diff --git a/modules/gfx/src/impl/entity_detail.cc b/modules/gfx/src/impl/entity_detail.cc
index 1225df45778087ba1324815f30f8ea2188bc590b..572de5bb7e2b995fba33d204cf3e7745110a42f5 100644
--- a/modules/gfx/src/impl/entity_detail.cc
+++ b/modules/gfx/src/impl/entity_detail.cc
@@ -43,9 +43,9 @@ void GfxView::AddAtom(const AtomView& av)
AtomEntry ae(a,default_radius,
a.GetRadius(),
GfxObj::Ele2Color(a.GetElement()));
- atom_map[a.GetHashCode()]=ae;
+ atom_map[a.GetHandle().GetHashCode()]=ae;
if(av.GetBondCount()==0) {
- orphan_atom_list.push_back(a.GetHashCode());
+ orphan_atom_list.push_back(a.GetHandle().GetHashCode());
}
}
diff --git a/modules/mol/base/pymod/export_atom.cc b/modules/mol/base/pymod/export_atom.cc
index 83f2adc0648de4b6eaacccadfba7dbf0337d812b..c2133beb95fcc8cf280db30c176a075824eedf68 100644
--- a/modules/mol/base/pymod/export_atom.cc
+++ b/modules/mol/base/pymod/export_atom.cc
@@ -42,8 +42,6 @@ void export_Atom()
.add_property("qualified_name", &AtomBase::GetQualifiedName)
.def("IsValid", &AtomBase::IsValid)
.def(self_ns::str(self))
- .add_property("hash_code", &AtomBase::GetHashCode)
- .def("GetHashCode", &AtomBase::GetHashCode)
.def("GetAtomProps", &AtomBase::GetAtomProps,
return_value_policy<copy_const_reference>())
.def("SetAtomProps", &AtomBase::SetAtomProps, args("prop"))
@@ -86,10 +84,12 @@ void export_Atom()
.add_property("handle", &AtomHandle::GetHandle)
.add_property("entity", &AtomHandle::GetEntity)
.def("GetBondPartners", &AtomHandle::GetBondPartners)
+ .def("GetHashCode", &AtomHandle::GetHashCode)
.def("FindBondToAtom", &AtomHandle::FindBondToAtom, args("other_atom"))
.def(self==self)
.def(self!=self)
.def("__hash__", &AtomHandle::GetHashCode)
+ .add_property("hash_code", &AtomHandle::GetHashCode)
;
class_<AtomHandleList>("AtomHandleList", no_init)
diff --git a/modules/mol/base/pymod/export_atom_view.cc b/modules/mol/base/pymod/export_atom_view.cc
index af2dd063b8ea7db1f510ec39aca5df7ad7fce705..036a87ae056ded83b3f30b4803315aa9f3295a89 100644
--- a/modules/mol/base/pymod/export_atom_view.cc
+++ b/modules/mol/base/pymod/export_atom_view.cc
@@ -43,6 +43,9 @@ void export_AtomView()
.def("GetHandle", &AtomView::GetHandle)
.def("GetBondCount", &AtomView::GetBondCount)
.def("GetBondList", &AtomView::GetBondList)
+ .def("GetHashCode", &AtomView::GetHashCode)
+ .def("__hash__", &AtomView::GetHashCode)
+ .add_property("hash_code", &AtomView::GetHashCode)
.def("GetBondPartners", &AtomView::GetBondPartners)
;
class_<AtomViewList>("AtomViewList", init<>())
diff --git a/modules/mol/base/src/atom_base.cc b/modules/mol/base/src/atom_base.cc
index 8eaff3164a27365f42b981a80495e6eb1c9f93f1..2818844b012bb0ac1d8ef0d2f088fb7435128434 100644
--- a/modules/mol/base/src/atom_base.cc
+++ b/modules/mol/base/src/atom_base.cc
@@ -120,12 +120,6 @@ void AtomBase::CheckValidity() const
throw InvalidHandle();
}
-long AtomBase::GetHashCode() const
-{
- this->CheckValidity();
- return reinterpret_cast<long>(Impl().get());
-}
-
std::ostream& operator<<(std::ostream& os, const AtomBase& atom)
{
if (atom.IsValid()) {
diff --git a/modules/mol/base/src/atom_base.hh b/modules/mol/base/src/atom_base.hh
index 142f1a9db2acab1949bef593ff7a99b5715230c1..9777aea714732f090c4b2def487086e4031ad26f 100644
--- a/modules/mol/base/src/atom_base.hh
+++ b/modules/mol/base/src/atom_base.hh
@@ -153,11 +153,6 @@ public:
/// \brief get atom implementation
impl::AtomImplPtr& Impl();
- /// \brief Get unique identifier for atom
- ///
- /// Get hash code that uniquely identifies every atom. The hash code is
- /// identical for all atom views pointing to a given atom.
- long GetHashCode() const;
protected:
GenericPropContainerImpl* GpImpl();
diff --git a/modules/mol/base/src/atom_handle.cc b/modules/mol/base/src/atom_handle.cc
index 486441683eb4deb5913d8830ae9aba18d1cce020..61c975724e70f6c913321947ff31e406133aa5a8 100644
--- a/modules/mol/base/src/atom_handle.cc
+++ b/modules/mol/base/src/atom_handle.cc
@@ -116,6 +116,12 @@ AtomHandle AtomHandle::GetHandle() const
return *this;
}
+long AtomHandle::GetHashCode() const
+{
+ this->CheckValidity();
+ return reinterpret_cast<long>(Impl().get());
+}
+
}} // ns
diff --git a/modules/mol/base/src/atom_handle.hh b/modules/mol/base/src/atom_handle.hh
index 7d817f8e169a7f1f38581b41a53697bc0bad2a66..6ea9094c0db51dab69bc7c46b8a5913c2402404b 100644
--- a/modules/mol/base/src/atom_handle.hh
+++ b/modules/mol/base/src/atom_handle.hh
@@ -81,6 +81,13 @@ public:
///
/// Useful for duck-typing in Python and templated code.
AtomHandle GetHandle() const;
+
+ /// \brief Get unique identifier for atom
+ ///
+ /// Get hash code that uniquely identifies every atom. The hash code is
+ /// identical for all atom views pointing to a given atom.
+ long GetHashCode() const;
+
bool operator==(const AtomHandle& ref) const;
bool operator!=(const AtomHandle& ref) const;
diff --git a/modules/mol/base/src/atom_view.cc b/modules/mol/base/src/atom_view.cc
index 25518778e9164600b08b817e17c48bf3cbb4a0c3..5811a2d5567ea3db1de2ebe8eede8fb4c9a7c631 100644
--- a/modules/mol/base/src/atom_view.cc
+++ b/modules/mol/base/src/atom_view.cc
@@ -115,7 +115,7 @@ mol::AtomViewList AtomView::GetBondPartners() const
mol::AtomViewList avl;
mol::BondHandleList::const_iterator i;
for (i=data_->bonds.begin();i!=data_->bonds.end();++i) {
- if (i->GetFirst()!=*this) {
+ if (i->GetFirst().GetHandle()!=this->GetHandle()) {
avl.push_back(this->GetEntity().FindAtom(i->GetFirst()));
} else {
avl.push_back(this->GetEntity().FindAtom(i->GetSecond()));
@@ -156,7 +156,13 @@ void AtomView::RemoveBondInternal(const BondHandle& bond)
data_->bonds.erase(i);
}
}
-
+
+long AtomView::GetHashCode() const
+{
+ this->CheckValidity();
+ return reinterpret_cast<long>(data_.get());
+}
+
}} // ns
diff --git a/modules/mol/base/src/atom_view.hh b/modules/mol/base/src/atom_view.hh
index ad65accc6f155ee28c54248b9178fb2b502fb563..a9e2d9937986b83b3b10d6e547afe2b90c1c6e53 100644
--- a/modules/mol/base/src/atom_view.hh
+++ b/modules/mol/base/src/atom_view.hh
@@ -69,6 +69,11 @@ public:
void Apply(EntityVisitor& visitor);
void Apply(EntityViewVisitor& visitor);
+ /// \brief get unique id
+ ///
+ /// The unique id is the same for all AtomViews pointing to the same atom
+ /// view data.
+ long GetHashCode() const;
bool operator==(const AtomView& rhs) const;
bool operator!=(const AtomView& rhs) const;
protected:
diff --git a/modules/mol/base/src/coord_source.cc b/modules/mol/base/src/coord_source.cc
index 9b9f853e32e18e1f237a98458f7bfc85e24545ea..0afa3597dacfba19e28d790f0a606d7311256877 100644
--- a/modules/mol/base/src/coord_source.cc
+++ b/modules/mol/base/src/coord_source.cc
@@ -95,7 +95,7 @@ void CoordSource::CaptureInto(int pos)
e=atoms_.end(); i!=e; ++i) {
coords.push_back(i->GetPos());
}
- if(pos<0 || pos>=GetFrameCount()) {
+ if(pos<0 || pos>=static_cast<int>(this->GetFrameCount())) {
this->AddFrame(coords);
} else {
this->InsertFrame(pos,coords);
diff --git a/modules/mol/base/tests/test_view.cc b/modules/mol/base/tests/test_view.cc
index 33bda815dc7a85e6039bd3dcf4d93b33db7777c7..26399e10e1c240182d87f59a453a605d69dd3902 100644
--- a/modules/mol/base/tests/test_view.cc
+++ b/modules/mol/base/tests/test_view.cc
@@ -77,6 +77,17 @@ BOOST_AUTO_TEST_CASE(gen_full_view)
BOOST_CHECK_EQUAL(avl[1].GetBondCount(),2);
BOOST_CHECK_EQUAL(avl[2].GetBondCount(),2);
BOOST_CHECK_EQUAL(avl[3].GetBondCount(),1);
+
+ mol::AtomView av1=avl[0];
+ mol::AtomView av2=avl[1];
+
+ BOOST_CHECK(av1!=av2);
+ BOOST_CHECK(av1.GetHashCode()!=av2.GetHashCode());
+ BOOST_CHECK(av1.GetHandle().GetHashCode()!=av1.GetHashCode());
+
+ mol::AtomView av3=av1;
+ BOOST_CHECK(av1==av3);
+ BOOST_CHECK_EQUAL(av1.GetHashCode(), av3.GetHashCode());
}
BOOST_AUTO_TEST_SUITE_END()
diff --git a/modules/seq/base/pymod/export_sequence.cc b/modules/seq/base/pymod/export_sequence.cc
index ce0e19864e6e6d4ee182b4f74391f31c32a078bf..0eb5ce9f29eae682b494d5ffd2cb73f1b981fded 100644
--- a/modules/seq/base/pymod/export_sequence.cc
+++ b/modules/seq/base/pymod/export_sequence.cc
@@ -38,7 +38,6 @@
using namespace ost;
using namespace ost::seq;
using namespace boost::python;
-
namespace {
void (SequenceHandle::*attach_one)(const mol::EntityView&)=&SequenceHandle::AttachView;