diff --git a/modules/base/tests/test_generic_property.cc b/modules/base/tests/test_generic_property.cc
index 754d5ead4438d6c8a9c5780170e625bf65983c72..48fa0d63addd1ff12f5e446a1f0a2e8586a7fcbd 100644
--- a/modules/base/tests/test_generic_property.cc
+++ b/modules/base/tests/test_generic_property.cc
@@ -53,8 +53,8 @@ BOOST_AUTO_TEST_CASE( test_generic_property )
EntityView ev = eh.CreateFullView();
ChainView chv = ev.FindChain("A");
- ResidueView resv = ev.FindResidue(res);
- AtomView atomv = ev.FindAtom(atom);
+ ResidueView resv = ev.ViewForHandle(res);
+ AtomView atomv = ev.ViewForHandle(atom);
BOOST_CHECK(ev.GetStringProp("a")=="123");
BOOST_CHECK(chv.GetFloatProp("b")==1.5);
diff --git a/modules/gfx/src/entity.cc b/modules/gfx/src/entity.cc
index 0154907216fc4940b726707307db806981cb7a2f..7920cd4eb8fdad036d4bed302dbbf9e845afadd0 100644
--- a/modules/gfx/src/entity.cc
+++ b/modules/gfx/src/entity.cc
@@ -443,7 +443,7 @@ bool Entity::OnSelect(const geom::Line3& line, geom::Vec3& result,
return true;
}
if(smode==1) {
- AtomView av = sel_.FindAtom(sel.GetHandle());
+ AtomView av = sel_.ViewForHandle(sel.GetHandle());
if(av.IsValid()) {
LOG_DEBUG("de-selected atom: " << sel);
sel_.RemoveAtom(av);
@@ -456,8 +456,8 @@ bool Entity::OnSelect(const geom::Line3& line, geom::Vec3& result,
}
result = sel.GetPos();
} else if(smode==2) {
- AtomView av=sel_.FindAtom(sel);
- ResidueView rv=sel_.FindResidue(sel.GetResidue());
+ AtomView av=sel_.ViewForHandle(sel);
+ ResidueView rv=sel_.ViewForHandle(sel.GetResidue());
if(av.IsValid() && rv.IsValid()) {
LOG_DEBUG("de-selected residue: " << sel.GetResidue());
sel_.RemoveResidue(rv);
@@ -472,7 +472,7 @@ bool Entity::OnSelect(const geom::Line3& line, geom::Vec3& result,
return false;
}
ChainHandle chain=sel.GetHandle().GetResidue().GetChain();
- ChainView cv = sel_.FindChain(chain);
+ ChainView cv = sel_.ViewForHandle(chain);
if(cv.IsValid()) {
LOG_DEBUG("de-selected chain: " << chain);
sel_.RemoveChain(cv);
diff --git a/modules/gfx/src/impl/backbone_trace.cc b/modules/gfx/src/impl/backbone_trace.cc
index ad9e8c961b0cedea3073cdd8183fc636662b5397..9ff14e1f45280f6e9be0ccac54c1a7507586cee1 100644
--- a/modules/gfx/src/impl/backbone_trace.cc
+++ b/modules/gfx/src/impl/backbone_trace.cc
@@ -253,7 +253,7 @@ BackboneTrace BackboneTrace::CreateSubset(const mol::EntityView& subview)
NodeEntryList new_nlist;
const NodeEntryList& nlist=*nitnit;
for(NodeEntryList::const_iterator nit=nlist.begin();nit!=nlist.end();++nit) {
- if(subview.FindAtom(nit->atom).IsValid()) {
+ if(subview.ViewForHandle(nit->atom).IsValid()) {
if(!new_nlist.empty()) {
if(!in_sequence(new_nlist.back().atom.GetResidue(),nit->atom.GetResidue(),seq_hack_)) {
if(new_nlist.size()>1) {
diff --git a/modules/gfx/src/impl/connect_renderer_base.cc b/modules/gfx/src/impl/connect_renderer_base.cc
index fd70d9968b67270d14c837de128fcbce9a003460..5f0ed4a6b8f821866eb587ac7110a0df28a307d4 100644
--- a/modules/gfx/src/impl/connect_renderer_base.cc
+++ b/modules/gfx/src/impl/connect_renderer_base.cc
@@ -145,7 +145,7 @@ inline void apply_color_op(ConnectRendererBase* rend, GfxView* v, T1 get_col, co
view = op.GetView();
}
for(AtomEntryMap::iterator it=v->atom_map.begin();it!=v->atom_map.end();++it){
- if(view.FindAtom(it->second.atom)){
+ if(view.ViewForHandle(it->second.atom)){
it->second.color=get_col.ColorOfAtom(it->second.atom).second;
}
}
diff --git a/modules/gfx/src/impl/line_trace_renderer.cc b/modules/gfx/src/impl/line_trace_renderer.cc
index 8e650b9876e4ee1d065bde84962bd75a7377702f..bb6622ac84e6de1d5138c3810760975d2744dffb 100644
--- a/modules/gfx/src/impl/line_trace_renderer.cc
+++ b/modules/gfx/src/impl/line_trace_renderer.cc
@@ -92,7 +92,7 @@ void LineTraceRenderer::PrepareRendering(const BackboneTrace& trace_subset,
if(nl.size()<1) continue;
for(unsigned int i=0;i<nl.size();++i) {
const NodeEntry& entry=nl[i];
- if(sel_.FindAtom(entry.atom).IsValid()) {
+ if(sel_.ViewForHandle(entry.atom).IsValid()) {
geom::Vec3 apos = entry.atom.GetPos();
VertexID p0=va.Add(apos, geom::Vec3(),sel_clr);
if(i>0) {
diff --git a/modules/gfx/src/impl/trace_renderer.cc b/modules/gfx/src/impl/trace_renderer.cc
index 49ee1c7ab258f9b51aa2432d019b78f809a3fd43..f901c77cdf7fa93424bcf6557e02557fd67377f3 100644
--- a/modules/gfx/src/impl/trace_renderer.cc
+++ b/modules/gfx/src/impl/trace_renderer.cc
@@ -64,7 +64,7 @@ void TraceRenderer::PrepareRendering(BackboneTrace& trace_subset,
const NodeEntryList& nl=trace_subset.GetList(node_list);
for(unsigned int i=0;i<nl.size();++i) {
mol::AtomHandle ah=nl[i].atom;
- if(sel_.FindAtom(ah).IsValid()) {
+ if(sel_.ViewForHandle(ah).IsValid()) {
geom::Vec3 apos = ah.GetPos();
va.AddSphere(SpherePrim(apos,
options_->GetTubeRadius()+0.05,
diff --git a/modules/gfx/src/impl/trace_renderer_base.cc b/modules/gfx/src/impl/trace_renderer_base.cc
index b77b426913f5aaab3628371554d842e0d31932c6..1b4c47fe5320f3a118d8ffff66a26412640b9201 100644
--- a/modules/gfx/src/impl/trace_renderer_base.cc
+++ b/modules/gfx/src/impl/trace_renderer_base.cc
@@ -63,7 +63,7 @@ inline void apply_color_op(TraceRendererBase* rend, BackboneTrace& trace_subset,
for (int node_list=0; node_list<trace_subset.GetListCount(); ++node_list) {
NodeEntryList& nl=trace_subset.GetList(node_list);
for (unsigned int i=0; i<nl.size();++i) {
- if(view.FindAtom(nl[i].atom)){
+ if(view.ViewForHandle(nl[i].atom)){
std::pair<bool,Color> clr =get_col.ColorOfAtom(nl[i].atom);
if(clr.first) {
set_node_entry_color(nl[i],mask,clr.second);
diff --git a/modules/gui/src/gl_canvas.cc b/modules/gui/src/gl_canvas.cc
index 2d631931bafc912c9137587f28df24c1b9a0b9c0..f94bff0458c4fbfe746c489e424ebc467c9137d2 100644
--- a/modules/gui/src/gl_canvas.cc
+++ b/modules/gui/src/gl_canvas.cc
@@ -369,7 +369,7 @@ void GLCanvas::CopySelectionToClipboard()
if (!rv.IsPeptideLinking() || rv.GetOneLetterCode()=='?')
continue;
seq1 << rv.GetOneLetterCode();
- if (sel.FindResidue(rv.GetHandle()).IsValid()) {
+ if (sel.ViewForHandle(rv.GetHandle()).IsValid()) {
seq2 << rv.GetOneLetterCode();
} else {
seq2 << '-';
diff --git a/modules/gui/src/sequence_viewer/sequence_view_object.cc b/modules/gui/src/sequence_viewer/sequence_view_object.cc
index f9303f8ddce335f16dbf4fd4f48cef5eb3bfaa16..97993f0cdf11d45967377249f0793cf01e37ea50 100644
--- a/modules/gui/src/sequence_viewer/sequence_view_object.cc
+++ b/modules/gui/src/sequence_viewer/sequence_view_object.cc
@@ -168,7 +168,7 @@ QMap<int, QList<int> > SequenceViewObject::GetIndexesForView(const mol::EntityVi
// for each residue in the selection deduce index in sequence
for (mol::ResidueViewList::const_iterator j=src_chain.GetResidueList().begin(),
e2=src_chain.GetResidueList().end(); j!=e2; ++j) {
- mol::ResidueView dst_res=dst_chain.FindResidue(j->GetHandle());
+ mol::ResidueView dst_res=dst_chain.ViewForHandle(j->GetHandle());
assert(dst_res.IsValid());
int p=dst_res.GetIndex()+1;
assert(p>=0 && p<=seq.GetLength());
diff --git a/modules/mol/base/pymod/export_chain_view.cc b/modules/mol/base/pymod/export_chain_view.cc
index e8c54c9a4a9436585531da168bdcbeab4130d3b2..70ee5d1d1a216c56ad6757ffa681094141d85b41 100644
--- a/modules/mol/base/pymod/export_chain_view.cc
+++ b/modules/mol/base/pymod/export_chain_view.cc
@@ -34,7 +34,8 @@ typedef ResidueView (ChainView::*RnumMethod)(const ResNum&) const;
typedef ResidueView (ChainView::*HandleMethod)(const ResidueHandle&) const;
RnumMethod rnum_find_residue=&ChainView::FindResidue;
-HandleMethod handle_find_residue=&ChainView::FindResidue;
+HandleMethod handle_find_residue=&ChainView::FindResidue;
+HandleMethod view_for_rh=&ChainView::ViewForHandle;
typedef ResidueView (ChainView::*HM)(const ResidueHandle&, ViewAddFlags);
typedef ResidueView (ChainView::*VM)(const ResidueView&, ViewAddFlags);
@@ -48,9 +49,11 @@ BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(X_add_atom_overloads,
ChainView::AddAtom, 1, 2)
AtomView (ChainView::*find_atom_a)(const ResNum&, const String&) const=&ChainView::FindAtom;
-AtomView (ChainView::*find_atom_b)(const AtomHandle&) const=&ChainView::FindAtom;
+AtomView (ChainView::*find_atom_b)(const AtomHandle&) const=&ChainView::FindAtom;
+AtomView (ChainView::*view_for_ah)(const AtomHandle&) const=&ChainView::ViewForHandle;
typedef EntityView (ChainView::*QueryMethod)(const Query&, uint) const;
typedef EntityView (ChainView::*StringMethod)(const String&, uint) const;
+
QueryMethod select_query=&ChainView::Select;
StringMethod select_string=&ChainView::Select;
}
@@ -71,8 +74,10 @@ void export_ChainView()
.def("GetEntity", &ChainView::GetEntity)
.def("FindResidue",rnum_find_residue, arg("residue_number"))
.def("FindResidue", handle_find_residue, arg("residue_handle"))
+ .def("ViewForHandle", view_for_rh, arg("residue_handle"))
.def("FindAtom", find_atom_a)
- .def("FindAtom", find_atom_b)
+ .def("FindAtom", find_atom_b)
+ .def("ViewForHandle", view_for_ah)
.def("AddAtom", &ChainView::AddAtom,
X_add_atom_overloads(args("atom_handle", "view_add_flags")))
.def("AddResidue", hm,
diff --git a/modules/mol/base/pymod/export_entity_view.cc b/modules/mol/base/pymod/export_entity_view.cc
index e0b4c9b097097d4dbfd7dcf50ae7b6f8c8d9c184..9d724a57982f024103e2949ad56b7eda5e57eea4 100644
--- a/modules/mol/base/pymod/export_entity_view.cc
+++ b/modules/mol/base/pymod/export_entity_view.cc
@@ -54,6 +54,7 @@ VM vm=&EntityView::AddChain;
HM hm=&EntityView::AddChain;
HandleMethod find_chain_hnd=&EntityView::FindChain;
+HandleMethod view_for_ch=&EntityView::ViewForHandle;
StringMethod find_chain_str=&EntityView::FindChain;
QSMethod select_string=&EntityView::Select;
QueryMethod select_query=&EntityView::Select;
@@ -91,8 +92,16 @@ BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(X_add_chain_overloads,
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(X_add_atom_overloads,
EntityView::AddAtom, 1, 2)
-AtomView (EntityView::*find_atom_a)(const String&, const ResNum&, const String&) const=&EntityView::FindAtom;
+AtomView (EntityView::*find_atom_a)(const String&, const ResNum&,
+ const String&) const=&EntityView::FindAtom;
AtomView (EntityView::*find_atom_b)(const AtomHandle&) const=&EntityView::FindAtom;
+AtomView (EntityView::*view_for_ah)(const AtomHandle&) const=&EntityView::ViewForHandle;
+
+ResidueView (EntityView::*find_res_a)(const ResidueHandle&) const=&EntityView::FindResidue;
+ResidueView (EntityView::*find_res_b)(const String&,
+ const ResNum&) const=&EntityView::FindResidue;
+
+ResidueView (EntityView::*view_for_rh)(const ResidueHandle&) const=&EntityView::ViewForHandle;
}
@@ -115,9 +124,15 @@ void export_EntityView()
.def("ExtendViewToResidues", &EntityView::ExtendViewToResidues)
.def("ExtendViewToSurrounding", &EntityView::ExtendViewToSurrounding)
.def("FindChain", find_chain_str)
- .def("FindResidue", &EntityView::FindResidue)
+ .def("FindChain", find_chain_hnd)
+ .def("ViewForHandle", view_for_rh)
+ .def("ViewForHandle", view_for_ch)
.def("FindAtom", find_atom_a)
- .def("FindAtom", find_atom_b)
+ .def("FindAtom", find_atom_b)
+ .def("FindResidue", find_res_a)
+ .def("FindResidue", find_res_b)
+
+ .def("ViewForHandle", view_for_ah)
.def("GetAtomCount", &EntityView::GetAtomCount)
.def("GetGeometricStart", geom_start<EntityView>)
.def("GetGeometricEnd", geom_end<EntityView>)
diff --git a/modules/mol/base/pymod/export_residue_view.cc b/modules/mol/base/pymod/export_residue_view.cc
index 89c6eddc428833b3dfe3d019b109b0e558c95ed7..79d167996ed18eb6d53d0ae57e66df3f8c2c695a 100644
--- a/modules/mol/base/pymod/export_residue_view.cc
+++ b/modules/mol/base/pymod/export_residue_view.cc
@@ -35,6 +35,7 @@ typedef AtomView (ResidueView::*HandleMethodNonConst)(const AtomHandle&, ViewAdd
StringMethod string_find_atom=&ResidueView::FindAtom;
HandleMethod handle_find_atom=&ResidueView::FindAtom;
+HandleMethod view_for_ah=&ResidueView::ViewForHandle;
HandleMethodNonConst add_atom_handle=&ResidueView::AddAtom;
ViewMethod add_atom_view=&ResidueView::AddAtom;
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(X_add_atom_overloads,
@@ -67,6 +68,7 @@ void export_ResidueView()
.def("AddAtom", add_atom_handle, X_add_atom_overloads(args("atom_handle", "flags")))
.def("AddAtom", add_atom_view, X_add_atom_overloads(args("atom_view", "flags")))
.def("FindAtom", handle_find_atom, args("atom_handle"))
+ .def("ViewForHandle", view_for_ah, arg("atom_handle"))
.def("IsAtomIncluded", &ResidueView::IsAtomIncluded, args("atom_handle"))
.def("GetIndex", &ResidueView::GetIndex)
.add_property("index", &ResidueView::GetIndex)
diff --git a/modules/mol/base/src/atom_view.cc b/modules/mol/base/src/atom_view.cc
index 2d81e4aec04be48a8310209fc05250139e71709e..ed16ac0f82f314a452cddbc8b35fd8fe5842b2ab 100644
--- a/modules/mol/base/src/atom_view.cc
+++ b/modules/mol/base/src/atom_view.cc
@@ -120,9 +120,9 @@ mol::AtomViewList AtomView::GetBondPartners() const
mol::BondHandleList::const_iterator i;
for (i=data_->bonds.begin();i!=data_->bonds.end();++i) {
if (i->GetFirst().GetHandle()!=this->GetHandle()) {
- avl.push_back(this->GetEntity().FindAtom(i->GetFirst()));
+ avl.push_back(this->GetEntity().ViewForHandle(i->GetFirst()));
} else {
- avl.push_back(this->GetEntity().FindAtom(i->GetSecond()));
+ avl.push_back(this->GetEntity().ViewForHandle(i->GetSecond()));
}
}
return avl;
@@ -138,9 +138,9 @@ void AtomView::RemoveBonds()
BondHandle b=*i;
AtomView av;
if (b.GetFirst()==this->GetHandle()) {
- av=ent.FindAtom(b.GetSecond());
+ av=ent.ViewForHandle(b.GetSecond());
} else {
- av=ent.FindAtom(b.GetFirst());
+ av=ent.ViewForHandle(b.GetFirst());
}
ent.RemoveBond(b);
}
diff --git a/modules/mol/base/src/chain_view.cc b/modules/mol/base/src/chain_view.cc
index 4727e31ddce6764bcdfc0e78bb5e7c3c31e0d83f..355bd6cf5963f68a3a42fdf587c7ec60f2ed9c80 100644
--- a/modules/mol/base/src/chain_view.cc
+++ b/modules/mol/base/src/chain_view.cc
@@ -18,8 +18,8 @@
//------------------------------------------------------------------------------
#include <algorithm>
#include <limits>
-
#include <boost/bind.hpp>
+#include <ost/log.hh>
#include <ost/mol/bond_handle.hh>
#include <ost/mol/residue_handle.hh>
#include <ost/mol/chain_view.hh>
@@ -176,7 +176,13 @@ ResidueView ChainView::FindResidue(const ResNum& number) const {
}
}
-ResidueView ChainView::FindResidue(const ResidueHandle& handle) const {
+ResidueView ChainView::FindResidue(const ResidueHandle& residue) const {
+ LOG_WARNING("ChainView::FindResidue(handle) is deprecated. "
+ "Use ChainView::ViewForHandle instead.");
+ return this->ViewForHandle(residue);
+}
+
+ResidueView ChainView::ViewForHandle(const ResidueHandle& handle) const {
this->CheckValidity();
const ResidueViewList& l=data_->residues;
ResidueViewList::const_iterator i;
@@ -187,7 +193,7 @@ ResidueView ChainView::FindResidue(const ResidueHandle& handle) const {
bool ChainView::IsResidueIncluded(const ResidueHandle& handle) const {
this->CheckValidity();
- return this->FindResidue(handle).IsValid();
+ return this->ViewForHandle(handle).IsValid();
}
ResidueView ChainView::AddResidue(const ResidueHandle& residue_handle,
@@ -195,7 +201,7 @@ ResidueView ChainView::AddResidue(const ResidueHandle& residue_handle,
this->CheckValidity();
ResidueView rv;
if ((flags & ViewAddFlag::CHECK_DUPLICATES) &&
- (rv=this->FindResidue(residue_handle)))
+ (rv=this->ViewForHandle(residue_handle)))
return rv;
rv=ResidueView(*this, residue_handle);
if (!data_->residues.empty()) {
@@ -213,12 +219,18 @@ ResidueView ChainView::AddResidue(const ResidueHandle& residue_handle,
}
AtomView ChainView::FindAtom(const AtomHandle& atom) const {
+ LOG_WARNING("ChainView::FindAtom(handle) is deprecated. "
+ "Use ChainView::ViewForHandle instead.");
+ return this->ViewForHandle(atom);
+}
+
+AtomView ChainView::ViewForHandle(const AtomHandle& atom) const {
ResidueHandle residue=atom.GetResidue();
if (atom.GetEntity()!=this->GetEntity().GetHandle())
return AtomView();
ResidueView v=this->FindResidue(residue.GetNumber());
- return v.IsValid() ? v.FindAtom(atom) : AtomView();
+ return v.IsValid() ? v.ViewForHandle(atom) : AtomView();
}
AtomView ChainView::AddAtom(const AtomHandle& atom_handle,
@@ -262,7 +274,7 @@ ResidueView ChainView::AddResidue(const ResidueView& residue_view,
this->CheckValidity();
ResidueView rv;
if ((flags & ViewAddFlag::CHECK_DUPLICATES) &&
- (rv=this->FindResidue(residue_view.GetHandle()))) {
+ (rv=this->ViewForHandle(residue_view.GetHandle()))) {
if (!(flags & ViewAddFlag::INCLUDE_ATOMS)) {
return rv;
}
diff --git a/modules/mol/base/src/chain_view.hh b/modules/mol/base/src/chain_view.hh
index 72ed7a72e47877f485931994c2d4f501bc95a925..70bd305aa1c17884f062a2b0721c97cb1cea7340 100644
--- a/modules/mol/base/src/chain_view.hh
+++ b/modules/mol/base/src/chain_view.hh
@@ -125,12 +125,15 @@ public:
ResidueView FindResidue(const ResNum& number) const;
/// \brief Find view for given atom handle
- AtomView FindAtom(const AtomHandle& atom) const;
+ /// Deprecated: Use ViewForHandle instead
+ AtomView FindAtom(const AtomHandle& atom) const;
+ AtomView ViewForHandle(const AtomHandle& atom) const;
AtomView FindAtom(const ResNum& num, const String& name) const;
/// \brief Find residue by residue handle
- ResidueView FindResidue(const ResidueHandle& handle) const;
+ ResidueView ViewForHandle(const ResidueHandle& handle) const;
+ ResidueView FindResidue(const ResidueHandle& handle) const;
/// \brief Check whether the view includes the given residue.
bool IsResidueIncluded(const ResidueHandle& handle) const;
diff --git a/modules/mol/base/src/entity_view.cc b/modules/mol/base/src/entity_view.cc
index a88f0b39553a438c0d51359fee91cacf9d85a7a1..d81940ee1bfc89228a9db78163ac410b95a96738 100644
--- a/modules/mol/base/src/entity_view.cc
+++ b/modules/mol/base/src/entity_view.cc
@@ -1,4 +1,5 @@
//------------------------------------------------------------------------------
+//
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2011 by the OpenStructure authors
@@ -207,7 +208,7 @@ ChainView EntityView::AddChain(const ChainHandle& chain_handle,
this->CheckValidity();
ChainView cv;
if (flags & ViewAddFlag::CHECK_DUPLICATES &&
- (cv=this->FindChain(chain_handle)))
+ (cv=this->ViewForHandle(chain_handle)))
return cv;
cv=ChainView(*this, chain_handle);
data_->chains.push_back(cv);
@@ -256,14 +257,14 @@ ChainView EntityView::FindChain(const String& chain_name) const{
}
-ResidueView EntityView::FindResidue(const ResidueHandle& residue) const {
+ResidueView EntityView::ViewForHandle(const ResidueHandle& residue) const {
ChainHandle chain=residue.GetChain();
- ChainView v=this->FindChain(chain);
- return v.IsValid() ? v.FindResidue(residue) : ResidueView();
+ ChainView v=this->ViewForHandle(chain);
+ return v.IsValid() ? v.ViewForHandle(residue) : ResidueView();
}
-AtomView EntityView::FindAtom(const AtomHandle& atom) const
+AtomView EntityView::ViewForHandle(const AtomHandle& atom) const
{
this->CheckValidity();
return data_->ViewForHandle(atom);
@@ -409,7 +410,7 @@ EntityView EntityView::Select(const Query& query, QueryFlags flags) const
return view;
}
-ChainView EntityView::FindChain(const ChainHandle& chain) const {
+ChainView EntityView::ViewForHandle(const ChainHandle& chain) const {
this->CheckValidity();
ChainViewList::const_iterator i;
i=std::find_if(data_->chains.begin(), data_->chains.end(),
@@ -421,7 +422,7 @@ ChainView EntityView::FindChain(const ChainHandle& chain) const {
bool EntityView::IsChainIncluded(const ChainHandle& chain) const
{
this->CheckValidity();
- return this->FindChain(chain).IsValid();
+ return this->ViewForHandle(chain).IsValid();
}
@@ -584,7 +585,7 @@ ChainView EntityView::AddChain(const ChainView& chain_view,
this->CheckValidity();
ChainView cv;
if (flags & ViewAddFlag::CHECK_DUPLICATES &&
- (cv=this->FindChain(chain_view.GetHandle()))) {
+ (cv=this->ViewForHandle(chain_view.GetHandle()))) {
if (!(flags & ViewAddFlag::INCLUDE_RESIDUES)) {
return cv;
}
@@ -627,7 +628,7 @@ AtomViewList EntityView::FindWithin(const geom::Vec3& center, Real radius) const
AtomHandleList ahl=this->GetHandle().FindWithin(center, radius);
AtomViewList avl;
for (AtomHandleList::iterator i=ahl.begin(), e=ahl.end(); i!=e; ++i) {
- if (AtomView v=this->FindAtom(*i)) {
+ if (AtomView v=this->ViewForHandle(*i)) {
avl.push_back(v);
}
}
@@ -721,7 +722,7 @@ AtomView EntityView::AddXAtom(const AtomHandle& ah, ViewAddFlags flags)
}
AtomView EntityView::FindXAtom(const AtomHandle& ah)
{
- return this->FindAtom(ah);
+ return this->ViewForHandle(ah);
}
#endif
@@ -737,6 +738,18 @@ AtomView EntityView::FindAtom(const String& chain_name,
}
return AtomView();
}
+
+ResidueView EntityView::FindResidue(const String& chain,
+ const ResNum& num) const
+{
+ this->CheckValidity();
+ ChainView ch=this->FindChain(chain);
+ if (ch.IsValid()) {
+ return ch.FindResidue(num);
+ }
+ return ResidueView();
+}
+
geom::AlignedCuboid EntityView::GetBounds() const
{
this->CheckValidity();
@@ -878,5 +891,26 @@ String EntityView::Dump() const
return stream.str();
}
+ChainView EntityView::FindChain(const ChainHandle& chain) const
+{
+ LOG_WARNING("EntityView::FindChain is deprecated. "
+ "Use EntityView::ViewForHandle instead");
+ return this->ViewForHandle(chain);
+}
+
+ResidueView EntityView::FindResidue(const ResidueHandle& residue) const
+{
+ LOG_WARNING("EntityView::FindResidue is deprecated. "
+ "Use EntityView::ViewForHandle instead");
+ return this->ViewForHandle(residue);
+}
+
+AtomView EntityView::FindAtom(const AtomHandle& atom) const
+{
+ LOG_WARNING("EntityView::FindAtom(handle) is deprecated. "
+ "Use EntityView::ViewForHandle instead");
+ return this->ViewForHandle(atom);
+}
+
}} // ns
diff --git a/modules/mol/base/src/entity_view.hh b/modules/mol/base/src/entity_view.hh
index 6e5b2371695064033bfa4637d7a5e533e6c9957b..56136733b06abfca2abc5bf12c3f299f6de9e002 100644
--- a/modules/mol/base/src/entity_view.hh
+++ b/modules/mol/base/src/entity_view.hh
@@ -221,16 +221,39 @@ public:
ChainView FindChain(const String& chain_name) const;
/// \brief Find atom for given residue handle
+ ///
+ /// deprecated. Use ViewForHandle instead
ResidueView FindResidue(const ResidueHandle& residue) const;
+ ResidueView FindResidue(const String& chain, const ResNum& num) const;
+
+ /// \brief locate residue view for given residue handle
+ ///
+ /// returns an invalid ResidueView if the residue could not be
+ /// located in the structure
+ ResidueView ViewForHandle(const ResidueHandle& residue) const;
/// \brief Find view for given atom handle
+ ///
+ /// deprecated. Use ViewForHandle instead
AtomView FindAtom(const AtomHandle& atom) const;
+ AtomView ViewForHandle(const AtomHandle& atom) const;
+ /// \brief locate atom view for given atom handle
+ ///
+ /// returns an invalid AtomView if the residue could not be
+ /// located in the structure
AtomView FindAtom(const String& chain_name, const ResNum& num,
const String& atom_name) const;
/// \brief Find chain for given chain handle
- ChainView FindChain(const ChainHandle& chain) const;
+ ///
+ /// deprecated: Use ViewForHandle instead
+ ChainView FindChain(const ChainHandle& chain) const;
+ /// \brief locate chain view for given chain handle
+ ///
+ /// returns an invalid AtomView if the residue could not be
+ /// located in the structure
+ ChainView ViewForHandle(const ChainHandle& chain) const;
/// \brief Check whether the view includes the given chain
/// \return True, if the chain is included in the view, false if not.
bool IsChainIncluded(const ChainHandle& chain) const;
diff --git a/modules/mol/base/src/residue_view.cc b/modules/mol/base/src/residue_view.cc
index 4bd75ba32e1701750d89a28a04ab9169c5ce9dc2..406854a1f0f077c61080c320320e82577765e625 100644
--- a/modules/mol/base/src/residue_view.cc
+++ b/modules/mol/base/src/residue_view.cc
@@ -20,7 +20,7 @@
#include <limits>
#include <boost/bind.hpp>
-
+#include <ost/log.hh>
#include <ost/mol/bond_handle.hh>
#include <ost/mol/chain_view.hh>
#include <ost/mol/atom_view.hh>
@@ -96,7 +96,7 @@ AtomView ResidueView::AddAtom(const AtomHandle& atom_handle,
this->CheckValidity();
AtomView v;
if ((flags & ViewAddFlag::CHECK_DUPLICATES) &&
- (v=this->FindAtom(atom_handle))) {
+ (v=this->ViewForHandle(atom_handle))) {
return v;
}
v=AtomView(*this, atom_handle);
@@ -118,7 +118,7 @@ AtomView ResidueView::FindAtom(const String& atom_name) const {
return i==data_->atoms.end() ? AtomView() : *i;
}
-AtomView ResidueView::FindAtom(const AtomHandle& handle) const {
+AtomView ResidueView::ViewForHandle(const AtomHandle& handle) const {
this->CheckValidity();
const AtomViewList& l=data_->atoms;
AtomViewList::const_iterator i;
@@ -128,7 +128,7 @@ AtomView ResidueView::FindAtom(const AtomHandle& handle) const {
bool ResidueView::IsAtomIncluded(const AtomHandle& handle) const {
// validity is checked by FindAtom
- return this->FindAtom(handle).IsValid();
+ return this->ViewForHandle(handle).IsValid();
}
@@ -274,4 +274,11 @@ EntityView ResidueView::Select(const String& q, QueryFlags flags) const {
return this->GetEntity().Select(Query(s.str()), flags);
}
+AtomView ResidueView::FindAtom(const AtomHandle& handle) const
+{
+ LOG_WARNING("ResidueView::FindAtom(handle) is deprecated. "
+ "Use ResidueView::ViewForHandle instead.");
+ return this->ViewForHandle(handle);
+}
+
}} //ns
diff --git a/modules/mol/base/src/residue_view.hh b/modules/mol/base/src/residue_view.hh
index 8efe0c97f8739a5e8c64a1d1f84f3db357e94835..1727e87719c93b1d437352d861e8674c6cd72963 100644
--- a/modules/mol/base/src/residue_view.hh
+++ b/modules/mol/base/src/residue_view.hh
@@ -118,6 +118,7 @@ public:
AtomView FindAtom(const String& atom_name) const;
/// \brief Find residue by residue handle
+ AtomView ViewForHandle(const AtomHandle& handle) const;
AtomView FindAtom(const AtomHandle& handle) const;
/// \brief Check whether the view includes the the given atom.
diff --git a/modules/mol/base/src/view_op.cc b/modules/mol/base/src/view_op.cc
index 973fa768662d38a4992874bf40917a768810d19a..6e4227e741d0faa02d5b1a902b1d63be0050aee2 100644
--- a/modules/mol/base/src/view_op.cc
+++ b/modules/mol/base/src/view_op.cc
@@ -64,14 +64,14 @@ mol::EntityView Union(const mol::EntityView& ev1, const mol::EntityView& ev2)
mol::ChainViewList::const_iterator c_it=ev2.GetChainList().begin();
for ( ; c_it!=ev2.GetChainList().end(); ++c_it) {
mol::ChainView cv=*c_it;
- mol::ChainView cv2=merge.FindChain(cv.GetHandle());
+ mol::ChainView cv2=merge.ViewForHandle(cv.GetHandle());
if (!cv2) {
cv2=merge.AddChain(cv, mol::ViewAddFlag::INCLUDE_ALL);
} else {
mol::ResidueViewList::const_iterator r_it=cv.GetResidueList().begin();
for (; r_it!=cv.GetResidueList().end(); ++r_it) {
mol::ResidueView rv=*r_it;
- mol::ResidueView rv2=cv2.FindResidue(rv.GetHandle());
+ mol::ResidueView rv2=cv2.ViewForHandle(rv.GetHandle());
if (!rv2) {
rv2=cv2.AddResidue(rv, mol::ViewAddFlag::INCLUDE_ALL);
} else {
@@ -115,7 +115,7 @@ mol::EntityView Difference(const mol::EntityView& ev1,
mol::ChainViewList::const_iterator c_it=ev1.GetChainList().begin();
for ( ; c_it!=ev1.GetChainList().end(); ++c_it) {
mol::ChainView cv=*c_it;
- mol::ChainView cv2=ev2.FindChain(cv.GetHandle());
+ mol::ChainView cv2=ev2.ViewForHandle(cv.GetHandle());
if (!cv2) {
diff.AddChain(cv,mol::ViewAddFlag::INCLUDE_ALL);
} else {
@@ -123,7 +123,7 @@ mol::EntityView Difference(const mol::EntityView& ev1,
mol::ResidueViewList::const_iterator r_it=cv.GetResidueList().begin();
for (; r_it!=cv.GetResidueList().end(); ++r_it) {
mol::ResidueView rv=*r_it;
- mol::ResidueView rv2=cv2.FindResidue(rv.GetHandle());
+ mol::ResidueView rv2=cv2.ViewForHandle(rv.GetHandle());
if (!rv2) {
if(!chain_added){
diff.AddChain(cv);
@@ -134,7 +134,7 @@ mol::EntityView Difference(const mol::EntityView& ev1,
bool residue_added = false;
mol::AtomViewList::const_iterator a_it=rv.GetAtomList().begin();
for (; a_it!=rv.GetAtomList().end(); ++a_it) {
- if (!rv2.FindAtom((*a_it).GetHandle())) {
+ if (!rv2.ViewForHandle((*a_it).GetHandle())) {
if(!residue_added){
diff.AddResidue(rv);
residue_added = true;
@@ -182,7 +182,7 @@ mol::EntityView Intersection(const mol::EntityView& ev1,
BondHandleList bonds_to_add;
for (AtomViewIter a=ev1.AtomsBegin(),e=ev1.AtomsEnd(); a!=e; ++a) {
AtomView av=*a;
- AtomView av2=ev2.FindAtom(av.GetHandle());
+ AtomView av2=ev2.ViewForHandle(av.GetHandle());
if (av2.IsValid()) {
intersection.AddAtom(av.GetHandle());
bl=av.GetBondList();
diff --git a/modules/mol/base/tests/test_view_op.cc b/modules/mol/base/tests/test_view_op.cc
index 7d084e6fbb2816a8e49b73727160e79b4c6e845a..61fff1ff0955baac7eaa11e775d42e19f35179c5 100644
--- a/modules/mol/base/tests/test_view_op.cc
+++ b/modules/mol/base/tests/test_view_op.cc
@@ -81,20 +81,20 @@ BOOST_AUTO_TEST_CASE(test_difference)
BOOST_CHECK(diff_view.FindChain("B"));
// check residues
- BOOST_CHECK(!diff_view.FindResidue(ent.FindResidue("A", mol::ResNum(1))));
- BOOST_CHECK(diff_view.FindResidue(ent.FindResidue("A", mol::ResNum(2))));
- BOOST_CHECK(diff_view.FindResidue(ent.FindResidue("B", mol::ResNum(1))));
- BOOST_CHECK(diff_view.FindResidue(ent.FindResidue("B", mol::ResNum(2))));
+ BOOST_CHECK(!diff_view.ViewForHandle(ent.FindResidue("A", mol::ResNum(1))));
+ BOOST_CHECK(diff_view.ViewForHandle(ent.FindResidue("A", mol::ResNum(2))));
+ BOOST_CHECK(diff_view.ViewForHandle(ent.FindResidue("B", mol::ResNum(1))));
+ BOOST_CHECK(diff_view.ViewForHandle(ent.FindResidue("B", mol::ResNum(2))));
// check atoms
- BOOST_CHECK(!diff_view.FindAtom(ent.FindAtom("A", mol::ResNum(1), "A")));
- BOOST_CHECK(!diff_view.FindAtom(ent.FindAtom("A", mol::ResNum(1), "B")));
- BOOST_CHECK(!diff_view.FindAtom(ent.FindAtom("A", mol::ResNum(2), "C")));
- BOOST_CHECK(diff_view.FindAtom(ent.FindAtom("A", mol::ResNum(2), "D")));
- BOOST_CHECK(diff_view.FindAtom(ent.FindAtom("B", mol::ResNum(1), "E")));
- BOOST_CHECK(diff_view.FindAtom(ent.FindAtom("B", mol::ResNum(1), "F")));
- BOOST_CHECK(diff_view.FindAtom(ent.FindAtom("B", mol::ResNum(2), "G")));
- BOOST_CHECK(diff_view.FindAtom(ent.FindAtom("B", mol::ResNum(2), "H")));
+ BOOST_CHECK(!diff_view.ViewForHandle(ent.FindAtom("A", mol::ResNum(1), "A")));
+ BOOST_CHECK(!diff_view.ViewForHandle(ent.FindAtom("A", mol::ResNum(1), "B")));
+ BOOST_CHECK(!diff_view.ViewForHandle(ent.FindAtom("A", mol::ResNum(2), "C")));
+ BOOST_CHECK(diff_view.ViewForHandle(ent.FindAtom("A", mol::ResNum(2), "D")));
+ BOOST_CHECK(diff_view.ViewForHandle(ent.FindAtom("B", mol::ResNum(1), "E")));
+ BOOST_CHECK(diff_view.ViewForHandle(ent.FindAtom("B", mol::ResNum(1), "F")));
+ BOOST_CHECK(diff_view.ViewForHandle(ent.FindAtom("B", mol::ResNum(2), "G")));
+ BOOST_CHECK(diff_view.ViewForHandle(ent.FindAtom("B", mol::ResNum(2), "H")));
// check bonds
BondHandleList bonds=diff_view.GetBondList();
@@ -132,21 +132,21 @@ BOOST_AUTO_TEST_CASE(test_union_a)
BOOST_CHECK(un.FindChain("B"));
// test residues
- BOOST_CHECK(un.FindResidue(ent.FindResidue("A", mol::ResNum(1))));
- BOOST_CHECK(un.FindResidue(ent.FindResidue("A", mol::ResNum(2))));
- BOOST_CHECK(un.FindResidue(ent.FindResidue("B", mol::ResNum(1))));
- BOOST_CHECK(un.FindResidue(ent.FindResidue("B", mol::ResNum(2))));
+ BOOST_CHECK(un.ViewForHandle(ent.FindResidue("A", mol::ResNum(1))));
+ BOOST_CHECK(un.ViewForHandle(ent.FindResidue("A", mol::ResNum(2))));
+ BOOST_CHECK(un.ViewForHandle(ent.FindResidue("B", mol::ResNum(1))));
+ BOOST_CHECK(un.ViewForHandle(ent.FindResidue("B", mol::ResNum(2))));
// test atoms
- BOOST_CHECK(!un.FindAtom(ent.FindAtom("A", mol::ResNum(1), "A")));
- BOOST_CHECK(un.FindAtom(ent.FindAtom("A", mol::ResNum(1), "B")));
- BOOST_CHECK(un.FindAtom(ent.FindAtom("A", mol::ResNum(2), "C")));
- BOOST_CHECK(!un.FindAtom(ent.FindAtom("A", mol::ResNum(2), "D")));
+ BOOST_CHECK(!un.ViewForHandle(ent.FindAtom("A", mol::ResNum(1), "A")));
+ BOOST_CHECK(un.ViewForHandle(ent.FindAtom("A", mol::ResNum(1), "B")));
+ BOOST_CHECK(un.ViewForHandle(ent.FindAtom("A", mol::ResNum(2), "C")));
+ BOOST_CHECK(!un.ViewForHandle(ent.FindAtom("A", mol::ResNum(2), "D")));
- BOOST_CHECK(!un.FindAtom(ent.FindAtom("B", mol::ResNum(1), "E")));
- BOOST_CHECK(un.FindAtom(ent.FindAtom("B", mol::ResNum(1), "F")));
- BOOST_CHECK(un.FindAtom(ent.FindAtom("B", mol::ResNum(2), "G")));
- BOOST_CHECK(!un.FindAtom(ent.FindAtom("B", mol::ResNum(2), "H")));
+ BOOST_CHECK(!un.ViewForHandle(ent.FindAtom("B", mol::ResNum(1), "E")));
+ BOOST_CHECK(un.ViewForHandle(ent.FindAtom("B", mol::ResNum(1), "F")));
+ BOOST_CHECK(un.ViewForHandle(ent.FindAtom("B", mol::ResNum(2), "G")));
+ BOOST_CHECK(!un.ViewForHandle(ent.FindAtom("B", mol::ResNum(2), "H")));
// bonds
BondHandleList bonds=un.GetBondList();
@@ -186,21 +186,21 @@ BOOST_AUTO_TEST_CASE(test_union_b)
BOOST_CHECK(un.FindChain("B"));
// test residues
- BOOST_CHECK(un.FindResidue(ent.FindResidue("A", mol::ResNum(1))));
- BOOST_CHECK(un.FindResidue(ent.FindResidue("A", mol::ResNum(2))));
- BOOST_CHECK(un.FindResidue(ent.FindResidue("B", mol::ResNum(1))));
- BOOST_CHECK(un.FindResidue(ent.FindResidue("B", mol::ResNum(2))));
+ BOOST_CHECK(un.ViewForHandle(ent.FindResidue("A", mol::ResNum(1))));
+ BOOST_CHECK(un.ViewForHandle(ent.FindResidue("A", mol::ResNum(2))));
+ BOOST_CHECK(un.ViewForHandle(ent.FindResidue("B", mol::ResNum(1))));
+ BOOST_CHECK(un.ViewForHandle(ent.FindResidue("B", mol::ResNum(2))));
// test atoms
- BOOST_CHECK(un.FindAtom(ent.FindAtom("A", mol::ResNum(1), "A")));
- BOOST_CHECK(un.FindAtom(ent.FindAtom("A", mol::ResNum(1), "B")));
- BOOST_CHECK(un.FindAtom(ent.FindAtom("A", mol::ResNum(2), "C")));
- BOOST_CHECK(!un.FindAtom(ent.FindAtom("A", mol::ResNum(2), "D")));
+ BOOST_CHECK(un.ViewForHandle(ent.FindAtom("A", mol::ResNum(1), "A")));
+ BOOST_CHECK(un.ViewForHandle(ent.FindAtom("A", mol::ResNum(1), "B")));
+ BOOST_CHECK(un.ViewForHandle(ent.FindAtom("A", mol::ResNum(2), "C")));
+ BOOST_CHECK(!un.ViewForHandle(ent.FindAtom("A", mol::ResNum(2), "D")));
- BOOST_CHECK(!un.FindAtom(ent.FindAtom("B", mol::ResNum(1), "E")));
- BOOST_CHECK(un.FindAtom(ent.FindAtom("B", mol::ResNum(1), "F")));
- BOOST_CHECK(un.FindAtom(ent.FindAtom("B", mol::ResNum(2), "G")));
- BOOST_CHECK(!un.FindAtom(ent.FindAtom("B", mol::ResNum(2), "H")));
+ BOOST_CHECK(!un.ViewForHandle(ent.FindAtom("B", mol::ResNum(1), "E")));
+ BOOST_CHECK(un.ViewForHandle(ent.FindAtom("B", mol::ResNum(1), "F")));
+ BOOST_CHECK(un.ViewForHandle(ent.FindAtom("B", mol::ResNum(2), "G")));
+ BOOST_CHECK(!un.ViewForHandle(ent.FindAtom("B", mol::ResNum(2), "H")));
// bonds
BondHandleList bonds=un.GetBondList();
@@ -240,22 +240,22 @@ BOOST_AUTO_TEST_CASE(test_intersection_a)
BOOST_CHECK(is.FindChain("B"));
// test residues
- BOOST_CHECK(!is.FindResidue(ent.FindResidue("A", mol::ResNum(1))));
- BOOST_CHECK(is.FindResidue(ent.FindResidue("A", mol::ResNum(2))));
- BOOST_CHECK(is.FindResidue(ent.FindResidue("B", mol::ResNum(1))));
- BOOST_CHECK(is.FindResidue(ent.FindResidue("B", mol::ResNum(2))));
+ BOOST_CHECK(!is.ViewForHandle(ent.FindResidue("A", mol::ResNum(1))));
+ BOOST_CHECK(is.ViewForHandle(ent.FindResidue("A", mol::ResNum(2))));
+ BOOST_CHECK(is.ViewForHandle(ent.FindResidue("B", mol::ResNum(1))));
+ BOOST_CHECK(is.ViewForHandle(ent.FindResidue("B", mol::ResNum(2))));
// test atoms
- BOOST_CHECK(!is.FindAtom(ent.FindAtom("A", mol::ResNum(1), "A")));
- BOOST_CHECK(!is.FindAtom(ent.FindAtom("A", mol::ResNum(1), "B")));
- BOOST_CHECK(is.FindAtom(ent.FindAtom("A", mol::ResNum(2), "C")));
- BOOST_CHECK(!is.FindAtom(ent.FindAtom("A", mol::ResNum(2), "D")));
+ BOOST_CHECK(!is.ViewForHandle(ent.FindAtom("A", mol::ResNum(1), "A")));
+ BOOST_CHECK(!is.ViewForHandle(ent.FindAtom("A", mol::ResNum(1), "B")));
+ BOOST_CHECK(is.ViewForHandle(ent.FindAtom("A", mol::ResNum(2), "C")));
+ BOOST_CHECK(!is.ViewForHandle(ent.FindAtom("A", mol::ResNum(2), "D")));
- BOOST_CHECK(!is.FindAtom(ent.FindAtom("B", mol::ResNum(1), "E")));
- BOOST_CHECK(is.FindAtom(ent.FindAtom("B", mol::ResNum(1), "F")));
+ BOOST_CHECK(!is.ViewForHandle(ent.FindAtom("B", mol::ResNum(1), "E")));
+ BOOST_CHECK(is.ViewForHandle(ent.FindAtom("B", mol::ResNum(1), "F")));
- BOOST_CHECK(is.FindAtom(ent.FindAtom("B", mol::ResNum(2), "G")));
- BOOST_CHECK(!is.FindAtom(ent.FindAtom("B", mol::ResNum(2), "H")));
+ BOOST_CHECK(is.ViewForHandle(ent.FindAtom("B", mol::ResNum(2), "G")));
+ BOOST_CHECK(!is.ViewForHandle(ent.FindAtom("B", mol::ResNum(2), "H")));
// bonds
BondHandleList bonds=is.GetBondList();
@@ -295,22 +295,22 @@ BOOST_AUTO_TEST_CASE(test_intersection_b)
BOOST_CHECK(is.FindChain("B"));
// test residues
- BOOST_CHECK(!is.FindResidue(ent.FindResidue("A", mol::ResNum(1))));
- BOOST_CHECK(!is.FindResidue(ent.FindResidue("A", mol::ResNum(2))));
- BOOST_CHECK(is.FindResidue(ent.FindResidue("B", mol::ResNum(1))));
- BOOST_CHECK(is.FindResidue(ent.FindResidue("B", mol::ResNum(2))));
+ BOOST_CHECK(!is.ViewForHandle(ent.FindResidue("A", mol::ResNum(1))));
+ BOOST_CHECK(!is.ViewForHandle(ent.FindResidue("A", mol::ResNum(2))));
+ BOOST_CHECK(is.ViewForHandle(ent.FindResidue("B", mol::ResNum(1))));
+ BOOST_CHECK(is.ViewForHandle(ent.FindResidue("B", mol::ResNum(2))));
// test atoms
- BOOST_CHECK(!is.FindAtom(ent.FindAtom("A", mol::ResNum(1), "A")));
- BOOST_CHECK(!is.FindAtom(ent.FindAtom("A", mol::ResNum(1), "B")));
- BOOST_CHECK(!is.FindAtom(ent.FindAtom("A", mol::ResNum(2), "C")));
- BOOST_CHECK(!is.FindAtom(ent.FindAtom("A", mol::ResNum(2), "D")));
+ BOOST_CHECK(!is.ViewForHandle(ent.FindAtom("A", mol::ResNum(1), "A")));
+ BOOST_CHECK(!is.ViewForHandle(ent.FindAtom("A", mol::ResNum(1), "B")));
+ BOOST_CHECK(!is.ViewForHandle(ent.FindAtom("A", mol::ResNum(2), "C")));
+ BOOST_CHECK(!is.ViewForHandle(ent.FindAtom("A", mol::ResNum(2), "D")));
- BOOST_CHECK(!is.FindAtom(ent.FindAtom("B", mol::ResNum(1), "E")));
- BOOST_CHECK(is.FindAtom(ent.FindAtom("B", mol::ResNum(1), "F")));
+ BOOST_CHECK(!is.ViewForHandle(ent.FindAtom("B", mol::ResNum(1), "E")));
+ BOOST_CHECK(is.ViewForHandle(ent.FindAtom("B", mol::ResNum(1), "F")));
- BOOST_CHECK(is.FindAtom(ent.FindAtom("B", mol::ResNum(2), "G")));
- BOOST_CHECK(!is.FindAtom(ent.FindAtom("B", mol::ResNum(2), "H")));
+ BOOST_CHECK(is.ViewForHandle(ent.FindAtom("B", mol::ResNum(2), "G")));
+ BOOST_CHECK(!is.ViewForHandle(ent.FindAtom("B", mol::ResNum(2), "H")));
// bonds
BondHandleList bonds=is.GetBondList();