diff --git a/code_fragments/entity/gfx_symmetry.py b/code_fragments/entity/gfx_symmetry.py
index a0d795ece75923058688a6a3ebabc2c9a3f8012e..bfef9fb1b8ba5511e32e970fdd244e572b86aa7e 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 1e4215f456887ce75341d2a2ac6ff8074dc6a054..242ba49b1b5b5bb6092728ef6a59a42154e6ad1f 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 bf269d55258f21ba21a56c010654ae3a3ab9e47d..ed69d1ae49011918f196cce57ac6e22cc8f06955 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 1e48f270c9417419adeb1096ca02acbc049d0740..e84c2b64a73f5bfe4a4d712028b1454127474f59 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 fecac337051c6b0f8fbe05eab6212ba6eef8fac8..1e534f1d100d4f3bca4b74ca87b21f36982acb5a 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 ceba5546acd05db0131eacfb4dc359d14216af6d..59706446935595833c11ecd2732556c3c855451e 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 0000000000000000000000000000000000000000..9182f67ee274e924e18ce2bd2538bcac55672c06
--- /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 a0c603fd799f3aea911aab9bba8bc661e405cb6d..1e2e59285e209914f56789b6545ab195bd8af489 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 ee6753b52d420cf3ae5ef360425a5390132cd464..471b592a13421b259427e56a8d0ce4939f45bed1 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 a8fa1c8d86ff6990c1e4ae838c0c24915e3dc0c2..b0df16c0c9065f8084127b48a1055cd29090d849 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 aaa75efb730ad624934bb3d1c1cf510bf6fa915e..3b3eadab25854ee278194bd82119bfb2861e291e 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 532f4b0a2b2d3e23a79ea73f8c59d130ab15685a..ef844831cb222c399cf5a4405803be9224c2c48e 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 63bd1c746a19ad3135852649cc25eebf6c7f9725..f8dbd089628879641e24731629afe92a108e4403 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 8fd6a49d80e043d7a82618b54a6ec58603dddbf0..15473b5def7f392e90962d048e1a2bde18e35a74 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 842017ae4ba00bee32ec4238239f211a39786f90..1f0e8094c10c8f95f5e6e71d48fb675f9ee63091 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 0faa7ee8fc2f691b3acc86d539300b93ca211843..6337818deeebc8356c1a08421173edc39da076ee 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 fac143b8527ef1c880c615f9fc5ff47808516fb9..1c5ba252e6c3d526ac711bb99f8031d860bda5e5 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 3be942a5648cbb4f51a5a909e577a1e255c1d4e4..800d1fc82434898e2cd1bd436e8df4dfb1f5be8b 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 b7fad67139096c0e07aa5323cb0fcf1929870b72..17c47cd81112c92ef308c598cf7c03202a1c6648 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 9bb291d8ea21cd21907ee65ec4d20b09ed1d99e7..540425c70219e49396c29ce19ef54850712edd70 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 b6c5deabc1defba0b2c8cf3976b449fd53d0ff4c..6be3145f35ac93cdfe8c4432a6978098b395aa42 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 e55894da5fa97e37911942c0151abd01f8ce2eab..6e3aa7bf8b07f102436f172e0ce1ff2ce618c724 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 02f4636c1cc5e60865ad92b5e7ddcd3901a23ed0..8b9d74876df5e0ad9e98f7fdcfd3dfc327efd49a 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 644bed1e734d8594620164051c80060eb1a33295..1737ca4f587a76e52d99617809cd3e148f8598d5 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 e717342227cc929559b261a672fed9ea26b181f4..8d17d4a133d641a88afb3cd81a5722223105eb9a 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 ca83cf254b3b0c6c8315260a719261105c488a1f..ae1208f5e4bb70b8f603055fb7f0d98299e70d9c 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 bfee304770bcb5ec53443cda276127dc1458b074..225c5a974ba2768ddb6fadea26d7d2876a9f44a8 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 22e816b6e851d79f2c4f56dedaddf23ae7cd4fef..0e03937674307b4b3b625c417bb86fa2046320c9 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 1719708c9a0e52b9a6892bfc9b8b3560150547d0..6c9e007d80a2d52ea1f69a981f81e5416adf283c 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 0d85e6e7fd460be23d463f1c7210da729e74edee..57b7c56192d3bdb9b0b9aa125e3eb4ec659d9b8b 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 72c5ff76fbd08034f744229f76c24e975ba4ee1d..53e0a3eaa79126ebbd6095a3c69719196a8d6c09 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 0cd381e86e08046fa59456b6e7cf48f44bfabd03..d771a95ce09a0ba448eaca0be2a391e53020ecdd 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