diff --git a/modules/mol/base/src/chain_handle.cc b/modules/mol/base/src/chain_handle.cc
index 156eca176a4d4b8b54a120e56f1f384bb87e78f2..4581eb7806890f1a12da761cfd6ac18ba906857e 100644
--- a/modules/mol/base/src/chain_handle.cc
+++ b/modules/mol/base/src/chain_handle.cc
@@ -125,17 +125,18 @@ bool ChainHandle::operator!=(const ChainHandle& ref) const
ResidueHandleIter ChainHandle::ResiduesBegin() const {
this->CheckValidity();
impl::ChainImplPtr c=Impl();
- impl::ChainImplMap::iterator cc=c->GetEntity()->GetChainMap().find(c->GetName());
- return ResidueHandleIter(cc, c->GetResidueList().begin(), c->GetEntity());
+ impl::ChainImplList::iterator cc=c->GetEntity()->GetChain(this->GetName());
+ return ResidueHandleIter(cc, c->GetResidueList().begin(),
+ c->GetEntity());
}
ResidueHandleIter ChainHandle::ResiduesEnd() const {
this->CheckValidity();
impl::ChainImplPtr c=Impl();
- impl::ChainImplMap::iterator cc=c->GetEntity()->GetChainMap().find(c->GetName());
- impl::ChainImplMap::iterator nc=cc; ++nc;
- if (nc!=c->GetEntity()->GetChainMap().end()) {
- return ResidueHandleIter(nc, nc->second->GetResidueList().begin(),
+ impl::ChainImplList::iterator cc=c->GetEntity()->GetChain(this->GetName());
+ impl::ChainImplList::iterator nc=cc; ++nc;
+ if (nc!=c->GetEntity()->GetChainList().end()) {
+ return ResidueHandleIter(nc, (*nc)->GetResidueList().begin(),
c->GetEntity());
} else {
return ResidueHandleIter(cc, c->GetResidueList().end(),
@@ -151,7 +152,7 @@ AtomHandleIter ChainHandle::AtomsBegin() const
return AtomHandleIter();
}
- impl::ChainImplMap::iterator cc=c->GetEntity()->GetChainMap().find(c->GetName());
+ impl::ChainImplList::iterator cc=c->GetEntity()->GetChain(this->GetName());
return AtomHandleIter(cc, c->GetResidueList().begin(),
c->GetResidueList().front()->GetAtomList().begin(),
c->GetEntity(), true);
@@ -164,10 +165,10 @@ AtomHandleIter ChainHandle::AtomsEnd() const {
if (c->GetResidueList().empty()) {
return AtomHandleIter();
}
- impl::ChainImplMap::iterator cc=c->GetEntity()->GetChainMap().find(c->GetName());
- impl::ChainImplMap::iterator nc=cc; ++nc;
- impl::ResidueImplList& rc=nc->second->GetResidueList();
- if (nc!=c->GetEntity()->GetChainMap().end()) {
+ impl::ChainImplList::iterator cc=c->GetEntity()->GetChain(this->GetName());
+ impl::ChainImplList::iterator nc=cc; ++nc;
+ impl::ResidueImplList& rc=(*nc)->GetResidueList();
+ if (nc!=c->GetEntity()->GetChainList().end()) {
return AtomHandleIter(nc, rc.begin(), rc.front()->GetAtomList().begin(),
c->GetEntity(), false);
} else {
diff --git a/modules/mol/base/src/entity_handle.cc b/modules/mol/base/src/entity_handle.cc
index b0ac01f09e135c5110bf970af372b13ebbf14590..8686df88c286c726648bad9abec259514414a9c2 100644
--- a/modules/mol/base/src/entity_handle.cc
+++ b/modules/mol/base/src/entity_handle.cc
@@ -257,48 +257,48 @@ AtomHandle EntityHandle::FindAtom(const String& chain_name,
ResidueHandleIter EntityHandle::ResiduesBegin() const {
this->CheckValidity();
- if (Impl()->GetChainMap().empty()) {
+ if (Impl()->GetChainList().empty()) {
return ResidueHandleIter();
}
impl::EntityImplPtr i=Impl();
- impl::ChainImplPtr chain=i->GetChainMap().begin()->second;
- return ResidueHandleIter(i->GetChainMap().begin(),
+ impl::ChainImplPtr chain=i->GetChainList().front();
+ return ResidueHandleIter(i->GetChainList().begin(),
chain->GetResidueList().begin(), i);
}
ResidueHandleIter EntityHandle::ResiduesEnd() const {
this->CheckValidity();
- if (Impl()->GetChainMap().empty()) {
+ if (Impl()->GetChainList().empty()) {
return ResidueHandleIter();
}
impl::EntityImplPtr i=Impl();
- impl::ChainImplPtr chain=i->GetChainMap().rbegin()->second;
- return ResidueHandleIter(i->GetChainMap().end(),
+ impl::ChainImplPtr chain=i->GetChainList().back();
+ return ResidueHandleIter(i->GetChainList().end(),
chain->GetResidueList().end(), i);
}
ChainHandleIter EntityHandle::ChainsBegin() const {
this->CheckValidity();
- return ChainHandleIter(Impl()->GetChainMap().begin());
+ return ChainHandleIter(Impl()->GetChainList().begin());
}
ChainHandleIter EntityHandle::ChainsEnd() const {
- return ChainHandleIter(Impl()->GetChainMap().end());
+ return ChainHandleIter(Impl()->GetChainList().end());
}
AtomHandleIter EntityHandle::AtomsBegin() const {
this->CheckValidity();
impl::EntityImplPtr ent=Impl();
- if (ent->GetChainMap().empty()) {
+ if (ent->GetChainList().empty()) {
return AtomHandleIter();
}
- impl::ResidueImplList& r=ent->GetChainMap().begin()->second->GetResidueList();
+ impl::ResidueImplList& r=ent->GetChainList().front()->GetResidueList();
if (r.empty()) {
return AtomHandleIter();
}
- return AtomHandleIter(ent->GetChainMap().begin(), r.begin(),
+ return AtomHandleIter(ent->GetChainList().begin(), r.begin(),
r.front()->GetAtomList().begin(), ent, true);
}
@@ -306,14 +306,14 @@ AtomHandleIter EntityHandle::AtomsEnd() const
{
this->CheckValidity();
impl::EntityImplPtr ent=Impl();
- if (ent->GetChainMap().empty()) {
+ if (ent->GetChainList().empty()) {
return AtomHandleIter();
}
- impl::ResidueImplList& r=ent->GetChainMap().rbegin()->second->GetResidueList();
+ impl::ResidueImplList& r=ent->GetChainList().back()->GetResidueList();
if (r.empty()) {
return AtomHandleIter();
}
- return AtomHandleIter(ent->GetChainMap().end(), r.end(),
+ return AtomHandleIter(ent->GetChainList().end(), r.end(),
r.back()->GetAtomList().end(), ent, false);
}
diff --git a/modules/mol/base/src/entity_view.cc b/modules/mol/base/src/entity_view.cc
index 34f7d506421cef9b32aeaec3c46a0470d89c3f2c..a3819e1020d4c8dd975f9b2e799d4bf248092a34 100644
--- a/modules/mol/base/src/entity_view.cc
+++ b/modules/mol/base/src/entity_view.cc
@@ -76,9 +76,9 @@ EntityView::EntityView(const EntityHandle& entity,
ViewAddFlags flags)
: EntityBase(entity.Impl()), data_(new EntityViewData()) {
if (flags & ViewAddFlag::INCLUDE_CHAINS) {
- impl::ChainImplMap::const_iterator i=entity.Impl()->GetChainMap().begin();
- for (; i!=entity.Impl()->GetChainMap().end(); ++i) {
- this->AddChain(ChainHandle(i->second), flags);
+ impl::ChainImplList::const_iterator i=entity.Impl()->GetChainList().begin();
+ for (; i!=entity.Impl()->GetChainList().end(); ++i) {
+ this->AddChain(ChainHandle(*i), flags);
}
}
}
diff --git a/modules/mol/base/src/impl/chain_impl_fw.hh b/modules/mol/base/src/impl/chain_impl_fw.hh
index 00f22561b72845bea621bd31f90c1587e886631d..2ba9c725dbf40038cf67f76b6749bdd5f0293fa2 100644
--- a/modules/mol/base/src/impl/chain_impl_fw.hh
+++ b/modules/mol/base/src/impl/chain_impl_fw.hh
@@ -28,7 +28,6 @@ namespace ost { namespace mol { namespace impl {
class ChainImpl;
typedef boost::shared_ptr<ChainImpl> ChainImplPtr;
typedef boost::weak_ptr<ChainImpl> ChainImplW;
-typedef std::list<ChainImplPtr> ChainImplList;
}}} // ns
diff --git a/modules/mol/base/src/impl/entity_impl.cc b/modules/mol/base/src/impl/entity_impl.cc
index 29fdad970ebddf5f8a8a49e54a436182bbc1c068..8b13c433fdfc368904fc663ccf79f410e879d933 100644
--- a/modules/mol/base/src/impl/entity_impl.cc
+++ b/modules/mol/base/src/impl/entity_impl.cc
@@ -64,7 +64,7 @@ namespace ost { namespace mol { namespace impl {
EntityImpl::EntityImpl():
atom_map_(),
- chain_map_(),
+ chain_list_(),
connector_map_(),
torsion_map_(),
transformation_matrix_(),
@@ -104,9 +104,9 @@ mol::BondHandleList EntityImpl::GetBondList() const
int EntityImpl::GetResidueCount() const
{
int count=0;
- for (ChainImplMap::const_iterator i=chain_map_.begin(),
- e=chain_map_.end(); i!=e; ++i) {
- count+=i->second->GetResidueCount();
+ for (ChainImplList::const_iterator i=chain_list_.begin(),
+ e=chain_list_.end(); i!=e; ++i) {
+ count+=(*i)->GetResidueCount();
}
return count;
}
@@ -133,9 +133,9 @@ ChainImplPtr EntityImpl::InsertChain(const ChainImplPtr& chain)
void EntityImpl::ReplicateHierarchy(EntityImplPtr dest)
{
- for (ChainImplMap::const_iterator i=chain_map_.begin(),
- e1=chain_map_.end(); i!=e1; ++i) {
- ChainImplPtr src_chain=i->second;
+ for (ChainImplList::const_iterator i=chain_list_.begin(),
+ e1=chain_list_.end(); i!=e1; ++i) {
+ ChainImplPtr src_chain=*i;
ChainImplPtr dst_chain=dest->InsertChain(src_chain);
// copy generic properties
dst_chain->Assign(*src_chain.get());
@@ -176,10 +176,10 @@ AtomImplPtr lookup_atom(const AtomImplPtr& atom, EntityImplPtr dest,
void EntityImpl::DoCopyBondsAndTorsions(EntityImplPtr dest)
{
- for (ChainImplMap::const_iterator i=chain_map_.begin(),
- i2=dest->chain_map_.begin(), e1=chain_map_.end(); i!=e1; ++i, ++i2) {
- ChainImplPtr src_chain=i->second;
- ChainImplPtr dst_chain=i2->second;
+ for (ChainImplList::const_iterator i=chain_list_.begin(),
+ i2=dest->chain_list_.begin(), e1=chain_list_.end(); i!=e1; ++i, ++i2) {
+ ChainImplPtr src_chain=*i;
+ ChainImplPtr dst_chain=*i2;
for (ResidueImplList::iterator j=src_chain->GetResidueList().begin(),
j2=dst_chain->GetResidueList().begin(),
e2=src_chain->GetResidueList().end(); j!=e2; ++j, ++j2) {
@@ -236,7 +236,7 @@ void EntityImpl::DoCopy(EntityImplPtr dest)
int EntityImpl::GetChainCount() const
{
- return static_cast<int>(chain_map_.size());
+ return static_cast<int>(chain_list_.size());
}
const geom::Mat4& EntityImpl::GetTransfMatrix() const
@@ -384,17 +384,19 @@ ResidueImplPtr EntityImpl::CreateResidue(const ChainImplPtr& cp,
ChainImplPtr EntityImpl::InsertChain(const String& cname)
{
- ChainImplMap::iterator i=chain_map_.find(cname);
- if (i!=chain_map_.end()) {
- throw IntegrityError("Can't insert chain. A chain with name '"+cname+
- "' already exists");
+ for (ChainImplList::iterator
+ i=chain_list_.begin(), e=chain_list_.end(); i!=e; ++i) {
+ if ((*i)->GetName()==cname) {
+ throw IntegrityError("Can't insert chain. A chain with name '"+cname+
+ "' already exists");
+ }
}
#if MAKE_SHARED_AVAILABLE
ChainImplPtr cp=boost::make_shared<ChainImpl>(shared_from_this(), cname);
#else
ChainImplPtr cp(new ChainImpl(shared_from_this(), cname));
#endif
- chain_map_.insert(ChainImplMap::value_type(cp->GetName(),cp));
+ chain_list_.push_back(cp);
return cp;
}
@@ -767,8 +769,9 @@ void EntityImpl::Apply(EntityVisitor& v)
{
LOG_TRACE("visitor @" << &v << " visiting entity impl @" << this << std::endl);
v.OnEntry();
- for(ChainImplMap::iterator it = chain_map_.begin();it!=chain_map_.end();++it) {
- it->second->Apply(v);
+ for(ChainImplList::iterator
+ it = chain_list_.begin();it!=chain_list_.end();++it) {
+ (*it)->Apply(v);
}
for(ConnectorImplMap::iterator it = connector_map_.begin();it!=connector_map_.end();++it) {
@@ -821,7 +824,7 @@ void EntityImpl::NotifyObserver()
void EntityImpl::Swap(EntityImpl& impl)
{
atom_map_.swap(impl.atom_map_);
- chain_map_.swap(impl.chain_map_);
+ chain_list_.swap(impl.chain_list_);
connector_map_.swap(impl.connector_map_);
torsion_map_.swap(impl.torsion_map_);
std::swap(transformation_matrix_,impl.transformation_matrix_);
@@ -830,15 +833,6 @@ void EntityImpl::Swap(EntityImpl& impl)
observer_map_.swap(impl.observer_map_);
}
-ChainImplList EntityImpl::GetChainList() const {
- ChainImplList cl;
- ChainImplMap::const_iterator i;
- for (i=chain_map_.begin(); i!=chain_map_.end(); ++i) {
- cl.push_back(i->second);
- }
- return cl;
-}
-
TorsionImplP EntityImpl::FindTorsion(const AtomImplPtr& a1,
const AtomImplPtr& a2,
@@ -895,19 +889,15 @@ EntityView EntityImpl::do_selection(const EntityHandle& eh,
EntityHandle myself(const_cast<impl::EntityImpl*>(this)->shared_from_this());
QueryState qs(query.CreateQueryState(myself));
LOGN_DUMP("entering chain loop");
- for (ChainImplMap::const_iterator ch_it = chain_map_.begin();
- ch_it!=chain_map_.end();++ch_it) {
- if(!ch_it->second) {
- LOGN_DUMP("found invalid chain shared_ptr");
- continue;
- }
- LOGN_DUMP("checking chain " << ch_it->second->GetName());
+ for (ChainImplList::const_iterator
+ ch_it=chain_list_.begin(); ch_it!=chain_list_.end();++ch_it) {
+ LOGN_DUMP("checking chain " << ch_it->GetName());
c_added = false;
- tribool c = always_true ? tribool(true) : qs.EvalChain(ch_it->second);
+ tribool c = always_true ? tribool(true) : qs.EvalChain(*ch_it);
if (c == true) {
LOGN_DUMP("chain is selected");
// Include all residues
- const ChainImplPtr& ci=ch_it->second;
+ const ChainImplPtr& ci=*ch_it;
++chain_count;
ChainView chain=view.AddChain(ci);
ResidueImplList::const_iterator re_it = ci->GetResidueList().begin();
@@ -930,7 +920,7 @@ EntityView EntityImpl::do_selection(const EntityHandle& eh,
} else if (indeterminate(c)) {
// Test residues
r_added = false;
- const ChainImplPtr& ci = ch_it->second;
+ const ChainImplPtr& ci = *ch_it;
ChainView chain;
ResidueImplList::const_iterator re_it = ci->GetResidueList().begin();
@@ -1042,10 +1032,10 @@ EntityView EntityImpl::CreateFullView(const EntityHandle& h) const
}
ChainImplPtr EntityImpl::FindChain(const String& name) const {
- ChainImplMap::const_iterator i;
- for(i=chain_map_.begin(); i!=chain_map_.end();++i) {
- if (i->second->GetName()==name)
- return i->second;
+ ChainImplList::const_iterator i;
+ for(i=chain_list_.begin(); i!=chain_list_.end();++i) {
+ if ((*i)->GetName()==name)
+ return *i;
}
return ChainImplPtr();
}
@@ -1078,7 +1068,7 @@ TorsionImplMap& EntityImpl::GetTorsionMap() {
void EntityImpl::DeleteChain(const ChainImplPtr& chain) {
if (chain && chain->GetEntity().get()==this) {
chain->DeleteAllResidues();
- chain_map_.erase(chain->GetName());
+ chain_list_.erase(this->GetChain(chain->GetName()));
}
}
@@ -1191,24 +1181,26 @@ void EntityImpl::DecICSEditorCount()
}
}
+impl::ChainImplList::iterator EntityImpl::GetChain(const String& name)
+{
+ impl::ChainImplList& cc=this->GetChainList();
+ for (impl::ChainImplList::iterator i=cc.begin(), e=cc.end(); i!=e; ++i) {
+ if ((*i)->GetName()==name) {
+ return i;
+ }
+ }
+ return cc.end();
+}
void EntityImpl::RenameChain(ChainImplPtr chain, const String& new_name)
{
- ChainImplMap::iterator i, j;
- j=chain_map_.find(new_name);
-
- if (j!=chain_map_.end() && j->second!=chain) {
+ ChainImplList::iterator i;
+ ChainImplPtr ch=this->FindChain(new_name);
+ if (ch) {
throw IntegrityError("unable to rename chain '"+chain->GetName()+
"' to '"+new_name+"', since there is already a chain "
"with that name");
}
- for(i=chain_map_.begin(); i!=chain_map_.end();++i) {
- if (i->second==chain) {
- chain_map_.erase(i);
- chain_map_.insert(std::make_pair(new_name, chain));
- chain->SetName(new_name);
- break;
- }
- }
+ chain->SetName(new_name);
}
void EntityImpl::UpdateTransformedPos(){
diff --git a/modules/mol/base/src/impl/entity_impl.hh b/modules/mol/base/src/impl/entity_impl.hh
index 63504c74987765914620394ab72515b64031090c..81f533bf0a9f3c696276b7e5e487e14a7125bfaa 100644
--- a/modules/mol/base/src/impl/entity_impl.hh
+++ b/modules/mol/base/src/impl/entity_impl.hh
@@ -56,7 +56,7 @@ typedef std::map<AtomImpl*,AtomImplPtr> AtomImplMap;
/// \internal
typedef std::map<ResidueImpl*,ResidueImplPtr> ResidueImplMap;
/// \internal
-typedef std::map<String,ChainImplPtr> ChainImplMap;
+typedef std::vector<ChainImplPtr> ChainImplList;
/// \internal
typedef std::map<ConnectorImpl*,ConnectorImplP> ConnectorImplMap;
/// \internal
@@ -201,10 +201,9 @@ public:
bool IsTransfIdentity() const;
- ChainImplList GetChainList() const;
+ const ChainImplList& GetChainList() const { return chain_list_; }
- ChainImplMap& GetChainMap() {return chain_map_; }
- const ChainImplMap& GetChainMap() const {return chain_map_; }
+ ChainImplList& GetChainList() { return chain_list_; }
void DeleteFromConnMap(const ConnectorImplP& conn);
@@ -241,6 +240,8 @@ public:
const String& GetName() const;
+ impl::ChainImplList::iterator GetChain(const String& name);
+
void SetName(const String& ent_name);
private:
@@ -251,7 +252,7 @@ private:
void DoCopyBondsAndTorsions(EntityImplPtr dest);
AtomImplMap atom_map_;
- ChainImplMap chain_map_;
+ ChainImplList chain_list_;
ConnectorImplMap connector_map_;
TorsionImplMap torsion_map_;
diff --git a/modules/mol/base/src/iterator.cc b/modules/mol/base/src/iterator.cc
index 26fc516444fcfc4000b66f75da3e4d2021dd5ff8..74ff90c6514b1fd86517d68aba1ceddfd604694c 100644
--- a/modules/mol/base/src/iterator.cc
+++ b/modules/mol/base/src/iterator.cc
@@ -28,21 +28,21 @@ namespace ost { namespace mol {
ResidueHandleIter& ResidueHandleIter::operator++() {
++cur_res_;
- if (cur_res_==cur_chain_->second->GetResidueList().end()) {
+ if (cur_res_==(*cur_chain_)->GetResidueList().end()) {
// we have to skip over empty chains otherwise we end up pointing to an
// invalid residue.
do {
++cur_chain_;
- if (ent_->GetChainMap().end()==cur_chain_) {
+ if (ent_->GetChainList().end()==cur_chain_) {
break;
}
- cur_res_=cur_chain_->second->GetResidueList().begin();
- } while (cur_chain_->second->GetResidueList().empty());
+ cur_res_=(*cur_chain_)->GetResidueList().begin();
+ } while ((*cur_chain_)->GetResidueList().empty());
}
return *this;
}
-ResidueHandleIter::ResidueHandleIter(impl::ChainImplMap::iterator chain_it,
+ResidueHandleIter::ResidueHandleIter(impl::ChainImplList::iterator chain_it,
impl::ResidueImplList::iterator res_it,
impl::EntityImplPtr ent)
: cur_chain_(chain_it), cur_res_(res_it),
@@ -99,7 +99,7 @@ AtomHandleIter::AtomHandleIter()
#endif
{}
-AtomHandleIter::AtomHandleIter(impl::ChainImplMap::iterator chain_it,
+AtomHandleIter::AtomHandleIter(impl::ChainImplList::iterator chain_it,
impl::ResidueImplList::iterator res_it,
impl::AtomImplList::iterator atom_it,
impl::EntityImplPtr ent, bool skip_empty)
@@ -122,19 +122,19 @@ void AtomHandleIter::SkipEmpty()
// pointing to an invalid atom.
do {
++cur_res_;
- if (cur_chain_->second->GetResidueList().end()==cur_res_) {
+ if ((*cur_chain_)->GetResidueList().end()==cur_res_) {
do {
++cur_chain_;
- if (ent_->GetChainMap().end()==cur_chain_) {
+ if (ent_->GetChainList().end()==cur_chain_) {
return;
}
- cur_res_=cur_chain_->second->GetResidueList().begin();
- if (!cur_chain_->second->GetResidueList().empty())
+ cur_res_=(*cur_chain_)->GetResidueList().begin();
+ if (!(*cur_chain_)->GetResidueList().empty())
cur_atom_=(*cur_res_)->GetAtomList().begin();
else
cur_atom_=impl::AtomImplList::iterator();
- } while (cur_chain_->second->GetResidueList().empty());
+ } while ((*cur_chain_)->GetResidueList().empty());
} else {
cur_atom_=(*cur_res_)->GetAtomList().begin();
}
diff --git a/modules/mol/base/src/iterator.hh b/modules/mol/base/src/iterator.hh
index 4d75aec8b05e7245a2d382ee96ae51e5f5406c7e..7bbbe48396591eea4ba1af3f8fc991976b754dec 100644
--- a/modules/mol/base/src/iterator.hh
+++ b/modules/mol/base/src/iterator.hh
@@ -80,17 +80,17 @@ private:
namespace impl {
// forward declearation of chain impl map.
- typedef std::map<String, ChainImplPtr> ChainImplMap;
+ typedef std::vector<ChainImplPtr> ChainImplList;
}
class DLLEXPORT_OST_MOL ChainHandleIter : public std::iterator<std::forward_iterator_tag,
ChainHandle> {
public: // internally used constructors
- ChainHandleIter(impl::ChainImplMap::iterator chain_it)
+ ChainHandleIter(impl::ChainImplList::iterator chain_it)
: cur_(chain_it) {
}
public:
ChainHandle operator*() {
- return ChainHandle(cur_->second);
+ return ChainHandle(*cur_);
}
ChainHandleIter& operator++() {
@@ -106,7 +106,7 @@ public:
return !this->operator==(rhs);
}
private:
- impl::ChainImplMap::iterator cur_;
+ impl::ChainImplList::iterator cur_;
};
class DLLEXPORT_OST_MOL ResidueHandleIter : public std::iterator<std::forward_iterator_tag,
@@ -114,7 +114,7 @@ class DLLEXPORT_OST_MOL ResidueHandleIter : public std::iterator<std::forward_it
public:
ResidueHandleIter() {
}
- ResidueHandleIter(impl::ChainImplMap::iterator chain_it,
+ ResidueHandleIter(impl::ChainImplList::iterator chain_it,
impl::ResidueImplList::iterator res_it,
impl::EntityImplPtr ent);
bool operator==(const ResidueHandleIter& rhs) const {
@@ -133,7 +133,7 @@ public:
ResidueHandle operator*();
private:
- impl::ChainImplMap::iterator cur_chain_;
+ impl::ChainImplList::iterator cur_chain_;
impl::ResidueImplList::iterator cur_res_;
impl::EntityImplPtr ent_;
};
@@ -174,7 +174,7 @@ class DLLEXPORT_OST_MOL AtomHandleIter : public std::iterator<std::forward_itera
public:
AtomHandleIter();
- AtomHandleIter(impl::ChainImplMap::iterator chain_it,
+ AtomHandleIter(impl::ChainImplList::iterator chain_it,
impl::ResidueImplList::iterator res_it,
impl::AtomImplList::iterator atom_it,
impl::EntityImplPtr ent, bool skip_empty);
@@ -195,7 +195,7 @@ public:
AtomHandle operator*();
private:
void SkipEmpty();
- impl::ChainImplMap::iterator cur_chain_;
+ impl::ChainImplList::iterator cur_chain_;
impl::ResidueImplList::iterator cur_res_;
impl::AtomImplList::iterator cur_atom_;
impl::EntityImplPtr ent_;
diff --git a/modules/mol/base/src/residue_handle.cc b/modules/mol/base/src/residue_handle.cc
index b66c83250276d6301b4c9699c1f72483e1a70c8f..bfc57c1949c209f753e0592730669f82f179c020 100644
--- a/modules/mol/base/src/residue_handle.cc
+++ b/modules/mol/base/src/residue_handle.cc
@@ -181,7 +181,7 @@ AtomHandleIter ResidueHandle::AtomsBegin() const
impl::ResidueImplPtr r=Impl();
int index=this->GetIndex();
impl::ChainImplPtr c=r->GetChain();
- impl::ChainImplMap::iterator cc=r->GetEntity()->GetChainMap().find(c->GetName());
+ impl::ChainImplList::iterator cc=r->GetEntity()->GetChain(c->GetName());
return AtomHandleIter(cc, c->GetResidueList().begin()+index,
r->GetAtomList().begin(), r->GetEntity(), true);
}
@@ -192,7 +192,7 @@ AtomHandleIter ResidueHandle::AtomsEnd() const
impl::ResidueImplPtr r=Impl();
int index=this->GetIndex();
impl::ChainImplPtr c=r->GetChain();
- impl::ChainImplMap::iterator cc=r->GetEntity()->GetChainMap().find(c->GetName());
+ impl::ChainImplList::iterator cc=r->GetEntity()->GetChain(c->GetName());
if (c->GetResidueList().begin()+index+1==c->GetResidueList().end()) {
return AtomHandleIter(cc, c->GetResidueList().begin()+index,
r->GetAtomList().end(), r->GetEntity(), false);