diff --git a/modules/mol/base/pymod/export_residue.cc b/modules/mol/base/pymod/export_residue.cc
index c4c43e5d89ca06505a65a7b39035692d7150681e..1e1b9f74a60d94c224b9aad51153a9e873b2a4a7 100644
--- a/modules/mol/base/pymod/export_residue.cc
+++ b/modules/mol/base/pymod/export_residue.cc
@@ -43,13 +43,25 @@ namespace {
void set_sec_struct1(ResidueBase* b, const SecStructure& s) {b->SetSecStructure(s);}
void set_sec_struct2(ResidueBase* b, char c) {b->SetSecStructure(SecStructure(c));}
- void set_chemclass1(ResidueBase* b, const ChemClass& cc) {b->SetChemClass(cc);}
- void set_chemclass2(ResidueBase* b, char c) {b->SetChemClass(ChemClass(c));}
+ void set_chemclass(ResidueBase* b, object po)
+ {
+ extract<ChemClass> ex1(po);
+ if(ex1.check()) {
+ b->SetChemClass(ex1());
+ }
+ extract<char> ex2(po);
+ if(ex2.check()) {
+ b->SetChemClass(ChemClass(ex2()));
+ }
+ std::string st=extract<std::string>(po);
+ if(st.empty()) {
+ throw Error("expected non-empty string as chem class");
+ }
+ b->SetChemClass(ChemClass(st[0]));
+ }
}
-//BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(X_insert_overloads,
-// ResidueHandle::InsertAtom, 2, 3)
void export_Residue()
{
@@ -125,6 +137,11 @@ void export_Residue()
.def("IsPeptideLinking", &ResidueBase::IsPeptideLinking)
.add_property("peptide_linking", &ResidueBase::IsPeptideLinking)
+ .def("GetCentralAtom", &ResidueBase::GetCentralAtom)
+ .def("SetCentralAtom", &ResidueBase::SetCentralAtom)
+ .add_property("central_atom", &ResidueBase::GetCentralAtom, &ResidueBase::SetCentralAtom)
+ .add_property("central_normal", &ResidueBase::GetCentralNormal)
+
.def("GetKey", &ResidueBase::GetKey,
return_value_policy<copy_const_reference>())
.def("GetName", &ResidueBase::GetName,
@@ -132,8 +149,8 @@ void export_Residue()
.def("GetNumber", &ResidueBase::GetNumber,
return_value_policy<copy_const_reference>())
.def("GetChemClass", &ResidueBase::GetChemClass)
- .def("SetChemClass", set_chemclass1)
- .def("SetChemClass", set_chemclass2)
+ .def("SetChemClass", set_chemclass)
+ .add_property("chem_class",&ResidueBase::GetChemClass,set_chemclass)
.add_property("is_ligand", &ResidueBase::IsLigand, &ResidueBase::SetIsLigand)
.def("IsLigand", &ResidueBase::IsLigand)
.def("SetIsLigand", &ResidueBase::SetIsLigand)
@@ -186,7 +203,6 @@ void export_Residue()
.def("GetCenterOfMass", &ResidueHandle::GetCenterOfMass)
.def("GetCenterOfAtoms", &ResidueHandle::GetCenterOfAtoms)
.def("GetGeometricCenter", geom_center<ResidueHandle>)
- .def("GetCentralAtom", &ResidueHandle::GetCentralAtom)
.add_property("mass", &ResidueHandle::GetMass)
.add_property("center_of_mass", &ResidueHandle::GetCenterOfMass)
.add_property("center_of_atoms", &ResidueHandle::GetCenterOfAtoms)
diff --git a/modules/mol/base/src/impl/residue_impl.cc b/modules/mol/base/src/impl/residue_impl.cc
index d8ce7f6d3f97b6c0bfe9e452d0c2760d54bbd01c..28f0cc6f9047616848e8d0a334da946a6fdfea9f 100644
--- a/modules/mol/base/src/impl/residue_impl.cc
+++ b/modules/mol/base/src/impl/residue_impl.cc
@@ -43,7 +43,8 @@ ResidueImpl::ResidueImpl(const EntityImplPtr& ent,
atom_list_(),
sec_structure_(SecStructure::COIL),
olc_('?'),
- protein_(false), ligand_(false)
+ protein_(false), ligand_(false),
+ central_atom_()
{
}
@@ -163,6 +164,7 @@ EntityImplPtr ResidueImpl::GetEntity() const
AtomImplPtr ResidueImpl::GetCentralAtom() const
{
+ if(central_atom_) return central_atom_;
if (chem_class_.IsNucleotideLinking()) {
for (AtomImplList::const_iterator it=atom_list_.begin();
it!=atom_list_.end();++it) {
@@ -178,6 +180,12 @@ AtomImplPtr ResidueImpl::GetCentralAtom() const
return AtomImplPtr();
}
+void ResidueImpl::SetCentralAtom(const AtomImplPtr& a)
+{
+ central_atom_=a;
+}
+
+
char ResidueImpl::GetOneLetterCode() const
{
return olc_;
diff --git a/modules/mol/base/src/impl/residue_impl.hh b/modules/mol/base/src/impl/residue_impl.hh
index 560571f87d1ac8f9c492704a54d5b3dcfe6bee15..8b01d32d2f3d8873f8098805dbe62028334dc2ec 100644
--- a/modules/mol/base/src/impl/residue_impl.hh
+++ b/modules/mol/base/src/impl/residue_impl.hh
@@ -72,6 +72,13 @@ public:
ChainImplPtr GetChain() const;
AtomImplPtr GetCentralAtom() const;
+ /*!
+ explicitely set central atom
+
+ if this is set, it will override the heuristic encoded
+ in GetCentralAtom; pass an invalid ptr to deactivate again
+ */
+ void SetCentralAtom(const AtomImplPtr& a);
geom::Vec3 GetCentralNormal() const;
@@ -209,6 +216,7 @@ private:
void AddAltAtom(const String& group, const AtomImplPtr& atom,
const geom::Vec3& position);
void RemoveAltPositionsForAtom(const AtomImplPtr& atom);
+
String curr_group_;
AtomEntryGroups alt_groups_;
EntityImplW ent_;
@@ -221,8 +229,13 @@ private:
ChemClass chem_class_;
char olc_;
// whether the residue is part of the protein.
+ // TODO: this should be fixed to be a enum'ed type aka
+ // RESIDUE_TYPE type_;
+ // where enum is one of protein, ligand, dna, lipid, etc
bool protein_;
bool ligand_;
+ AtomImplPtr central_atom_;
+
};
}}} // ns
diff --git a/modules/mol/base/src/residue_base.cc b/modules/mol/base/src/residue_base.cc
index a1d321dee00bf9a43b1a92634d88897099831ba7..7d15ad5f6fff00b62a223b8f41417f25d0703d8d 100644
--- a/modules/mol/base/src/residue_base.cc
+++ b/modules/mol/base/src/residue_base.cc
@@ -44,6 +44,23 @@ const GenericPropContainerImpl* ResidueBase::GpImpl() const
return Impl().get();
}
+AtomHandle ResidueBase::GetCentralAtom() const
+{
+ this->CheckValidity();
+ return AtomHandle(Impl()->GetCentralAtom());
+}
+
+void ResidueBase::SetCentralAtom(const AtomHandle& a)
+{
+ this->CheckValidity();
+ impl_->SetCentralAtom(a.Impl());
+}
+
+geom::Vec3 ResidueBase::GetCentralNormal() const
+{
+ this->CheckValidity();
+ return impl_->GetCentralNormal();
+}
const ResNum& ResidueBase::GetNumber() const {
this->CheckValidity();
diff --git a/modules/mol/base/src/residue_base.hh b/modules/mol/base/src/residue_base.hh
index ea5a5f01081787d3fe6e177894f288cfb8699f99..c994b9a3098b48479300c811d55583cc213ad16c 100644
--- a/modules/mol/base/src/residue_base.hh
+++ b/modules/mol/base/src/residue_base.hh
@@ -19,6 +19,8 @@
#ifndef OST_RESIDUE_BASE_HH
#define OST_RESIDUE_BASE_HH
+#include <ost/geom/geom.hh>
+
#include <ost/mol/module_config.hh>
#include <ost/mol/residue_prop.hh>
#include <ost/mol/impl/residue_impl_fw.hh>
@@ -90,6 +92,20 @@ public:
/// residue name and residue number
String GetQualifiedName() const;
+ /// \brief returns main atom, ie CA for amino acids
+ AtomHandle GetCentralAtom() const;
+
+ /*!
+ \brief set explicit central atom
+
+ overrides the heuristic of GetCentralAtom to explicitely
+ use the given one as the central atom; passing in an
+ invalid handle reverts back to the heurstic determination
+ */
+ void SetCentralAtom(const AtomHandle& a);
+
+ /// \return return specific normal of residue, usually CA-CB dir for AA
+ geom::Vec3 GetCentralNormal() const;
/// \brief whether the residue can form peptide bonds
bool IsPeptideLinking() const;
diff --git a/modules/mol/base/src/residue_handle.cc b/modules/mol/base/src/residue_handle.cc
index 809dbb8c64b9a1d604753e2feaa79174a8f71c96..d2ef00da17cd22fed12270d1dc783e9d8cc5cbe4 100644
--- a/modules/mol/base/src/residue_handle.cc
+++ b/modules/mol/base/src/residue_handle.cc
@@ -130,18 +130,6 @@ bool ResidueHandle::operator!=(const ResidueHandle& ref) const
return Impl()!=ref.Impl();
}
-AtomHandle ResidueHandle::GetCentralAtom() const
-{
- this->CheckValidity();
- return AtomHandle(Impl()->GetCentralAtom());
-}
-
-geom::Vec3 ResidueHandle::GetCentralNormal() const
-{
- this->CheckValidity();
- return Impl()->GetCentralNormal();
-}
-
int ResidueHandle::GetIndex() const
{
this->CheckValidity();
diff --git a/modules/mol/base/src/residue_handle.hh b/modules/mol/base/src/residue_handle.hh
index 54b9092a001e34a45aacdfffddf0ac33cc389665..5048a0804c960f535a7213b2a93c2e7324dac241 100644
--- a/modules/mol/base/src/residue_handle.hh
+++ b/modules/mol/base/src/residue_handle.hh
@@ -61,21 +61,15 @@ public:
: ResidueBase(impl) {}
EntityHandle GetEntity() const;
- /// \brief returns main atom, ie CA for amino acids
- AtomHandle GetCentralAtom() const;
-
- /// \return return specific normal of residue, usually CA-CB dir for AA
- geom::Vec3 GetCentralNormal() const;
-
- /// \brief Get entity's mass
+ /// \brief Get residue's mass
double GetMass() const;
- /// \brief Get entity's center of mass (mass weighted)
+ /// \brief Get residue's center of mass (mass weighted)
geom::Vec3 GetCenterOfMass() const;
- /// \brief Get entity's center of atoms (not mass weighted)
+ /// \brief Get residue's center of atoms (not mass weighted)
///
- /// Returns the center of all the atoms in an entity. This is
+ /// Returns the center of all the atoms in this residue. This is
/// similar to GetCenterOfMass(), but the atoms are not mass weighted
geom::Vec3 GetCenterOfAtoms() const;
diff --git a/modules/mol/base/src/residue_view.hh b/modules/mol/base/src/residue_view.hh
index 8c95c81c1fe372151a69a17f213ff6c398827072..8efe0c97f8739a5e8c64a1d1f84f3db357e94835 100644
--- a/modules/mol/base/src/residue_view.hh
+++ b/modules/mol/base/src/residue_view.hh
@@ -155,22 +155,20 @@ public:
/// \brief get parent chain view.
ChainView GetChain() const;
-
- /// \brief Get entity's mass
+ /// \brief Get residue's mass
double GetMass() const;
- /// \brief Get entity's center of mass (mass weighted)
+ /// \brief Get residue's center of mass (mass weighted)
geom::Vec3 GetCenterOfMass() const;
- /// \brief Get entity's center of atoms (not mass weighted)
+ /// \brief Get residue's center of atoms (not mass weighted)
///
- /// Returns the center of all the atoms in an entity. This is
+ /// Returns the center of all the atoms in this residue. This is
/// similar to GetCenterOfMass(), but the atoms are not mass weighted
geom::Vec3 GetCenterOfAtoms() const;
- /// \brief Get entity's axis-aligned bounding box
+ /// \brief Get residue's axis-aligned bounding box
geom::AlignedCuboid GetBounds() const;
-
/// \brief return view based on a query object
/// \sa Query