diff --git a/examples/surf/test_rsurf.py b/examples/surf/test_rsurf.py
index f1f2b9c2a17c7296b210343d9f22e69948430f7e..e8818bdac3f3b8338a53db871608c0871e72d880 100644
--- a/examples/surf/test_rsurf.py
+++ b/examples/surf/test_rsurf.py
@@ -15,7 +15,7 @@ scene.Add(gs)
# for debug reasons
rs=mol.RSurf(1.5)
for a in ev.GetAtomList():
- rs.AddSphere(a.GetPos(),a.GetProp().Radius,str(a))
+ rs.AddSphere(a.GetPos(),a.GetRadius(),str(a))
rs.Build()
rs.Triangulate(60.0*3.1415/180.0)
gr=gfx.RSurface("r",rs)
diff --git a/modules/bindings/pymod/msms.py b/modules/bindings/pymod/msms.py
index 6f36ab9fdf10a3ee70d86127e4c656ca48189ee5..5698652f4dc4d6bf479f657a8530c1e2ab8143dd 100644
--- a/modules/bindings/pymod/msms.py
+++ b/modules/bindings/pymod/msms.py
@@ -55,7 +55,7 @@ def _SetupFiles(entity, selection):
for a in entity_view.GetAtomList():
position=a.GetPos()
tmp_file_handle.write('%8.3f %8.3f %8.3f %4.2f\n' % (position[0],
- position[1], position[2], a.GetProp().radius))
+ position[1], position[2], a.GetAtomProps().radius))
tmp_file_handle.close()
return (tmp_dir_name, tmp_file_name)
diff --git a/modules/conop/src/builder.cc b/modules/conop/src/builder.cc
index f82eede9bdbd91314f8808d3b6ca98c743363d49..14c103e55d29f8a69758663b38cefb99b498c06f 100644
--- a/modules/conop/src/builder.cc
+++ b/modules/conop/src/builder.cc
@@ -65,13 +65,13 @@ bool Builder::IsBondFeasible(const mol::AtomHandle& atom_a,
{
Real len=geom::Length2(atom_a.GetPos()-atom_b.GetPos());
Real radii=0.0;
- if (atom_a.GetProp().radius>0.0) {
- radii=atom_a.GetProp().radius;
+ if (atom_a.GetRadius()>0.0) {
+ radii=atom_a.GetRadius();
} else {
return false;
}
- if (atom_b.GetProp().radius>0.0) {
- radii+=atom_b.GetProp().radius;
+ if (atom_b.GetRadius()>0.0) {
+ radii+=atom_b.GetRadius();
} else {
return false;
}
diff --git a/modules/conop/src/heuristic_builder.cc b/modules/conop/src/heuristic_builder.cc
index 00e7f251bd58c2c7a145399e7917be61c619eddd..5c27610eaa153c19c58ff6b51c68bb0fa23871a4 100644
--- a/modules/conop/src/heuristic_builder.cc
+++ b/modules/conop/src/heuristic_builder.cc
@@ -458,10 +458,9 @@ bool HeuristicBuilder::IsResidueComplete(const mol::ResidueHandle& rh)
void HeuristicBuilder::FillAtomProps(mol::AtomHandle atom)
{
- mol::AtomProp prop=atom.GetProp();
+ mol::AtomProp prop=atom.GetAtomProps();
if (prop.element=="") {
- prop.element=Builder::GuessAtomElement(atom.GetName(),
- atom.GetProp().is_hetatm);
+ prop.element=Builder::GuessAtomElement(atom.GetName(), prop.is_hetatm);
}
Conopology& conop_inst=Conopology::Instance();
if (prop.radius==0.0) {
@@ -470,7 +469,7 @@ void HeuristicBuilder::FillAtomProps(mol::AtomHandle atom)
if (prop.mass==0.0) {
prop.mass=conop_inst.GetDefaultAtomMass(prop.element);
}
- atom.SetProp(prop);
+ atom.SetAtomProps(prop);
}
}} // ns
diff --git a/modules/conop/src/rule_based_builder.cc b/modules/conop/src/rule_based_builder.cc
index 0f12cbc634f7d2a8d0200babc34d395a5e27687c..f2a8fd18f28672d36bf6f1e9a816f6b1c231ac9c 100644
--- a/modules/conop/src/rule_based_builder.cc
+++ b/modules/conop/src/rule_based_builder.cc
@@ -61,7 +61,7 @@ void RuleBasedBuilder::CheckResidueCompleteness(const mol::ResidueHandle& rh) {
void RuleBasedBuilder::FillAtomProps(mol::AtomHandle atom, const AtomSpec& spec)
{
- mol::AtomProp props=atom.GetProp();
+ mol::AtomProp props=atom.GetAtomProps();
if (props.element=="") {
props.element=spec.element;
}
@@ -72,7 +72,7 @@ void RuleBasedBuilder::FillAtomProps(mol::AtomHandle atom, const AtomSpec& spec)
if (props.mass==0.0) {
props.mass=conop_inst.GetDefaultAtomMass(spec.element);
}
- atom.SetProp(props);
+ atom.SetAtomProps(props);
}
void RuleBasedBuilder::FillResidueProps(mol::ResidueHandle residue) {
@@ -265,7 +265,7 @@ void RuleBasedBuilder::FillAtomProps(mol::AtomHandle atom)
bool RuleBasedBuilder::OnUnknownAtom(mol::AtomHandle atom)
{
- mol::AtomProp props=atom.GetProp();
+ mol::AtomProp props=atom.GetAtomProps();
if (props.element=="") {
props.element=Builder::GuessAtomElement(atom.GetName(), props.is_hetatm);
}
@@ -276,7 +276,7 @@ bool RuleBasedBuilder::OnUnknownAtom(mol::AtomHandle atom)
if (props.mass==0.0) {
props.mass=conop_inst.GetDefaultAtomMass(props.element);
}
- atom.SetProp(props);
+ atom.SetAtomProps(props);
return false;
}
diff --git a/modules/conop/src/sanitizer.cc b/modules/conop/src/sanitizer.cc
index 17cf91874a925044fcba1bfe649b9a66d6bfb3b7..d7d8d42783840f49014d92e315dd9ed901360598 100644
--- a/modules/conop/src/sanitizer.cc
+++ b/modules/conop/src/sanitizer.cc
@@ -42,12 +42,12 @@ bool Sanitizer::VisitResidue(const mol::ResidueHandle& residue) {
}
void Sanitizer::FillAtomProps(mol::AtomHandle atom, const AtomSpec& spec) {
- mol::AtomProp props=atom.GetProp();
+ mol::AtomProp props=atom.GetAtomProps();
if (props.element!=spec.element) {
props.element=spec.element;
LOGN_MESSAGE("Correcting element for " << atom.GetQualifiedName() <<
" (now " << spec.element << ", was " << props.element << ")");
- atom.SetProp(props);
+ atom.SetAtomProps(props);
}
}
diff --git a/modules/gfx/src/gl_include.hh b/modules/gfx/src/gl_include.hh
index 10a682dee2d39ff49c1168684e909290b8a7ae82..2295ca6a336ad91753b2ce6bb95c252c1a0baf7e 100644
--- a/modules/gfx/src/gl_include.hh
+++ b/modules/gfx/src/gl_include.hh
@@ -29,7 +29,6 @@
#ifdef _MSC_VER
#include <windows.h>
-#undef GetProp
# ifdef FindAtom
# undef FindAtom
# endif
diff --git a/modules/gfx/src/impl/backbone_trace.cc b/modules/gfx/src/impl/backbone_trace.cc
index 28ebb3842557e98b72eed9e6c9fb805d37cfad49..d4314bea8901f49678e55af9fa2cff6f791bfe1d 100644
--- a/modules/gfx/src/impl/backbone_trace.cc
+++ b/modules/gfx/src/impl/backbone_trace.cc
@@ -58,8 +58,8 @@ public:
// determine atom to add to list
mol::AtomHandle ca = res.GetCentralAtom();
if (ca) {
- NodeEntry entry={ca, GfxObj::Ele2Color(ca.GetProp().element),
- GfxObj::Ele2Color(ca.GetProp().element),
+ NodeEntry entry={ca, GfxObj::Ele2Color(ca.GetAtomProps().element),
+ GfxObj::Ele2Color(ca.GetAtomProps().element),
geom::Vec3(0.0,0.0,0.0), // this will be set by the gfx trace obj
res.GetCentralNormal(),
1.0,
diff --git a/modules/gfx/src/impl/connect_renderer_base.cc b/modules/gfx/src/impl/connect_renderer_base.cc
index 36df3b365b4a069c6fe4f6dc9a22ad226ac11c42..bc1dab565c98ebee107ca2787c7b841247d763e8 100644
--- a/modules/gfx/src/impl/connect_renderer_base.cc
+++ b/modules/gfx/src/impl/connect_renderer_base.cc
@@ -49,7 +49,7 @@ public:
if(mode==SEL_ATOM) {
float d=geom::Distance(line_,atom.GetPos());
if((fixed_radius && d<=dlim_) ||
- (!fixed_radius && d<=atom.GetProp().radius)) {
+ (!fixed_radius && d<=atom.GetRadius())) {
geom::Vec3 v=Scene::Instance().Project(atom.GetPos());
if(v[2]>0.0 && v[2]<zmin_) {
zmin_=v[2];
diff --git a/modules/gfx/src/impl/entity_detail.cc b/modules/gfx/src/impl/entity_detail.cc
index 52f34fcabd25210c087216dfb34151bee7a9e917..1d5a3c226c70b674bf9076388272bea46de76fd1 100644
--- a/modules/gfx/src/impl/entity_detail.cc
+++ b/modules/gfx/src/impl/entity_detail.cc
@@ -41,8 +41,8 @@ void GfxView::AddAtom(const AtomView& av)
{
AtomHandle a=av.GetHandle();
AtomEntry ae(a,default_radius,
- a.GetProp().radius,
- GfxObj::Ele2Color(a.GetProp().element));
+ a.GetRadius(),
+ GfxObj::Ele2Color(a.GetElement()));
atom_map[a.GetHashCode()]=ae;
if(av.GetBondCount()==0) {
orphan_atom_list.push_back(a.GetHashCode());
@@ -70,16 +70,16 @@ void GfxView::AddBond(const BondHandle& b)
if (ae1 && !ae2) {
AtomHandle a=b.GetSecond();
AtomEntry ae(a,default_radius,
- a.GetProp().radius,
- GfxObj::Ele2Color(a.GetProp().element));
+ a.GetRadius(),
+ GfxObj::Ele2Color(a.GetElement()));
atom_map[a.GetHashCode()]=ae;
ae2=&atom_map[a.GetHashCode()];
}
if (!ae1 && ae2) {
AtomHandle a=b.GetFirst();
AtomEntry ae(a,default_radius,
- a.GetProp().radius,
- GfxObj::Ele2Color(a.GetProp().element));
+ a.GetRadius(),
+ GfxObj::Ele2Color(a.GetElement()));
atom_map[a.GetHashCode()]=ae;
ae1=&atom_map[a.GetHashCode()];
}
diff --git a/modules/gfx/src/impl/entity_renderer.hh b/modules/gfx/src/impl/entity_renderer.hh
index db0825dd59640d78b382d72ef592d69d615fc562..2fa91e110442b022a0c64d3ad0cc2963d10f1641 100644
--- a/modules/gfx/src/impl/entity_renderer.hh
+++ b/modules/gfx/src/impl/entity_renderer.hh
@@ -24,8 +24,8 @@
*/
-#if defined(GetProp)
-#undef GetProp
+#if defined(GetAtomProps)
+#undef GetAtomProps
#endif
#include <vector>
@@ -185,7 +185,7 @@ protected:
//Simplify color ops
struct ByElementGetCol {
Color ColorOfAtom(mol::AtomHandle& atom) const{
- return GfxObj::Ele2Color(atom.GetProp().element);
+ return GfxObj::Ele2Color(atom.GetElement());
}
};
diff --git a/modules/io/src/mol/entity_io_crd_handler.cc b/modules/io/src/mol/entity_io_crd_handler.cc
index e89b294f93f3f7d1f8d28240c1727766513bbd10..2fd39293ff0fe11c929e97915a59735edb034742 100644
--- a/modules/io/src/mol/entity_io_crd_handler.cc
+++ b/modules/io/src/mol/entity_io_crd_handler.cc
@@ -191,7 +191,7 @@ bool CRDWriter::VisitAtom(const mol::AtomHandle& atom)
<< format("%10.5f") % atom.GetPos().GetZ() << " "
<< format("%-4s") % e_name << " "
<< format("%-5i") % res.GetNumber() << " "
- << format("%8.5f") % atom.GetProp().b_factor
+ << format("%8.5f") % atom.GetBFactor()
<< std::endl;
return true;
diff --git a/modules/io/src/mol/entity_io_sdf_handler.cc b/modules/io/src/mol/entity_io_sdf_handler.cc
index bbd703bc1dd262cf49d98a9fca72aae1fd61bbb9..f9c49479ffbebaf52a4d03a18cafe4cb69a20c67 100644
--- a/modules/io/src/mol/entity_io_sdf_handler.cc
+++ b/modules/io/src/mol/entity_io_sdf_handler.cc
@@ -280,7 +280,7 @@ namespace {
ostr_ << format("%10.4f") % atom.GetPos()[0]
<< format("%10.4f") % atom.GetPos()[1]
<< format("%10.4f ") % atom.GetPos()[2]
- << format("%-3s") % atom.GetProp().element
+ << format("%-3s") % atom.GetElement()
<< " 0 0 0 0 0 0"
<< std::endl;
return true;
diff --git a/modules/io/src/mol/pdb_reader.cc b/modules/io/src/mol/pdb_reader.cc
index 33de62cdd94f6242185b04d938cdbb704b4dd46e..f26e77672d2ff4aa62c49f8ead2c7d98544423bc 100644
--- a/modules/io/src/mol/pdb_reader.cc
+++ b/modules/io/src/mol/pdb_reader.cc
@@ -363,7 +363,7 @@ void PDBReader::ParseAnisou(const StringRef& line, int line_num,
throw IOException(str(format(fmt_str) % line_num));
}
//get properties which are already set and extend them by adding the ANISOU info
- mol::AtomProp aprop=atom.GetProp();
+ mol::AtomProp aprop=atom.GetAtomProps();
geom::Mat3 mat(anisou[0], anisou[3], anisou[4],
anisou[3], anisou[1], anisou[5],
anisou[4], anisou[5], anisou[2]);
@@ -371,7 +371,7 @@ void PDBReader::ParseAnisou(const StringRef& line, int line_num,
//divide by 10**4 to actually reflect the real values
aprop.anisou/=10000;
aprop.has_anisou=true;
- atom.SetProp(aprop);
+ atom.SetAtomProps(aprop);
return;
}
diff --git a/modules/io/src/mol/pdb_writer.cc b/modules/io/src/mol/pdb_writer.cc
index 36f9ce9e2f8fae5081204e6546f4077022313b54..cc8cd4bf50d828ecd40c658a65aafee0aa9796f9 100644
--- a/modules/io/src/mol/pdb_writer.cc
+++ b/modules/io/src/mol/pdb_writer.cc
@@ -36,7 +36,7 @@ void write_atom(std::ostream& ostr, const mol::AtomHandle& atom, int atomnum,
{
mol::ResidueHandle res=atom.GetResidue();
char ins_code=res.GetNumber().GetInsCode();
- String record_name=atom.GetProp().is_hetatm ? "HETATM" : "ATOM ";
+ String record_name=atom.GetAtomProps().is_hetatm ? "HETATM" : "ATOM ";
String aname_str=atom.GetName();
if(aname_str.length()<4) {
aname_str=" "+aname_str;
@@ -54,13 +54,13 @@ void write_atom(std::ostream& ostr, const mol::AtomHandle& atom, int atomnum,
<< " "
<< format("%8.3f%8.3f%8.3f") % p[0] % p[1] % p[2];
if(is_pqr) {
- ostr << format("%6.2f") % atom.GetProp().charge
- << format("%6.2f") % atom.GetProp().radius;
+ ostr << format("%6.2f") % atom.GetAtomProps().charge
+ << format("%6.2f") % atom.GetAtomProps().radius;
} else {
- ostr << format("%6.2f") % atom.GetProp().occupancy
- << format("%6.2f") % atom.GetProp().b_factor;
+ ostr << format("%6.2f") % atom.GetAtomProps().occupancy
+ << format("%6.2f") % atom.GetAtomProps().b_factor;
}
- ostr << format("%10s%2s") % "" % atom.GetProp().element
+ ostr << format("%10s%2s") % "" % atom.GetAtomProps().element
<< std::endl
;
} else {
@@ -77,13 +77,13 @@ void write_atom(std::ostream& ostr, const mol::AtomHandle& atom, int atomnum,
<< " "
<< format("%8.3f%8.3f%8.3f") % p[0] % p[1] % p[2];
if(is_pqr) {
- ostr << format("%6.2f") % atom.GetProp().charge
- << format("%6.2f") % atom.GetProp().radius;
+ ostr << format("%6.2f") % atom.GetAtomProps().charge
+ << format("%6.2f") % atom.GetAtomProps().radius;
} else {
- ostr << format("%6.2f") % atom.GetProp().occupancy
- << format("%6.2f") % atom.GetProp().b_factor;
+ ostr << format("%6.2f") % atom.GetAtomProps().occupancy
+ << format("%6.2f") % atom.GetAtomProps().b_factor;
}
- ostr << format("%10s%2s") % "" % atom.GetProp().element
+ ostr << format("%10s%2s") % "" % atom.GetAtomProps().element
<< std::endl
;
}
diff --git a/modules/io/tests/test_io_pdb.cc b/modules/io/tests/test_io_pdb.cc
index 8086022d66d9ada41930b0c3ffb1edd82f3b55e0..811c459a891d1f08e8400242ef896979a3829fbb 100644
--- a/modules/io/tests/test_io_pdb.cc
+++ b/modules/io/tests/test_io_pdb.cc
@@ -64,10 +64,10 @@ BOOST_AUTO_TEST_CASE(atom_record)
BOOST_CHECK_EQUAL(a1.GetResidue().GetChain().GetName(), "A");
BOOST_CHECK_EQUAL(a1.GetPos(), geom::Vec3(16.0, 64.0, 8.0));
- BOOST_CHECK_EQUAL(a1.GetProp().b_factor, 1.0);
- BOOST_CHECK_EQUAL(a1.GetProp().occupancy, 0.5);
- BOOST_CHECK_EQUAL(a1.GetProp().element, "N");
- BOOST_CHECK_EQUAL(a1.GetProp().is_hetatm, false);
+ BOOST_CHECK_EQUAL(a1.GetAtomProps().b_factor, 1.0);
+ BOOST_CHECK_EQUAL(a1.GetAtomProps().occupancy, 0.5);
+ BOOST_CHECK_EQUAL(a1.GetAtomProps().element, "N");
+ BOOST_CHECK_EQUAL(a1.GetAtomProps().is_hetatm, false);
mol::AtomHandle a2=ent.FindAtom(" ", mol::ResNum(1), "CA");
BOOST_REQUIRE(a2.IsValid());
BOOST_CHECK_EQUAL(a2.GetName(), "CA");
@@ -75,10 +75,10 @@ BOOST_AUTO_TEST_CASE(atom_record)
BOOST_CHECK_EQUAL(a2.GetResidue().GetChain().GetName(), " ");
BOOST_CHECK_EQUAL(a2.GetPos(), geom::Vec3(32.0, -128.0, -2.5));
- BOOST_CHECK_EQUAL(a2.GetProp().b_factor, 128.0);
- BOOST_CHECK_EQUAL(a2.GetProp().occupancy, 1.0);
- BOOST_CHECK_EQUAL(a2.GetProp().element, "C");
- BOOST_CHECK_EQUAL(a2.GetProp().is_hetatm, true);
+ BOOST_CHECK_EQUAL(a2.GetAtomProps().b_factor, 128.0);
+ BOOST_CHECK_EQUAL(a2.GetAtomProps().occupancy, 1.0);
+ BOOST_CHECK_EQUAL(a2.GetAtomProps().element, "C");
+ BOOST_CHECK_EQUAL(a2.GetAtomProps().is_hetatm, true);
}
BOOST_AUTO_TEST_CASE(end_record)
@@ -159,7 +159,7 @@ BOOST_AUTO_TEST_CASE(anisou_record)
BOOST_REQUIRE(ent.GetAtomCount()==1);
mol::AtomHandle a1=ent.FindAtom("A", mol::ResNum(7), "N");
BOOST_REQUIRE(a1.IsValid());
- mol::AtomProp props=a1.GetProp();
+ mol::AtomProp props=a1.GetAtomProps();
BOOST_CHECK_CLOSE( 0.0100, props.anisou(0, 0), 1e-4);
BOOST_CHECK_CLOSE(-0.0016, props.anisou(1, 0), 1e-4);
BOOST_CHECK_CLOSE(-0.0026, props.anisou(2, 0), 1e-4);
diff --git a/modules/mol/base/pymod/export_atom.cc b/modules/mol/base/pymod/export_atom.cc
index bb8c9fe31afea70a0ff111b82de719df2c186ab0..83f2adc0648de4b6eaacccadfba7dbf0337d812b 100644
--- a/modules/mol/base/pymod/export_atom.cc
+++ b/modules/mol/base/pymod/export_atom.cc
@@ -44,12 +44,12 @@ void export_Atom()
.def(self_ns::str(self))
.add_property("hash_code", &AtomBase::GetHashCode)
.def("GetHashCode", &AtomBase::GetHashCode)
- .def("GetProp", &AtomBase::GetProp,
+ .def("GetAtomProps", &AtomBase::GetAtomProps,
return_value_policy<copy_const_reference>())
- .def("SetProp", &AtomBase::SetProp, args("prop"))
+ .def("SetAtomProps", &AtomBase::SetAtomProps, args("prop"))
.def("GetIndex", &AtomBase::GetIndex)
.add_property("prop",
- make_function(&AtomBase::GetProp,
+ make_function(&AtomBase::GetAtomProps,
return_value_policy<copy_const_reference>()))
.add_property("pos",
make_function(&AtomBase::GetPos,
@@ -59,7 +59,19 @@ void export_Atom()
return_value_policy<copy_const_reference>()),
&AtomBase::SetName)
.add_property("index",&AtomBase::GetIndex)
-
+
+ .def("GetRadius", &AtomBase::GetRadius)
+ .def("GetElement", &AtomBase::GetElement,
+ return_value_policy<copy_const_reference>())
+ .def("GetCharge", &AtomBase::GetCharge)
+ .def("GetMass", &AtomBase::GetMass)
+ .def("IsHetAtom", &AtomBase::IsHetAtom)
+ .add_property("radius", &AtomBase::GetRadius)
+ .add_property("element", make_function(&AtomBase::GetElement,
+ return_value_policy<copy_const_reference>()))
+ .add_property("is_hetatom", &AtomBase::IsHetAtom)
+ .add_property("charge", &AtomBase::GetCharge)
+ .add_property("mass", &AtomBase::GetMass)
;
generic_prop_def<AtomBase>(atom_base);
diff --git a/modules/mol/base/src/atom_base.cc b/modules/mol/base/src/atom_base.cc
index ac0a63e731e88d33e355e1669f03c4469d5a2f6d..8eaff3164a27365f42b981a80495e6eb1c9f93f1 100644
--- a/modules/mol/base/src/atom_base.cc
+++ b/modules/mol/base/src/atom_base.cc
@@ -76,16 +76,16 @@ std::vector<String> AtomBase::GetAltGroupNames() const
}
-const AtomProp& AtomBase::GetProp() const
+const AtomProp& AtomBase::GetAtomProps() const
{
this->CheckValidity();
- return impl_->GetProp();
+ return impl_->GetAtomProps();
}
-void AtomBase::SetProp(const AtomProp& prop)
+void AtomBase::SetAtomProps(const AtomProp& prop)
{
this->CheckValidity();
- impl_->GetProp()=prop;
+ impl_->GetAtomProps()=prop;
}
impl::AtomImplPtr& AtomBase::Impl()
@@ -137,6 +137,51 @@ std::ostream& operator<<(std::ostream& os, const AtomBase& atom)
}
+Real AtomBase::GetRadius() const
+{
+ this->CheckValidity();
+ return Impl()->GetAtomProps().radius;
+}
+
+
+const String& AtomBase::GetElement() const
+{
+ this->CheckValidity();
+ return Impl()->GetAtomProps().element;
+}
+
+
+bool AtomBase::IsHetAtom() const
+{
+ this->CheckValidity();
+ return Impl()->GetAtomProps().is_hetatm;
+}
+
+Real AtomBase::GetBFactor() const
+{
+ this->CheckValidity();
+ return Impl()->GetAtomProps().b_factor;
+}
+
+Real AtomBase::GetMass() const
+{
+ this->CheckValidity();
+ return Impl()->GetAtomProps().mass;
+}
+
+Real AtomBase::GetCharge() const
+{
+ this->CheckValidity();
+ return Impl()->GetAtomProps().charge;
+}
+
+Real AtomBase::GetOccupancy() const
+{
+ this->CheckValidity();
+ return Impl()->GetAtomProps().occupancy;
+}
+
+
String AtomBase::GetStringProperty(Prop::ID prop_id) const
{
this->CheckValidity();
diff --git a/modules/mol/base/src/atom_base.hh b/modules/mol/base/src/atom_base.hh
index 9744f00f8b06f87ab192c4ac9a293369b4d789a6..142f1a9db2acab1949bef593ff7a99b5715230c1 100644
--- a/modules/mol/base/src/atom_base.hh
+++ b/modules/mol/base/src/atom_base.hh
@@ -33,7 +33,7 @@ namespace ost { namespace mol {
/// Groups common functionality for AtomView and AtomHandle.
///
/// Most of the atom properties such as temperature factor, element, radius
-/// and charge can be accessed with #GetProp() that returns an object of
+/// and charge can be accessed with #GetAtomProps() that returns an object of
/// type AtomProp.
///
/// Like \ref ResidueBase residues, \ref ChainBase "chains" and
@@ -80,11 +80,11 @@ public:
/// \brief Get atom properties such as element name, radius crystallographic
/// occupancy and temperature factors.
///
- /// \sa #SetProp
- const AtomProp& GetProp() const;
+ /// \sa #SetAtomProps
+ const AtomProp& GetAtomProps() const;
/// \brief Set atom properties.
- void SetProp(const AtomProp& prop);
+ void SetAtomProps(const AtomProp& prop);
//@}
/// \name Handle validity
@@ -120,11 +120,36 @@ public:
/// \brief Get the internal index
unsigned long GetIndex() const;
+ /// \brief returns the van-der-Waals radius of the atom
+ Real GetRadius() const;
+
+ /// \brief returns the element name of the atom
+ const String& GetElement() const;
+
+ /// \brief whether the atom is a hetatm
+ bool IsHetAtom() const;
+
+ /// \brief Get isotropic temperature factor of atom
+ ///
+ /// The returned value may be zero for some structures
+ Real GetBFactor() const;
+
+ /// \brief get mass of atom
+ ///
+ /// The returned value may be zero
+ Real GetMass() const;
+
+ /// \brief get charge
+ Real GetCharge() const;
+
+ /// \brief get atom occupancy
+ Real GetOccupancy() const;
+
/// \brief get atom implementation.
///
/// Intended for internal use.
const impl::AtomImplPtr& Impl() const;
-
+
/// \brief get atom implementation
impl::AtomImplPtr& Impl();
diff --git a/modules/mol/base/src/chain_view.cc b/modules/mol/base/src/chain_view.cc
index dff4e770e074e261a0d3f60fcaa5c052a6c7f70b..87fd218701569abd1cf15260b93b8a09bcc081cb 100644
--- a/modules/mol/base/src/chain_view.cc
+++ b/modules/mol/base/src/chain_view.cc
@@ -313,7 +313,7 @@ Real ChainView::GetMass() const {
ResidueView r=*i;
for (AtomViewList::const_iterator j=r.GetAtomList().begin(),
e2=r.GetAtomList().end(); j!=e2; ++j) {
- mass+=j->GetProp().mass;
+ mass+=j->GetMass();
}
}
return mass;
@@ -388,7 +388,7 @@ geom::Vec3 ChainView::GetCenterOfMass() const
ResidueView r=*i;
for (AtomViewList::const_iterator j=r.GetAtomList().begin(),
e2=r.GetAtomList().end(); j!=e2; ++j) {
- center+=j->GetPos() * j->GetProp().mass;
+ center+=j->GetPos() * j->GetAtomProps().mass;
}
}
center/=mass;
diff --git a/modules/mol/base/src/entity_view.cc b/modules/mol/base/src/entity_view.cc
index 6616e3b985921427e5319d7c1b10176980339e0a..34f7d506421cef9b32aeaec3c46a0470d89c3f2c 100644
--- a/modules/mol/base/src/entity_view.cc
+++ b/modules/mol/base/src/entity_view.cc
@@ -185,7 +185,7 @@ geom::Vec3 EntityView::GetCenterOfMass() const
if (this->GetAtomCount()>0 && mass>0) {
AtomViewIter it=this->AtomsBegin();
for(; it!=this->AtomsEnd(); ++it) {
- center+=(*it).GetPos()*(*it).GetProp().mass;
+ center+=(*it).GetPos()*(*it).GetMass();
}
center/=mass;
}
@@ -197,7 +197,7 @@ Real EntityView::GetMass() const
Real mass = 0;
AtomViewIter it=this->AtomsBegin();
for(; it!=this->AtomsEnd(); ++it) {
- mass+=(*it).GetProp().mass;
+ mass+=(*it).GetMass();
}
return mass;
}
diff --git a/modules/mol/base/src/impl/atom_impl.hh b/modules/mol/base/src/impl/atom_impl.hh
index b24abc85c7d55e9f5eed8bca31cb1d3ee785ac94..9fcbbf77636a50e0871bf6b01ea70bc28c8a157d 100644
--- a/modules/mol/base/src/impl/atom_impl.hh
+++ b/modules/mol/base/src/impl/atom_impl.hh
@@ -71,9 +71,9 @@ public:
void SetOriginalPos(const geom::Vec3& pos) { pos_=pos; }
- const AtomProp& GetProp() const {return prop_;}
+ const AtomProp& GetAtomProps() const {return prop_;}
- AtomProp& GetProp() {return prop_;}
+ AtomProp& GetAtomProps() {return prop_;}
ResidueImplPtr GetResidue() const;
diff --git a/modules/mol/base/src/impl/chain_impl.cc b/modules/mol/base/src/impl/chain_impl.cc
index 72b1303772f9541ffe13038980fb58f47a63d462..02f4636c1cc5e60865ad92b5e7ddcd3901a23ed0 100644
--- a/modules/mol/base/src/impl/chain_impl.cc
+++ b/modules/mol/base/src/impl/chain_impl.cc
@@ -357,7 +357,7 @@ Real ChainImpl::GetMass() const
ResidueImplPtr r=*i;
for (AtomImplList::iterator j=r->GetAtomList().begin();
j!=r->GetAtomList().end(); ++j) {
- mass+=(*j)->GetProp().mass;
+ mass+=(*j)->GetAtomProps().mass;
}
}
return mass;
@@ -426,7 +426,7 @@ geom::Vec3 ChainImpl::GetCenterOfMass() const
ResidueImplPtr r=*i;
for (AtomImplList::iterator j=r->GetAtomList().begin();
j!=r->GetAtomList().end(); ++j) {
- center+=(*j)->GetPos() * (*j)->GetProp().mass;
+ center+=(*j)->GetPos() * (*j)->GetAtomProps().mass;
}
}
center/=mass;
diff --git a/modules/mol/base/src/impl/entity_impl.cc b/modules/mol/base/src/impl/entity_impl.cc
index 2a271f341946116568f34fb9fff8ca1a96e481d9..29fdad970ebddf5f8a8a49e54a436182bbc1c068 100644
--- a/modules/mol/base/src/impl/entity_impl.cc
+++ b/modules/mol/base/src/impl/entity_impl.cc
@@ -328,7 +328,7 @@ geom::Vec3 EntityImpl::GetCenterOfMass() const {
Real mass = this->GetMass();
if (this->GetAtomCount()>0 && mass>0) {
for(AtomImplMap::const_iterator it = atom_map_.begin();it!=atom_map_.end();++it) {
- center+=it->second->GetPos()*it->second->GetProp().mass;
+ center+=it->second->GetPos()*it->second->GetAtomProps().mass;
}
center/=mass;
}
@@ -339,7 +339,7 @@ Real EntityImpl::GetMass() const {
Real mass=0.0;
for (AtomImplMap::const_iterator it = atom_map_.begin();
it!=atom_map_.end();++it) {
- mass+=it->second->GetProp().mass;
+ mass+=it->second->GetAtomProps().mass;
}
return mass;
}
diff --git a/modules/mol/base/src/impl/query_ast.hh b/modules/mol/base/src/impl/query_ast.hh
index abdcbe1e582c060324b04c569bd8d50bcb074c5e..3abedd805027476c33c012d4dbab46cd2a338962 100644
--- a/modules/mol/base/src/impl/query_ast.hh
+++ b/modules/mol/base/src/impl/query_ast.hh
@@ -121,7 +121,7 @@ public:
virtual void Dump(int level=0) const;
- const Prop& GetProp() const {
+ const Prop& GetAtomProps() const {
return sel_;
}
CompOP GetCompOP() const {
diff --git a/modules/mol/base/src/impl/query_impl.cc b/modules/mol/base/src/impl/query_impl.cc
index 411f1d9bc18f3df563730a8551885a7a75a86343..312b38d6db7e483d0e419c2991919e1189997e1f 100644
--- a/modules/mol/base/src/impl/query_impl.cc
+++ b/modules/mol/base/src/impl/query_impl.cc
@@ -280,7 +280,7 @@ bool QueryImpl::IsAlwaysUndef(const Node* ast,
else {
const SelNode* sel_node = dynamic_cast<const SelNode*>(ast);
assert(sel_node);
- if ((int)target_level > (int)sel_node->GetProp().level) {
+ if ((int)target_level > (int)sel_node->GetAtomProps().level) {
return true;
}
}
@@ -296,7 +296,7 @@ void QueryImpl::ExtractSelStmts(const Node* ast) {
else {
const SelNode* sel_node = dynamic_cast<const SelNode*>(ast);
assert(sel_node);
- SelStmt val(sel_node->GetProp().id,
+ SelStmt val(sel_node->GetAtomProps().id,
sel_node->GetCompOP(),
sel_node->GetParm());
std::vector<SelStmt>::iterator i = std::find(sel_values_.begin(),
@@ -304,7 +304,7 @@ void QueryImpl::ExtractSelStmts(const Node* ast) {
if (i==sel_values_.end()) {
size_t idx = sel_values_.size();
sel_values_.push_back(val);
- indices_[(int)sel_node->GetProp().level].insert(idx);
+ indices_[(int)sel_node->GetAtomProps().level].insert(idx);
}
}
}
@@ -361,8 +361,8 @@ void QueryImpl::ASTToSelStack(const Node* src_ast,
}
else {
const SelNode* sel_node = dynamic_cast<const SelNode*>(src_ast);
- assert((int)target_level <= (int)sel_node->GetProp().level);
- SelStmt val(sel_node->GetProp().id,sel_node->GetCompOP(),
+ assert((int)target_level <= (int)sel_node->GetAtomProps().level);
+ SelStmt val(sel_node->GetAtomProps().id,sel_node->GetCompOP(),
sel_node->GetParm());
std::vector<SelStmt>::iterator i = std::find(sel_values_.begin(),
sel_values_.end(),val);
diff --git a/modules/mol/base/src/impl/residue_impl.cc b/modules/mol/base/src/impl/residue_impl.cc
index b45dae81083563c2d43c643bc61f4ee41534a445..bfee304770bcb5ec53443cda276127dc1458b074 100644
--- a/modules/mol/base/src/impl/residue_impl.cc
+++ b/modules/mol/base/src/impl/residue_impl.cc
@@ -59,7 +59,7 @@ AtomImplPtr ResidueImpl::InsertAtom(const AtomImplPtr& atom)
{
AtomImplPtr dst_atom=this->InsertAtom(atom->GetName(),
atom->GetPos(),
- atom->GetProp());
+ atom->GetAtomProps());
dst_atom->Assign(*atom.get());
dst_atom->SetState(atom->GetState());
return dst_atom;
@@ -70,7 +70,7 @@ Real ResidueImpl::GetAverageBFactor() const
Real sum=0;
for (AtomImplList::const_iterator i=atom_list_.begin(),
e=atom_list_.end(); i!=e; ++i) {
- sum+=(*i)->GetProp().b_factor;
+ sum+=(*i)->GetAtomProps().b_factor;
}
return atom_list_.size()>0 ? sum/atom_list_.size() : 0.0;
}
@@ -422,7 +422,7 @@ Real ResidueImpl::GetMass() const
Real mass = 0;
for (AtomImplList::const_iterator i=atom_list_.begin();
i!=atom_list_.end(); ++i) {
- mass+=(*i)->GetProp().mass;
+ mass+=(*i)->GetAtomProps().mass;
}
return mass;
}
@@ -474,7 +474,7 @@ geom::Vec3 ResidueImpl::GetCenterOfMass() const
if (this->GetAtomCount() > 0 && mass > 0) {
for (AtomImplList::const_iterator i=atom_list_.begin();
i!=atom_list_.end(); ++i) {
- center+=(*i)->GetPos()*(*i)->GetProp().mass;
+ center+=(*i)->GetPos()*(*i)->GetAtomProps().mass;
}
}
return center/mass;
diff --git a/modules/mol/base/src/query_state.cc b/modules/mol/base/src/query_state.cc
index 004af514f0c573ff6d180a7fe09b25a50789bbb0..c3e68560b175d21de8ad6591161e273a4b50f149 100644
--- a/modules/mol/base/src/query_state.cc
+++ b/modules/mol/base/src/query_state.cc
@@ -326,17 +326,17 @@ boost::logic::tribool QueryState::EvalAtom(const impl::AtomImplPtr& a) {
boost::get<float>(ss.param));
break;
case Prop::OCC:
- float_value=a->GetProp().occupancy;
+ float_value=a->GetAtomProps().occupancy;
s_[*i]=cmp_num<Real>(ss.comp_op, float_value,
boost::get<float>(ss.param));
break;
case Prop::ELE:
- str_value = a->GetProp().element;
+ str_value = a->GetAtomProps().element;
s_[*i] = cmp_string(ss.comp_op,str_value,
boost::get<String>(ss.param));
break;
case Prop::ABFAC:
- float_value=a->GetProp().b_factor;
+ float_value=a->GetAtomProps().b_factor;
s_[*i]=cmp_num<Real>(ss.comp_op, float_value,
boost::get<float>(ss.param));
break;
@@ -346,11 +346,11 @@ boost::logic::tribool QueryState::EvalAtom(const impl::AtomImplPtr& a) {
ss.comp_op);
break;
case Prop::ISHETATM:
- int_value = a->GetProp().is_hetatm;
+ int_value = a->GetAtomProps().is_hetatm;
s_[*i] = cmp_num<int>(ss.comp_op,int_value,boost::get<int>(ss.param));
break;
case Prop::ACHARGE:
- float_value=a->GetProp().charge;
+ float_value=a->GetAtomProps().charge;
s_[*i]=cmp_num<Real>(ss.comp_op, float_value,
boost::get<float>(ss.param));
break;
diff --git a/modules/mol/base/src/residue_view.cc b/modules/mol/base/src/residue_view.cc
index 29585678e9656899c480bf6eb22b5f6ff5f40407..e976652449b8cc15bf0d780c58f3fa8521e6f4c0 100644
--- a/modules/mol/base/src/residue_view.cc
+++ b/modules/mol/base/src/residue_view.cc
@@ -194,7 +194,7 @@ double ResidueView::GetMass() const
double mass = 0;
AtomViewList::const_iterator i;
for (i=data_->atoms.begin(); i!=data_->atoms.end(); ++i) {
- mass+=(*i).GetProp().mass;
+ mass+=(*i).GetAtomProps().mass;
}
return mass;
}
@@ -239,7 +239,7 @@ geom::Vec3 ResidueView::GetCenterOfMass() const
if (!data_->atoms.empty() && mass > 0) {
AtomViewList::const_iterator i;
for (i=data_->atoms.begin(); i!=data_->atoms.end(); ++i) {
- center+=(*i).GetPos()*(*i).GetProp().mass;
+ center+=(*i).GetPos()*(*i).GetAtomProps().mass;
}
center/=mass;
}
diff --git a/modules/mol/base/src/surface_builder.cc b/modules/mol/base/src/surface_builder.cc
index b989c7382b3364d3b6044e5ccd43ed0f275927c0..75214f3de4d24f215c1d93ac7260fa97f7422d49 100644
--- a/modules/mol/base/src/surface_builder.cc
+++ b/modules/mol/base/src/surface_builder.cc
@@ -32,7 +32,7 @@ SurfaceHandle BuildSurface(const EntityView& ev, Real probe_radius, Real patch_s
rsurf::RSurf rsurf(probe_radius);
for(AtomViewIter it=ev.AtomsBegin();it!=ev.AtomsEnd();++it) {
- rsurf.AddSphere((*it).GetPos(),(*it).GetProp().radius,(*it).GetQualifiedName());
+ rsurf.AddSphere((*it).GetPos(),(*it).GetAtomProps().radius,(*it).GetQualifiedName());
}
rsurf.Build();
diff --git a/modules/qa/src/clash_score.cc b/modules/qa/src/clash_score.cc
index 7ccfaafac069c36c09bea79da196c7f1872a5809..66b95c09635eefd8fbf2fdbde5db2e78cf5bf501 100644
--- a/modules/qa/src/clash_score.cc
+++ b/modules/qa/src/clash_score.cc
@@ -48,12 +48,12 @@ Real do_clash_score(const T& ent_a, const mol::EntityView& ent_b)
for (I i=ent_a.AtomsBegin(), e=ent_a.AtomsEnd(); i!=e; ++i) {
mol::AtomViewList clashees=ent_b.FindWithin((*i).GetPos(),
- (*i).GetProp().radius+1.7);
+ (*i).GetAtomProps().radius+1.7);
for (mol::AtomViewList::iterator j=clashees.begin(),
e2=clashees.end(); j!=e2; ++j) {
- energy+=StericEnergy((*j).GetPos(), (*j).GetProp().radius-0.25,
- (*i).GetPos(), (*i).GetProp().radius-0.25);
+ energy+=StericEnergy((*j).GetPos(), (*j).GetAtomProps().radius-0.25,
+ (*i).GetPos(), (*i).GetAtomProps().radius-0.25);
}
}
return energy;
@@ -75,11 +75,11 @@ Real ClashScore(const mol::AtomHandle& atom, const mol::EntityView& ent_b)
{
Real energy=0.0;
mol::AtomViewList clashees=ent_b.FindWithin(atom.GetPos(),
- atom.GetProp().radius+2.0);
+ atom.GetAtomProps().radius+2.0);
for (mol::AtomViewList::iterator j=clashees.begin(),
e2=clashees.end(); j!=e2; ++j) {
- energy+=StericEnergy((*j).GetPos(), (*j).GetProp().radius,
- atom.GetPos(), atom.GetProp().radius);
+ energy+=StericEnergy((*j).GetPos(), (*j).GetAtomProps().radius,
+ atom.GetPos(), atom.GetAtomProps().radius);
}
return energy;
}