView::GetGeometricCenter)
+ .def("GetGeometricCenter", geom_center<ChainView>)
+ .add_property("geometric_center", geom_center<ChainView>)
.add_property("mass", &ChainView::GetMass)
.add_property("center_of_mass", &ChainView::GetCenterOfMass)
.add_property("center_of_atoms", &ChainView::GetCenterOfAtoms)
.add_property("valid", &ChainView::IsValid)
.add_property("in_sequence", &ChainView::InSequence)
- .def("GetGeometricStart", &ChainView::GetGeometricStart)
- .def("GetGeometricEnd", &ChainView::GetGeometricEnd)
+ .def("GetGeometricStart", geom_start<ChainView>)
+ .def("GetGeometricEnd", geom_end<ChainView>)
+ .def("GetBounds", &ChainView::GetBounds)
+ .add_property("bounds", &ChainView::GetBounds)
;
diff --git a/modules/mol/base/pymod/export_entity.cc b/modules/mol/base/pymod/export_entity.cc
index a8fa1c8d8..b0df16c0c 100644
--- a/modules/mol/base/pymod/export_entity.cc
+++ b/modules/mol/base/pymod/export_entity.cc
@@ -23,7 +23,7 @@ using namespace boost::python;
#include <ost/mol/entity_view.hh>
#include <ost/mol/query.hh>
#include <ost/mol/mol.hh>
-
+#include "bounds.hh"
using namespace ost;
using namespace ost::mol;
@@ -55,6 +55,7 @@ BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(X_xcs_editor_overloads,
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(X_ics_editor_overloads,
EntityHandle::RequestICSEditor, 0, 1)
+
}
void export_Entity()
@@ -81,11 +82,13 @@ void export_Entity()
.def("GetMass", &EntityHandle::GetMass)
.def("GetCenterOfMass", &EntityHandle::GetCenterOfMass)
.def("GetCenterOfAtoms", &EntityHandle::GetCenterOfAtoms)
- .def("GetGeometricCenter", &EntityHandle::GetGeometricCenter)
- .add_property("geometric_center", &EntityHandle::GetGeometricCenter)
- .def("GetGeometricStart", &EntityHandle::GetGeometricStart)
- .def("GetGeometricEnd", &EntityHandle::GetGeometricEnd)
- .def("GetBoundarySize", &EntityHandle::GetBoundarySize)
+ .def("GetGeometricCenter", geom_center<EntityHandle>)
+ .add_property("geometric_center", geom_center<EntityHandle>)
+ .add_property("geometric_end", geom_end<EntityHandle>)
+ .add_property("geometric_start", geom_start<EntityHandle>)
+ .def("GetGeometricStart", geom_start<EntityHandle>)
+ .def("GetGeometricEnd", geom_end<EntityHandle>)
+ .def("GetBoundarySize", geom_size<EntityHandle>)
.def("GetResidueCount", &EntityHandle::GetResidueCount)
.def("GetAtomCount", &EntityHandle::GetAtomCount)
.def("GetBondCount", &EntityHandle::GetBondCount)
@@ -111,6 +114,8 @@ void export_Entity()
.add_property("chains", &EntityHandle::GetChainList)
.add_property("bonds", &EntityHandle::GetBondList)
.add_property("valid", &EntityHandle::IsValid)
+ .def("GetBounds", &EntityHandle::GetBounds)
+ .add_property("bounds", &EntityHandle::GetBounds)
.def("GetTransformationMatrix", &EntityHandle::GetTransformationMatrix,
return_value_policy<copy_const_reference>())
.add_property("transform",
diff --git a/modules/mol/base/pymod/export_entity_view.cc b/modules/mol/base/pymod/export_entity_view.cc
index aaa75efb7..3b3eadab2 100644
--- a/modules/mol/base/pymod/export_entity_view.cc
+++ b/modules/mol/base/pymod/export_entity_view.cc
@@ -26,6 +26,7 @@ using namespace boost::python;
#include <ost/mol/view_op.hh>
using namespace ost;
using namespace ost::mol;
+#include "bounds.hh"
namespace {
@@ -90,10 +91,10 @@ void export_EntityView()
.def("FindAtom", find_atom_a)
.def("FindAtom", find_atom_b)
.def("GetAtomCount", &EntityView::GetAtomCount)
- .def("GetGeometricStart", &EntityView::GetGeometricStart)
- .def("GetGeometricEnd", &EntityView::GetGeometricEnd)
- .def("GetGeometricCenter", &EntityView::GetGeometricCenter)
- .add_property("geometric_center", &EntityView::GetGeometricCenter)
+ .def("GetGeometricStart", geom_start<EntityView>)
+ .def("GetGeometricEnd", geom_end<EntityView>)
+ .def("GetGeometricCenter", geom_center<EntityView>)
+ .add_property("geometric_center", geom_center<EntityView>)
.def("GetCenterOfMass", &EntityView::GetCenterOfMass)
.def("GetCenterOfAtoms", &EntityView::GetCenterOfAtoms)
.def("GetMass", &EntityView::GetMass)
@@ -153,6 +154,8 @@ void export_EntityView()
.def(self==self)
.def(self!=self)
.def("Dump", &EntityView::Dump)
+ .def("GetBounds", &EntityView::GetBounds)
+ .add_property("bounds", &EntityView::GetBounds)
;
def("Union", &Union);
def("Difference", &Difference);
diff --git a/modules/mol/base/pymod/export_residue.cc b/modules/mol/base/pymod/export_residue.cc
index 532f4b0a2..ef844831c 100644
--- a/modules/mol/base/pymod/export_residue.cc
+++ b/modules/mol/base/pymod/export_residue.cc
@@ -27,7 +27,7 @@ using namespace ost;
using namespace ost::mol;
#include <ost/export_helper/generic_property_def.hh>
-
+#include "bounds.hh"
namespace {
@@ -165,20 +165,22 @@ void export_Residue()
.def("GetMass", &ResidueHandle::GetMass)
.def("GetCenterOfMass", &ResidueHandle::GetCenterOfMass)
.def("GetCenterOfAtoms", &ResidueHandle::GetCenterOfAtoms)
- .def("GetGeometricCenter", &ResidueHandle::GetGeometricCenter)
+ .def("GetGeometricCenter", geom_center<ResidueHandle>)
.add_property("mass", &ResidueHandle::GetMass)
.add_property("center_of_mass", &ResidueHandle::GetCenterOfMass)
.add_property("center_of_atoms", &ResidueHandle::GetCenterOfAtoms)
- .add_property("geometric_center", &ResidueHandle::GetGeometricCenter)
+ .add_property("geometric_center", geom_center<ResidueHandle>)
.add_property("phi_torsion", &ResidueHandle::GetPhiTorsion)
.add_property("psi_torsion", &ResidueHandle::GetPsiTorsion)
.add_property("omega_torsion", &ResidueHandle::GetOmegaTorsion)
.add_property("valid", &ResidueHandle::IsValid)
- .def("GetGeometricStart", &ResidueHandle::GetGeometricStart)
- .def("GetGeometricEnd", &ResidueHandle::GetGeometricEnd)
+ .def("GetGeometricStart", geom_start<ResidueHandle>)
+ .def("GetGeometricEnd", geom_end<ResidueHandle>)
.def(self==self)
.def(self!=self)
.def("__hash__", &ResidueHandle::GetHashCode)
+ .def("GetBounds", &ResidueHandle::GetBounds)
+ .add_property("bounds", &ResidueHandle::GetBounds)
;
class_<ResidueHandleList>("ResidueHandleList", no_init)
diff --git a/modules/mol/base/pymod/export_residue_view.cc b/modules/mol/base/pymod/export_residue_view.cc
index 63bd1c746..f8dbd0896 100644
--- a/modules/mol/base/pymod/export_residue_view.cc
+++ b/modules/mol/base/pymod/export_residue_view.cc
@@ -25,6 +25,7 @@ using namespace boost::python;
#include <ost/export_helper/vector.hh>
using namespace ost;
using namespace ost::mol;
+#include "bounds.hh"
namespace {
typedef AtomView (ResidueView::*StringMethod)(const String&) const;
@@ -79,14 +80,16 @@ void export_ResidueView()
.def("GetMass", &ResidueView::GetMass)
.def("GetCenterOfMass", &ResidueView::GetCenterOfMass)
.def("GetCenterOfAtoms", &ResidueView::GetCenterOfAtoms)
- .def("GetGeometricCenter", &ResidueView::GetGeometricCenter)
+ .def("GetGeometricCenter", geom_center<ResidueView>)
.add_property("mass", &ResidueView::GetMass)
.add_property("center_of_mass", &ResidueView::GetCenterOfMass)
.add_property("center_of_atoms", &ResidueView::GetCenterOfAtoms)
- .add_property("geometric_center", &ResidueView::GetGeometricCenter)
+ .add_property("geometric_center", geom_center<ResidueView>)
.add_property("valid", &ResidueView::IsValid)
- .def("GetGeometricStart", &ResidueView::GetGeometricStart)
- .def("GetGeometricEnd", &ResidueView::GetGeometricEnd)
+ .def("GetGeometricStart", geom_start<ResidueView>)
+ .def("GetGeometricEnd", geom_end<ResidueView>)
+ .def("GetBounds", &ResidueView::GetBounds)
+ .add_property("bounds", &ResidueView::GetBounds)
;
diff --git a/modules/mol/base/src/bounding_box.cc b/modules/mol/base/src/bounding_box.cc
index 8fd6a49d8..15473b5de 100644
--- a/modules/mol/base/src/bounding_box.cc
+++ b/modules/mol/base/src/bounding_box.cc
@@ -36,7 +36,7 @@ public:
PrincipalAxisCalc(const EntityHandle& ent):
natoms_(ent.GetAtomCount())
{
- mean_=ent.GetGeometricCenter();
+ mean_=ent.GetBounds().GetCenter();
cov_.setZero();
}
PrincipalAxisCalc(const AtomHandleList& atoms):
@@ -55,7 +55,7 @@ public:
PrincipalAxisCalc(const EntityView& ent):
natoms_(ent.GetAtomCount())
{
- mean_=ent.GetGeometricCenter();
+ mean_=ent.GetBounds().GetCenter();
cov_.setZero();
}
virtual bool VisitAtom(const AtomHandle& atom)
diff --git a/modules/mol/base/src/chain_handle.cc b/modules/mol/base/src/chain_handle.cc
index 842017ae4..1f0e8094c 100644
--- a/modules/mol/base/src/chain_handle.cc
+++ b/modules/mol/base/src/chain_handle.cc
@@ -197,22 +197,10 @@ void ChainHandle::AssignSecondaryStructure(SecStructure ss,
Impl()->AssignSecondaryStructure(ss, start, end);
}
-geom::Vec3 ChainHandle::GetGeometricCenter() const
+geom::AlignedCuboid ChainHandle::GetBounds() const
{
this->CheckValidity();
- return Impl()->GetGeometricCenter();
-}
-
-geom::Vec3 ChainHandle::GetGeometricStart() const
-{
- this->CheckValidity();
- return Impl()->GetGeometricStart();
-}
-
-geom::Vec3 ChainHandle::GetGeometricEnd() const
-{
- this->CheckValidity();
- return Impl()->GetGeometricEnd();
+ return Impl()->GetBounds();
}
geom::Vec3 ChainHandle::GetCenterOfMass() const
diff --git a/modules/mol/base/src/chain_handle.hh b/modules/mol/base/src/chain_handle.hh
index 0faa7ee8f..6337818de 100644
--- a/modules/mol/base/src/chain_handle.hh
+++ b/modules/mol/base/src/chain_handle.hh
@@ -166,18 +166,7 @@ public:
/// similar to GetCenterOfMass(), but the atoms are not mass weighted
geom::Vec3 GetCenterOfAtoms() const;
- /// \brief Get entity's geometric center
- ///
- /// Returns the geometric center of the entity's bounding box
- /// by calculating (GetGeometricStart()+GetGeometricEnd())/2
- geom::Vec3 GetGeometricCenter() const;
-
- /// \brief Get entity's minimum cartesian coordinates
- geom::Vec3 GetGeometricStart() const;
-
- /// \brief Get entity's maximum cartesian coordinates
- geom::Vec3 GetGeometricEnd() const;
-
+ geom::AlignedCuboid GetBounds() const;
/// \brief assign secondary structure to the inclusive residue range
/// start, end
void AssignSecondaryStructure(SecStructure ss,
diff --git a/modules/mol/base/src/chain_view.cc b/modules/mol/base/src/chain_view.cc
index fac143b85..1c5ba252e 100644
--- a/modules/mol/base/src/chain_view.cc
+++ b/modules/mol/base/src/chain_view.cc
@@ -327,44 +327,29 @@ Real ChainView::GetMass() const {
return mass;
}
-geom::Vec3 ChainView::GetGeometricStart() const
+geom::AlignedCuboid ChainView::GetBounds() const
{
this->CheckValidity();
- geom::Vec3 minimum(std::numeric_limits<Real>::max(),
- std::numeric_limits<Real>::max(),
- std::numeric_limits<Real>::max());
- ResidueViewList::const_iterator i;
- for (i=data_->residues.begin(); i!=data_->residues.end(); ++i) {
- ResidueView r=*i;
- for (AtomViewList::const_iterator j=r.GetAtomList().begin(),
- e2=r.GetAtomList().end(); j!=e2; ++j) {
- minimum=geom::Min(minimum, j->GetPos());
- }
- }
- return minimum;
-}
+ geom::Vec3 mmin( std::numeric_limits<Real>::max());
+ geom::Vec3 mmax(-std::numeric_limits<Real>::max());
-geom::Vec3 ChainView::GetGeometricEnd() const
-{
- this->CheckValidity();
- geom::Vec3 maximum(-std::numeric_limits<Real>::max(),
- -std::numeric_limits<Real>::max(),
- -std::numeric_limits<Real>::max());
- ResidueViewList::const_iterator i;
- for (i=data_->residues.begin(); i!=data_->residues.end(); ++i) {
+
+ bool atoms=false;
+ for (ResidueViewList::const_iterator
+ i=data_->residues.begin(); i!=data_->residues.end(); ++i) {
ResidueView r=*i;
for (AtomViewList::const_iterator j=r.GetAtomList().begin(),
e2=r.GetAtomList().end(); j!=e2; ++j) {
- maximum=geom::Max(maximum, j->GetPos());
+ mmin=geom::Min(mmin, j->GetPos());
+ mmax=geom::Max(mmax, j->GetPos());
+ atoms=true;
}
}
- return maximum;
-}
-
-geom::Vec3 ChainView::GetGeometricCenter() const
-{
- this->CheckValidity();
- return (this->GetGeometricStart() + this->GetGeometricEnd())/2;
+ if (atoms) {
+ return geom::AlignedCuboid(mmin, mmax);
+ } else {
+ return geom::AlignedCuboid(geom::Vec3(), geom::Vec3());
+ }
}
geom::Vec3 ChainView::GetCenterOfAtoms() const
diff --git a/modules/mol/base/src/chain_view.hh b/modules/mol/base/src/chain_view.hh
index 3be942a56..800d1fc82 100644
--- a/modules/mol/base/src/chain_view.hh
+++ b/modules/mol/base/src/chain_view.hh
@@ -143,14 +143,8 @@ public:
/// similar to GetCenterOfMass(), but the atoms are not mass weighted
geom::Vec3 GetCenterOfAtoms() const;
- /// \brief Get entity's geometric center
- ///
- /// Returns the geometric center of the entity's bounding box
- /// by calculating (GetGeometricStart()+GetGeometricEnd())/2
- geom::Vec3 GetGeometricCenter() const;
-
- geom::Vec3 GetGeometricStart() const;
- geom::Vec3 GetGeometricEnd() const;
+ /// \brief Get entity's axis aligned bounding box
+ geom::AlignedCuboid GetBounds() const;
/// /// \brief remove all residues from the view
void RemoveResidues();
diff --git a/modules/mol/base/src/entity_handle.cc b/modules/mol/base/src/entity_handle.cc
index b7fad6713..17c47cd81 100644
--- a/modules/mol/base/src/entity_handle.cc
+++ b/modules/mol/base/src/entity_handle.cc
@@ -55,25 +55,12 @@ geom::Vec3 EntityHandle::GetCenterOfAtoms() const {
return Impl()->GetCenterOfAtoms();
}
-geom::Vec3 EntityHandle::GetGeometricCenter() const {
- this->CheckValidity();
- return Impl()->GetGeometricCenter();
-}
-
-geom::Vec3 EntityHandle::GetGeometricStart() const {
- this->CheckValidity();
- return Impl()->GetGeometricStart();
-}
-
-geom::Vec3 EntityHandle::GetGeometricEnd() const {
+geom::AlignedCuboid EntityHandle::GetBounds() const
+{
this->CheckValidity();
- return Impl()->GetGeometricEnd();
+ return Impl()->GetBounds();
}
-geom::Vec3 EntityHandle::GetBoundarySize() const {
- this->CheckValidity();
- return Impl()->GetBoundarySize();
-}
EntityHandle::EntityHandle(const impl::EntityImplPtr& e)
: EntityBase(e)
diff --git a/modules/mol/base/src/entity_handle.hh b/modules/mol/base/src/entity_handle.hh
index 9bb291d8e..540425c70 100644
--- a/modules/mol/base/src/entity_handle.hh
+++ b/modules/mol/base/src/entity_handle.hh
@@ -84,20 +84,8 @@ public:
/// \brief Get entity's center of mass (mass weighted)
geom::Vec3 GetCenterOfMass() const;
- /// \brief Get entity's geometric center
- ///
- /// Returns the geometric center of the entity's bounding box
- /// by calculating (GetGeometricStart()+GetGeometricEnd())/2
- geom::Vec3 GetGeometricCenter() const;
-
- /// \brief Get entity's minimum cartesian coordinates
- geom::Vec3 GetGeometricStart() const;
-
- /// \brief Get entity's maximum cartesian coordinates
- geom::Vec3 GetGeometricEnd() const;
- /// \brief Get size of the entity
- geom::Vec3 GetBoundarySize() const;
+ geom::AlignedCuboid GetBounds() const;
//@}
/// \brief
diff --git a/modules/mol/base/src/entity_view.cc b/modules/mol/base/src/entity_view.cc
index b6c5deabc..6be3145f3 100644
--- a/modules/mol/base/src/entity_view.cc
+++ b/modules/mol/base/src/entity_view.cc
@@ -171,13 +171,6 @@ geom::Vec3 EntityView::GetCenterOfAtoms() const
return center;
}
-geom::Vec3 EntityView::GetGeometricCenter() const
-{
- geom::Vec3 center;
- center = (this->GetGeometricEnd() + this->GetGeometricStart())/2;
- return center;
-}
-
geom::Vec3 EntityView::GetCenterOfMass() const
{
geom::Vec3 center;
@@ -726,17 +719,6 @@ AtomView EntityView::FindXAtom(const AtomHandle& ah)
}
#endif
-geom::Vec3 EntityView::GetGeometricStart() const
-{
- this->CheckValidity();
- geom::Vec3 m(std::numeric_limits<Real>::max(),
- std::numeric_limits<Real>::max(),
- std::numeric_limits<Real>::max());
- for(AtomViewIter it=AtomsBegin(); it!=this->AtomsEnd(); ++it) {
- m=geom::Min(m, (*it).GetPos());
- }
- return m;
-}
AtomView EntityView::FindAtom(const String& chain_name,
const ResNum& num,
@@ -749,16 +731,20 @@ AtomView EntityView::FindAtom(const String& chain_name,
}
return AtomView();
}
-geom::Vec3 EntityView::GetGeometricEnd() const
+geom::AlignedCuboid EntityView::GetBounds() const
{
this->CheckValidity();
- geom::Vec3 m(-std::numeric_limits<Real>::max(),
- -std::numeric_limits<Real>::max(),
- -std::numeric_limits<Real>::max());
- for(AtomViewIter it=AtomsBegin(); it!=this->AtomsEnd(); ++it) {
- m=geom::Max(m, (*it).GetPos());
+ geom::Vec3 mmin( std::numeric_limits<Real>::max());
+ geom::Vec3 mmax(-std::numeric_limits<Real>::max());
+ if (this->GetAtomCount()) {
+ for(AtomViewIter it=AtomsBegin(); it!=this->AtomsEnd(); ++it) {
+ mmax=geom::Max(mmax, (*it).GetPos());
+ mmin=geom::Min(mmin, (*it).GetPos());
+ }
+ return geom::AlignedCuboid(mmin, mmax);
+ } else {
+ return geom::AlignedCuboid(geom::Vec3(), geom::Vec3());
}
- return m;
}
diff --git a/modules/mol/base/src/entity_view.hh b/modules/mol/base/src/entity_view.hh
index e55894da5..6e3aa7bf8 100644
--- a/modules/mol/base/src/entity_view.hh
+++ b/modules/mol/base/src/entity_view.hh
@@ -108,14 +108,8 @@ public:
/// similar to GetCenterOfMass(), but the atoms are not mass weighted
geom::Vec3 GetCenterOfAtoms() const;
- /// \brief Get entity's geometric center
- ///
- /// Returns the geometric center of the entity's bounding box
- /// by calculating (GetGeometricStart()+GetGeometricEnd())/2
- geom::Vec3 GetGeometricCenter() const;
-
- geom::Vec3 GetGeometricStart() const;
- geom::Vec3 GetGeometricEnd() const;
+ geom::AlignedCuboid GetBounds() const;
+
public:
/// \name Internal
//@{
diff --git a/modules/mol/base/src/impl/chain_impl.cc b/modules/mol/base/src/impl/chain_impl.cc
index 02f4636c1..8b9d74876 100644
--- a/modules/mol/base/src/impl/chain_impl.cc
+++ b/modules/mol/base/src/impl/chain_impl.cc
@@ -363,41 +363,27 @@ Real ChainImpl::GetMass() const
return mass;
}
-geom::Vec3 ChainImpl::GetGeometricStart() const
+geom::AlignedCuboid ChainImpl::GetBounds() const
{
- geom::Vec3 minimum(std::numeric_limits<Real>::infinity(),
- std::numeric_limits<Real>::infinity(),
- std::numeric_limits<Real>::infinity());
+ geom::Vec3 mmin( std::numeric_limits<Real>::infinity());
+ geom::Vec3 mmax(-std::numeric_limits<Real>::infinity());
+ bool atoms=false;
for (ResidueImplList::const_iterator i=residue_list_.begin();
i!=residue_list_.end(); ++i) {
ResidueImplPtr r=*i;
for (AtomImplList::iterator j=r->GetAtomList().begin();
j!=r->GetAtomList().end(); ++j) {
- minimum=geom::Min(minimum,(*j)->GetPos());
+ mmin=geom::Min(mmin, (*j)->GetPos());
+ mmax=geom::Max(mmax, (*j)->GetPos());
+ atoms=true;
}
}
- return minimum;
-}
-
-geom::Vec3 ChainImpl::GetGeometricEnd() const {
- geom::Vec3 maximum(-std::numeric_limits<Real>::infinity(),
- -std::numeric_limits<Real>::infinity(),
- -std::numeric_limits<Real>::infinity());
- for (ResidueImplList::const_iterator i=residue_list_.begin();
- i!=residue_list_.end(); ++i) {
- ResidueImplPtr r=*i;
- for (AtomImplList::iterator j=r->GetAtomList().begin();
- j!=r->GetAtomList().end(); ++j) {
- maximum=geom::Max(maximum,(*j)->GetPos());
- }
+ if (!atoms) {
+ return geom::AlignedCuboid(geom::Vec3(), geom::Vec3());
}
- return maximum;
+ return geom::AlignedCuboid(mmin, mmax);
}
-geom::Vec3 ChainImpl::GetGeometricCenter() const
-{
- return (this->GetGeometricStart() + this->GetGeometricEnd()) / 2;
-}
geom::Vec3 ChainImpl::GetCenterOfAtoms() const
{
diff --git a/modules/mol/base/src/impl/chain_impl.hh b/modules/mol/base/src/impl/chain_impl.hh
index 644bed1e7..1737ca4f5 100644
--- a/modules/mol/base/src/impl/chain_impl.hh
+++ b/modules/mol/base/src/impl/chain_impl.hh
@@ -81,9 +81,10 @@ public:
Real GetMass() const;
geom::Vec3 GetCenterOfMass() const;
geom::Vec3 GetCenterOfAtoms() const;
- geom::Vec3 GetGeometricCenter() const;
- geom::Vec3 GetGeometricStart() const;
- geom::Vec3 GetGeometricEnd() const;
+
+ /// \brief returns the axis-aligned bounding box of the entity
+ geom::AlignedCuboid GetBounds() const;
+
///\brief Get residue by number. Returns a invalid pointer if the chain
/// does not have any residue with this number.
diff --git a/modules/mol/base/src/impl/entity_impl.cc b/modules/mol/base/src/impl/entity_impl.cc
index e71734222..8d17d4a13 100644
--- a/modules/mol/base/src/impl/entity_impl.cc
+++ b/modules/mol/base/src/impl/entity_impl.cc
@@ -262,60 +262,29 @@ EntityImpl::~EntityImpl()
it->second->OnDestroy();
}
}
-
-geom::Vec3 EntityImpl::GetGeometricStart() const
+geom::AlignedCuboid EntityImpl::GetBounds() const
{
- geom::Vec3 minimum(std::numeric_limits<Real>::infinity(),
- std::numeric_limits<Real>::infinity(),
- std::numeric_limits<Real>::infinity());
- if (this->GetAtomCount()>0) {
- for(AtomImplMap::const_iterator it = atom_map_.begin();it!=atom_map_.end();++it) {
- minimum=geom::Min(minimum,it->second->GetPos());
- }
- }
- return minimum;
-}
-
-geom::Vec3 EntityImpl::GetGeometricEnd() const {
- geom::Vec3 maximum(-std::numeric_limits<Real>::infinity(),
- -std::numeric_limits<Real>::infinity(),
- -std::numeric_limits<Real>::infinity());
- if (this->GetAtomCount()>0) {
- for(AtomImplMap::const_iterator it = atom_map_.begin();it!=atom_map_.end();++it) {
- maximum=geom::Max(maximum,it->second->GetPos());
- }
- }
- return maximum;
-}
-geom::Vec3 EntityImpl::GetBoundarySize() const {
- geom::Vec3 size;
- geom::Vec3 minimum(std::numeric_limits<Real>::infinity(),
- std::numeric_limits<Real>::infinity(),
- std::numeric_limits<Real>::infinity());
- geom::Vec3 maximum(-std::numeric_limits<Real>::infinity(),
- -std::numeric_limits<Real>::infinity(),
- -std::numeric_limits<Real>::infinity());
if (this->GetAtomCount()>0) {
- for(AtomImplMap::const_iterator it = atom_map_.begin();it!=atom_map_.end();++it) {
- minimum=geom::Min(minimum,it->second->GetPos());
- maximum=geom::Max(maximum,it->second->GetPos());
+ geom::Vec3 mmin, mmax;
+ AtomImplMap::const_iterator it=atom_map_.begin();
+ mmin=mmax=it->second->GetPos();
+ for (++it; it!=atom_map_.end();++it) {
+ mmin=geom::Min(mmin,it->second->GetPos());
+ mmax=geom::Min(mmax,it->second->GetPos());
}
+ return geom::AlignedCuboid(mmin, mmax);
+ } else {
+ return geom::AlignedCuboid(geom::Vec3(), geom::Vec3());
}
- size=maximum-minimum;
- return size;
-}
-geom::Vec3 EntityImpl::GetGeometricCenter() const {
- geom::Vec3 center;
- center = (this->GetGeometricEnd() + this->GetGeometricStart())/2;
- return center;
}
geom::Vec3 EntityImpl::GetCenterOfAtoms() const {
geom::Vec3 center;
if (this->GetAtomCount()>0) {
- for(AtomImplMap::const_iterator it = atom_map_.begin();it!=atom_map_.end();++it) {
+ for (AtomImplMap::const_iterator it = atom_map_.begin();
+ it!=atom_map_.end();++it) {
center+=it->second->GetPos();
}
center/=static_cast<Real>(atom_map_.size());
diff --git a/modules/mol/base/src/impl/entity_impl.hh b/modules/mol/base/src/impl/entity_impl.hh
index ca83cf254..ae1208f5e 100644
--- a/modules/mol/base/src/impl/entity_impl.hh
+++ b/modules/mol/base/src/impl/entity_impl.hh
@@ -93,10 +93,11 @@ public:
Real GetMass() const;
geom::Vec3 GetCenterOfMass() const;
geom::Vec3 GetCenterOfAtoms() const;
- geom::Vec3 GetGeometricCenter() const;
- geom::Vec3 GetGeometricStart() const;
- geom::Vec3 GetGeometricEnd() const;
- geom::Vec3 GetBoundarySize() const;
+
+ /// \brief returns the axis-aligned bounding box of the entity
+ geom::AlignedCuboid GetBounds() const;
+
+
// default copy ctor and assignment op should work for now
AtomImplPtr CreateAtom(const ResidueImplPtr& rp, const String& name,
diff --git a/modules/mol/base/src/impl/residue_impl.cc b/modules/mol/base/src/impl/residue_impl.cc
index bfee30477..225c5a974 100644
--- a/modules/mol/base/src/impl/residue_impl.cc
+++ b/modules/mol/base/src/impl/residue_impl.cc
@@ -427,31 +427,23 @@ Real ResidueImpl::GetMass() const
return mass;
}
-geom::Vec3 ResidueImpl::GetGeometricEnd() const {
- geom::Vec3 maximum(-std::numeric_limits<Real>::infinity(),
- -std::numeric_limits<Real>::infinity(),
- -std::numeric_limits<Real>::infinity());
- for (AtomImplList::const_iterator i=atom_list_.begin();
- i!=atom_list_.end(); ++i) {
- maximum=geom::Max(maximum,(*i)->GetPos());
- }
- return maximum;
-}
-
-geom::Vec3 ResidueImpl::GetGeometricStart() const {
- geom::Vec3 minimum(std::numeric_limits<Real>::infinity(),
- std::numeric_limits<Real>::infinity(),
- std::numeric_limits<Real>::infinity());
- for (AtomImplList::const_iterator i=atom_list_.begin();
- i!=atom_list_.end(); ++i) {
- minimum=geom::Min(minimum,(*i)->GetPos());
- }
- return minimum;
-}
-
-geom::Vec3 ResidueImpl::GetGeometricCenter() const
+geom::AlignedCuboid ResidueImpl::GetBounds() const
{
- return (this->GetGeometricStart() + this->GetGeometricEnd())/2;
+
+ geom::Vec3 mmin( std::numeric_limits<Real>::infinity());
+ geom::Vec3 mmax(-std::numeric_limits<Real>::infinity());
+
+ if (atom_list_.size()>0) {
+ AtomImplList::const_iterator i=atom_list_.begin();
+ mmin=mmax=(*i)->GetPos();
+ for (++i; i!=atom_list_.end(); ++i) {
+ mmax=geom::Max(mmax,(*i)->GetPos());
+ mmin=geom::Min(mmin,(*i)->GetPos());
+ }
+ return geom::AlignedCuboid(mmin, mmax);
+ } else {
+ return geom::AlignedCuboid(geom::Vec3(), geom::Vec3());
+ }
}
geom::Vec3 ResidueImpl::GetCenterOfAtoms() const
diff --git a/modules/mol/base/src/impl/residue_impl.hh b/modules/mol/base/src/impl/residue_impl.hh
index 22e816b6e..0e0393767 100644
--- a/modules/mol/base/src/impl/residue_impl.hh
+++ b/modules/mol/base/src/impl/residue_impl.hh
@@ -131,9 +131,9 @@ public:
Real GetMass() const;
geom::Vec3 GetCenterOfMass() const;
geom::Vec3 GetCenterOfAtoms() const;
- geom::Vec3 GetGeometricCenter() const;
- geom::Vec3 GetGeometricStart() const;
- geom::Vec3 GetGeometricEnd() const;
+
+ geom::AlignedCuboid GetBounds() const;
+
void DeleteAtom(const AtomImplPtr& atom);
void DeleteAtoms(const String& atom_name);
diff --git a/modules/mol/base/src/residue_handle.cc b/modules/mol/base/src/residue_handle.cc
index 1719708c9..6c9e007d8 100644
--- a/modules/mol/base/src/residue_handle.cc
+++ b/modules/mol/base/src/residue_handle.cc
@@ -226,22 +226,10 @@ geom::Vec3 ResidueHandle::GetAltAtomPos(const AtomHandle& atom,
return Impl()->GetAltAtomPos(atom.Impl(), group);
}
-geom::Vec3 ResidueHandle::GetGeometricStart() const
+geom::AlignedCuboid ResidueHandle::GetBounds() const
{
this->CheckValidity();
- return Impl()->GetGeometricStart();
-}
-
-geom::Vec3 ResidueHandle::GetGeometricEnd() const
-{
- this->CheckValidity();
- return Impl()->GetGeometricEnd();
-}
-
-geom::Vec3 ResidueHandle::GetGeometricCenter() const
-{
- this->CheckValidity();
- return Impl()->GetGeometricCenter();
+ return Impl()->GetBounds();
}
geom::Vec3 ResidueHandle::GetCenterOfMass() const
diff --git a/modules/mol/base/src/residue_handle.hh b/modules/mol/base/src/residue_handle.hh
index 0d85e6e7f..57b7c5619 100644
--- a/modules/mol/base/src/residue_handle.hh
+++ b/modules/mol/base/src/residue_handle.hh
@@ -19,9 +19,11 @@
#ifndef OST_RESIDUE_HANDLE_HU
#define OST_RESIDUE_HANDLE_HU
+#include <ost/geom/vec3.hh>
+#include <ost/geom/aligned_cuboid.hh>
+
#include <ost/mol/query.hh>
#include <ost/mol/module_config.hh>
-#include <ost/geom/vec3.hh>
#include <ost/mol/residue_base.hh>
#include <ost/mol/atom_prop.hh>
#include <ost/mol/entity_visitor_fw.hh>
@@ -77,17 +79,8 @@ public:
/// similar to GetCenterOfMass(), but the atoms are not mass weighted
geom::Vec3 GetCenterOfAtoms() const;
- /// \brief Get entity's geometric center
- ///
- /// Returns the geometric center of the entity's bounding box
- /// by calculating (GetGeometricStart()+GetGeometricEnd())/2
- geom::Vec3 GetGeometricCenter() const;
-
- /// \brief Get entity's minimum cartesian coordinates
- geom::Vec3 GetGeometricStart() const;
-
- /// \brief Get entity's maximum cartesian coordinates
- geom::Vec3 GetGeometricEnd() const;
+ /// \brief get axis-aligned bounding box of residue
+ geom::AlignedCuboid GetBounds() const;
/// \brief The chain this residue is attached to
ChainHandle GetChain() const;
diff --git a/modules/mol/base/src/residue_view.cc b/modules/mol/base/src/residue_view.cc
index 72c5ff76f..53e0a3eaa 100644
--- a/modules/mol/base/src/residue_view.cc
+++ b/modules/mol/base/src/residue_view.cc
@@ -205,36 +205,17 @@ double ResidueView::GetMass() const
return mass;
}
-geom::Vec3 ResidueView::GetGeometricStart() const
+geom::AlignedCuboid ResidueView::GetBounds() const
{
this->CheckValidity();
- geom::Vec3 minimum(std::numeric_limits<Real>::max(),
- std::numeric_limits<Real>::max(),
- std::numeric_limits<Real>::max());
+ geom::Vec3 mmin( std::numeric_limits<Real>::max());
+ geom::Vec3 mmax(-std::numeric_limits<Real>::max());
AtomViewList::const_iterator i;
for (i=data_->atoms.begin(); i!=data_->atoms.end(); ++i) {
- minimum=geom::Min(minimum, (*i).GetPos());
+ mmin=geom::Min(mmin, (*i).GetPos());
+ mmax=geom::Max(mmax, (*i).GetPos());
}
- return minimum;
-}
-
-geom::Vec3 ResidueView::GetGeometricEnd() const
-{
- this->CheckValidity();
- geom::Vec3 maximum(-std::numeric_limits<Real>::max(),
- -std::numeric_limits<Real>::max(),
- -std::numeric_limits<Real>::max());
- AtomViewList::const_iterator i;
- for (i=data_->atoms.begin(); i!=data_->atoms.end(); ++i) {
- maximum=geom::Max(maximum, (*i).GetPos());
- }
- return maximum;
-}
-
-geom::Vec3 ResidueView::GetGeometricCenter() const
-{
- this->CheckValidity();
- return (this->GetGeometricStart() + this->GetGeometricEnd())/2;
+ return geom::AlignedCuboid(mmin, mmax);
}
geom::Vec3 ResidueView::GetCenterOfMass() const
diff --git a/modules/mol/base/src/residue_view.hh b/modules/mol/base/src/residue_view.hh
index 0cd381e86..d771a95ce 100644
--- a/modules/mol/base/src/residue_view.hh
+++ b/modules/mol/base/src/residue_view.hh
@@ -153,14 +153,9 @@ public:
/// similar to GetCenterOfMass(), but the atoms are not mass weighted
geom::Vec3 GetCenterOfAtoms() const;
- /// \brief Get entity's geometric center
- ///
- /// Returns the geometric center of the entity's bounding box
- /// by calculating (GetGeometricStart()+GetGeometricEnd())/2
- geom::Vec3 GetGeometricCenter() const;
+ /// \brief Get entity's axis-aligned bounding box
+ geom::AlignedCuboid GetBounds() const;
- geom::Vec3 GetGeometricStart() const;
- geom::Vec3 GetGeometricEnd() const;
/// \brief return view based on a query object
/// \sa Query
--
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