From 2539ad6faf5eef26587e91936bfa7b1aebac3457 Mon Sep 17 00:00:00 2001
From: Ansgar Philippsen <ansgar.philippsen@gmail.com>
Date: Fri, 27 Jul 2012 15:04:26 +0200
Subject: [PATCH] small fixes to entity impl deep copy code and tests
---
modules/mol/base/src/impl/chain_impl.hh | 4 +++-
modules/mol/base/src/impl/entity_impl.cc | 4 ++--
modules/mol/base/src/impl/entity_impl.hh | 4 +++-
modules/mol/base/src/view_op.cc | 2 +-
4 files changed, 9 insertions(+), 5 deletions(-)
diff --git a/modules/mol/base/src/impl/chain_impl.hh b/modules/mol/base/src/impl/chain_impl.hh
index 018c3b9e1..a2c607ec4 100644
--- a/modules/mol/base/src/impl/chain_impl.hh
+++ b/modules/mol/base/src/impl/chain_impl.hh
@@ -105,7 +105,9 @@ public:
/// \brief append new residue with exactly the same parameters as res, but
/// no atoms and bonds
- ResidueImplPtr AppendResidue(const ResidueImplPtr& res, bool deep=true);
+ // force deep to be set explicitely, because it is better than implicit
+ // (and since we are on the impl level interface consistency isn't that critical)
+ ResidueImplPtr AppendResidue(const ResidueImplPtr& res, bool deep);
ResidueImplPtr InsertResidueBefore(int index, const ResNum& n,
const ResidueKey& k);
diff --git a/modules/mol/base/src/impl/entity_impl.cc b/modules/mol/base/src/impl/entity_impl.cc
index 8b81293fb..4b4cb3a7a 100644
--- a/modules/mol/base/src/impl/entity_impl.cc
+++ b/modules/mol/base/src/impl/entity_impl.cc
@@ -145,13 +145,13 @@ void EntityImpl::ReplicateHierarchy(EntityImplPtr dest)
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);
+ ChainImplPtr dst_chain=dest->InsertChain(src_chain,false);
// copy generic properties
dst_chain->Assign(*src_chain.get());
for (ResidueImplList::iterator j=src_chain->GetResidueList().begin(),
e2=src_chain->GetResidueList().end(); j!=e2; ++j) {
ResidueImplPtr src_res=*j;
- ResidueImplPtr dst_res=dst_chain->AppendResidue(src_res);
+ ResidueImplPtr dst_res=dst_chain->AppendResidue(src_res, false);
for (AtomImplList::iterator k=src_res->GetAtomList().begin(),
e3=src_res->GetAtomList().end(); k!=e3; ++k) {
AtomImplPtr src_atom=*k;
diff --git a/modules/mol/base/src/impl/entity_impl.hh b/modules/mol/base/src/impl/entity_impl.hh
index a5f5cd805..c95bef408 100644
--- a/modules/mol/base/src/impl/entity_impl.hh
+++ b/modules/mol/base/src/impl/entity_impl.hh
@@ -109,7 +109,9 @@ public:
/// \brief insert a new chain based on parameters of the given chain
///
/// The chain will have no residues and atoms
- ChainImplPtr InsertChain(const ChainImplPtr& chain, bool deep=false);
+ // force deep to be set explicitely, because it is better than implicit
+ // (and since we are on the impl level interface consistency isn't that critical)
+ ChainImplPtr InsertChain(const ChainImplPtr& chain, bool deep);
ConnectorImplP Connect(const AtomImplPtr& first, const AtomImplPtr& second,
Real len, Real theta, Real phi,
unsigned char bond_order);
diff --git a/modules/mol/base/src/view_op.cc b/modules/mol/base/src/view_op.cc
index 6e4227e74..6b8aebad8 100644
--- a/modules/mol/base/src/view_op.cc
+++ b/modules/mol/base/src/view_op.cc
@@ -296,7 +296,7 @@ public:
virtual bool VisitResidue(const ResidueHandle& res)
{
- res_=chain_->AppendResidue(res.Impl());
+ res_=chain_->AppendResidue(res.Impl(),false);
return true;
}
--
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