From 7a49a6ccb596b58c3d819ffdf64dd02d2f492efb Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 3 Mar 2015 17:07:05 +0100
Subject: [PATCH] when making a deep copy, the alternative atom positions
should be handled.
This closes BZDNG-56
---
modules/mol/base/src/impl/chain_impl.cc | 67 ++++++++++++++++++++++---
1 file changed, 60 insertions(+), 7 deletions(-)
diff --git a/modules/mol/base/src/impl/chain_impl.cc b/modules/mol/base/src/impl/chain_impl.cc
index c6acf1a6a..e7012a796 100644
--- a/modules/mol/base/src/impl/chain_impl.cc
+++ b/modules/mol/base/src/impl/chain_impl.cc
@@ -71,15 +71,68 @@ ResidueImplPtr ChainImpl::AppendResidue(const ResidueImplPtr& res, bool deep)
dst_res->SetProtein(res->IsProtein());
dst_res->SetChemType(res->GetChemType());
dst_res->SetIsLigand(res->IsLigand());
- if(deep)
- {
+
+ if(deep){
AtomImplList::iterator it=res->GetAtomList().begin(),
- it_end=res->GetAtomList().end();
- for(;it!=it_end;++it)
- {
- AtomHandle atom=*it;
- dst_res->InsertAtom(atom.Impl());
+ it_end=res->GetAtomList().end();
+
+ if(res->HasAltAtoms()){
+
+ for(;it!=it_end;++it){
+
+ AtomImplPtr atom=*it;
+ std::vector<String> alt_gn = res->GetAltAtomGroupNames(atom);
+
+ if(alt_gn.empty()){
+ //there are no alternative locations for this atoms =>just add it
+ dst_res->InsertAtom(atom);
+ }
+
+ else{
+ AtomImplPtr dst_atom;
+
+ dst_atom = dst_res->InsertAltAtom(atom->GetName(),alt_gn[0],
+ res->GetAltAtomPos(atom,alt_gn[0]),
+ atom->GetElement(),
+ res->GetAltAtomOcc(atom,alt_gn[0]),
+ res->GetAltAtomBFactor(atom,alt_gn[0]));
+
+ //in the InsertAltAtom function only name, position and
+ //element get passed when inserting the actual atom into the residue.
+ //All the rest we have to map by ourself as we would call the
+ //dst_res->InsertAtom(atom) function
+ dst_atom->Assign(*atom.get());
+ dst_atom->SetState(atom->GetState());
+ dst_atom->SetBFactor(atom->GetBFactor());
+ dst_atom->SetOccupancy(atom->GetOccupancy());
+ dst_atom->SetHetAtom(atom->IsHetAtom());
+ dst_atom->SetIndex(atom->GetIndex());
+
+ if (!atom->HasDefaultProps()) {
+ dst_atom->SetRadius(atom->GetRadius());
+ dst_atom->SetCharge(atom->GetCharge());
+ dst_atom->SetMass(atom->GetMass());
+ dst_atom->SetAnisou(atom->GetAnisou());
+ }
+
+ //the pos for the first alt group name is already added in the
+ //InsertAltAtom function, all the others get added here
+ for(std::vector<String>::iterator alt_gn_it = alt_gn.begin() + 1,
+ alt_gn_it_e = alt_gn.end(); alt_gn_it != alt_gn_it_e; ++alt_gn_it){
+
+ dst_res->AddAltAtomPos(*alt_gn_it,dst_atom,
+ res->GetAltAtomPos(atom,*alt_gn_it),
+ res->GetAltAtomOcc(atom,*alt_gn_it),
+ res->GetAltAtomBFactor(atom,*alt_gn_it));
+ }
+ }
}
+ }
+ else{
+ for(;it!=it_end;++it){
+ dst_res->InsertAtom(*it);
+ }
+ }
}
return dst_res;
}
--
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