From a5e1745cd10191790757934a8fa3c3575f00842f Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Mon, 21 Mar 2011 18:58:00 +0100
Subject: [PATCH] improve calculation of ResidueImpl::GetIndex
Previously we were returning the wrong index for residues
in chains that contained a certain residue number more
than once. We were always returning the index of the first
residue. Among other things, this fixes BZDNG-229.
---
modules/mol/base/src/impl/chain_impl.cc | 93 +++++++++++++++--------
modules/mol/base/src/impl/chain_impl.hh | 12 +--
modules/mol/base/src/impl/residue_impl.cc | 3 +-
modules/mol/base/tests/test_residue.cc | 16 ++++
4 files changed, 88 insertions(+), 36 deletions(-)
diff --git a/modules/mol/base/src/impl/chain_impl.cc b/modules/mol/base/src/impl/chain_impl.cc
index 854b3d850..e0f51ada1 100644
--- a/modules/mol/base/src/impl/chain_impl.cc
+++ b/modules/mol/base/src/impl/chain_impl.cc
@@ -154,7 +154,7 @@ void ChainImpl::DeleteAllResidues() {
}
void ChainImpl::DeleteResidue(const ResNum& number) {
- int index=this->GetIndex(number);
+ int index=this->GetIndexForResNum(number);
if (index>=0) {
ResidueImplPtr r=residue_list_[index];
r->DeleteAllAtoms();
@@ -166,7 +166,13 @@ void ChainImpl::DeleteResidue(const ResNum& number) {
void ChainImpl::DeleteResidue(const ResidueImplPtr& residue) {
if (residue->GetChain().get()!=this)
return;
- this->DeleteResidue(residue->GetNumber());
+ int index=this->GetIndex(residue);
+ if (index>=0) {
+ ResidueImplPtr r=residue_list_[index];
+ r->DeleteAllAtoms();
+ residue_list_.erase(residue_list_.begin()+index);
+ this->UpdateShifts();
+ }
}
ResidueImplPtr ChainImpl::AppendResidue(const ResidueKey& key,
@@ -220,7 +226,7 @@ ResidueImplPtr ChainImpl::GetPrev(const ResidueImplPtr& r) const
{
if (!r)
return ResidueImplPtr();
- int index=this->GetIndex(r->GetNumber())-1;
+ int index=this->GetIndex(r)-1;
if (index>-1 && index<static_cast<int>(residue_list_.size())-1) {
return residue_list_[index];
}
@@ -256,7 +262,7 @@ ResidueImplPtr ChainImpl::GetNext(const ResidueImplPtr& r) const
{
if (!r)
return ResidueImplPtr();
- int index=this->GetIndex(r->GetNumber())+1;
+ int index=this->GetIndex(r)+1;
if (index>0 && index<=static_cast<int>(residue_list_.size())-1) {
return residue_list_[index];
}
@@ -282,7 +288,7 @@ void ChainImpl::Apply(EntityVisitor& v)
ResidueImplPtr ChainImpl::FindResidue(const ResNum& number) const
{
- int index=this->GetIndex(number);
+ int index=this->GetIndexForResNum(number);
bool invalid=index<0 || index>static_cast<int>(residue_list_.size())-1;
return invalid ? ResidueImplPtr() : residue_list_[index];
}
@@ -301,36 +307,63 @@ EntityImplPtr ChainImpl::GetEntity() const
{
return ent_.lock();
}
-
-int ChainImpl::GetIndex(const ResNum& number) const
+int ChainImpl::GetIndexForResNum(const ResNum& number) const
{
-
if (in_sequence_) {
- int pos=number.GetNum()-1;
- std::list<Shift>::const_iterator i;
- for (i=shifts_.begin(); i!=shifts_.end(); ++i) {
- const Shift& s=*i;
- if (pos<s.start) {
- break;
- } else if (pos<s.start+s.shift) {
- return -1;
- }
- pos-=s.shift;
- }
- while (pos>=0 && pos<static_cast<int>(residue_list_.size()) &&
- residue_list_[pos]->GetNumber()<number) {
- pos++;
- }
- if (pos<0 || pos>=static_cast<int>(residue_list_.size())) {
- return -1;
- }
- assert(residue_list_[pos]->GetNumber()==number);
- return pos;
+ return this->GetIndexForResNumInSequence(number);
} else {
- ResidueImplList::const_iterator k;
+ ResidueImplList::const_iterator k;
k=std::find_if(residue_list_.begin(),
residue_list_.end(),
bind(&ResidueImpl::GetNumber, _1)==number);
+
+ if (k==residue_list_.end())
+ return -1;
+ int pos=std::distance(residue_list_.begin(), k);
+ assert(residue_list_[pos]->GetNumber()==number);
+ return pos;
+ }
+}
+
+int ChainImpl::GetIndexForResNumInSequence(const ResNum& number) const
+{
+ int pos=number.GetNum()-1;
+ std::list<Shift>::const_iterator i;
+ for (i=shifts_.begin(); i!=shifts_.end(); ++i) {
+ const Shift& s=*i;
+ if (pos<s.start) {
+ break;
+ } else if (pos<s.start+s.shift) {
+ return -1;
+ }
+ pos-=s.shift;
+ }
+ while (pos>=0 && pos<static_cast<int>(residue_list_.size()) &&
+ residue_list_[pos]->GetNumber()<number) {
+ pos++;
+ }
+ if (pos<0 || pos>=static_cast<int>(residue_list_.size())) {
+ return -1;
+ }
+ assert(residue_list_[pos]->GetNumber()==number);
+ return pos;
+}
+
+int ChainImpl::GetIndex(const ResidueImplPtr& res) const
+{
+ if (!res) {
+ return -1;
+ }
+ ResNum number=res->GetNumber();
+ if (in_sequence_) {
+ return this->GetIndexForResNumInSequence(number);
+ } else {
+ ResidueImplList::const_iterator k=residue_list_.begin()-1;
+ do {
+ k=std::find_if(k+1, residue_list_.end(),
+ bind(&ResidueImpl::GetNumber, _1)==number);
+ } while(k!=residue_list_.end() && (*k)!=res);
+
if (k==residue_list_.end())
return -1;
int pos=std::distance(residue_list_.begin(), k);
@@ -343,7 +376,7 @@ void ChainImpl::AssignSecondaryStructure(SecStructure ss,
const ResNum& start,
const ResNum& end)
{
- int start_index=this->GetIndex(start);
+ int start_index=this->GetIndexForResNum(start);
int i=start_index;
bool found_end=false;
if (i>=0) {
diff --git a/modules/mol/base/src/impl/chain_impl.hh b/modules/mol/base/src/impl/chain_impl.hh
index cf7c1b838..d7d2ca64b 100644
--- a/modules/mol/base/src/impl/chain_impl.hh
+++ b/modules/mol/base/src/impl/chain_impl.hh
@@ -91,7 +91,7 @@ public:
ResidueImplPtr FindResidue(const ResNum& number) const;
AtomImplPtr FindAtom(const ResNum& number,
- const String& atom_name) const;
+ const String& atom_name) const;
//! Get number of residues of this chain
int GetResidueCount() const;
@@ -114,12 +114,14 @@ public:
void ReorderResidues();
- int GetIndex(const ResNum& number) const;
+ int GetIndex(const ResidueImplPtr& res) const;
+ void AssignSecondaryStructure(SecStructure ss,
+ const ResNum& start,
+ const ResNum& end);
+ int GetIndexForResNum(const ResNum& number) const;
- void AssignSecondaryStructure(SecStructure ss,
- const ResNum& start,
- const ResNum& end);
private:
+ int GetIndexForResNumInSequence(const ResNum& number) const;
void UpdateShifts();
typedef struct {
int start;
diff --git a/modules/mol/base/src/impl/residue_impl.cc b/modules/mol/base/src/impl/residue_impl.cc
index 4d22f927b..cf4729239 100644
--- a/modules/mol/base/src/impl/residue_impl.cc
+++ b/modules/mol/base/src/impl/residue_impl.cc
@@ -516,7 +516,8 @@ void ResidueImpl::AddAltAtomPos(const String& group,
}
int ResidueImpl::GetIndex() const {
- return this->GetChain()->GetIndex(this->GetNumber());
+ ResidueImplPtr res_impl=const_cast<ResidueImpl*>(this)->shared_from_this();
+ return this->GetChain()->GetIndex(res_impl);
}
bool ResidueImpl::HasAltAtomGroup(const String& group) const {
diff --git a/modules/mol/base/tests/test_residue.cc b/modules/mol/base/tests/test_residue.cc
index a5a31a2fc..3451f6f5b 100644
--- a/modules/mol/base/tests/test_residue.cc
+++ b/modules/mol/base/tests/test_residue.cc
@@ -46,6 +46,22 @@ BOOST_AUTO_TEST_CASE(test_in_sequence)
}
+BOOST_AUTO_TEST_CASE(test_res_index_bzdng227)
+{
+ std::cout << "HERE" << std::endl;
+ EntityHandle eh=CreateEntity();
+ XCSEditor e=eh.EditXCS();
+ ChainHandle ch1=e.InsertChain("A");
+ ResidueHandle ra = e.AppendResidue(ch1, "A", 1);
+ ResidueHandle rb = e.AppendResidue(ch1, "B", 2);
+ ResidueHandle rc = e.AppendResidue(ch1, "C", 1);
+
+ BOOST_CHECK_EQUAL(ra.GetIndex(), 0);
+ BOOST_CHECK_EQUAL(rb.GetIndex(), 1);
+ BOOST_CHECK_EQUAL(rc.GetIndex(), 2);
+}
+
+
BOOST_AUTO_TEST_CASE(throw_invalid_res_handle)
{
ChainHandle chain;
--
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