diff --git a/modelling/src/model.cc b/modelling/src/model.cc
index 98a7737b50a1eb9574a46ef0b8bc54e282037136..57c0fe4523be5413b27d0aac638de19b7f2b2f0a 100644
--- a/modelling/src/model.cc
+++ b/modelling/src/model.cc
@@ -17,10 +17,9 @@
#include <ctype.h>
#include <ost/log.hh>
#include <ost/dyn_cast.hh>
-#include <ost/conop/amino_acids.hh>
-#include <ost/conop/conop.hh>
#include <ost/mol/mol.hh>
#include <ost/seq/aligned_column.hh>
+#include <ost/conop/amino_acids.hh>
#include <ost/conop/rule_based.hh>
#include <ost/conop/heuristic.hh>
#include <ost/conop/conop.hh>
@@ -94,7 +93,7 @@ ModellingHandle ModellingHandle::Copy() const{
// All gaps have to be transferred to the new EntityHandle
for(StructuralGapList::const_iterator i = gaps.begin(); i != gaps.end(); ++i){
String chain_name = i->GetChainName();
- ost::mol::ChainHandle ch = r_mhandle.model.FindChain(chain_name);
+ mol::ChainHandle ch = r_mhandle.model.FindChain(chain_name);
r_mhandle.gaps.push_back(*i);
r_mhandle.gaps.back().Transfer(ch);
}
@@ -225,12 +224,12 @@ void MergeGaps(ModellingHandle& mhandle, uint index) {
String gap_seq = full_seq.substr(before_number,after_number-before_number-1);
//kill all residues in between the two new stems
- ost::mol::XCSEditor ed = mhandle.model.EditXCS(ost::mol::BUFFERED_EDIT);
- ost::mol::ChainHandle chain = mhandle.gaps[index].GetChain();
- ost::mol::ResNum i(before_number+1);
- ost::mol::ResNum e(after_number);
+ mol::XCSEditor ed = mhandle.model.EditXCS(mol::BUFFERED_EDIT);
+ mol::ChainHandle chain = mhandle.gaps[index].GetChain();
+ mol::ResNum i(before_number+1);
+ mol::ResNum e(after_number);
for(; i < e; ++i){
- ost::mol::ResidueHandle res = chain.FindResidue(i);
+ mol::ResidueHandle res = chain.FindResidue(i);
if(res.IsValid()) ed.DeleteResidue(res);
}
@@ -336,7 +335,7 @@ void SetupDefaultAllAtomScoring(ModellingHandle& mhandle){
}
void SetSequenceProfiles(ModellingHandle& mhandle,
- const ost::seq::ProfileHandleList& profiles){
+ const seq::ProfileHandleList& profiles){
// check whether the profiles match the internal SEQRES
if(static_cast<int>(profiles.size()) != mhandle.seqres.GetCount()){
@@ -533,7 +532,7 @@ void MergeMHandle(const ModellingHandle& source_mhandle,
}
ed.ReorderResidues(target_chain);
//fix torsions
- ost::conop::AssignBackboneTorsions(target_chain);
+ conop::AssignBackboneTorsions(target_chain);
//delete the gaps in the target mhandle or shorten them...
num.SetNum(start_resnum);
@@ -639,7 +638,7 @@ void MergeMHandle(const ModellingHandle& source_mhandle,
void InsertLoop(ModellingHandle& mhandle, const loop::BackboneList& bb_list,
uint start_resnum, uint chain_idx) {
// update model
- ost::mol::ChainHandleList chain_list = mhandle.model.GetChainList();
+ mol::ChainHandleList chain_list = mhandle.model.GetChainList();
bb_list.InsertInto(chain_list[chain_idx], start_resnum);
// update scoring
if (IsBackboneScoringSetUp(mhandle)) {
@@ -854,12 +853,12 @@ bool InsertDummyAtoms(ResidueHandle dst_res, XCSEditor& edi) {
return true;
}
-ModellingHandle BuildRawModel(const ost::seq::AlignmentHandle& aln,
+ModellingHandle BuildRawModel(const seq::AlignmentHandle& aln,
bool include_ligands,
const String& chain_names,
bool spdbv_style)
{
- ost::seq::AlignmentList l;
+ seq::AlignmentList l;
l.push_back(aln);
return BuildRawModel(l,
include_ligands,
@@ -867,7 +866,7 @@ ModellingHandle BuildRawModel(const ost::seq::AlignmentHandle& aln,
spdbv_style);
}
-ModellingHandle BuildRawModel(const ost::seq::AlignmentList& aln,
+ModellingHandle BuildRawModel(const seq::AlignmentList& aln,
bool include_ligands,
const String& chain_names,
bool spdbv_style)
@@ -882,7 +881,7 @@ ModellingHandle BuildRawModel(const ost::seq::AlignmentList& aln,
uint chain_name_idx = 0;
- for(ost::seq::AlignmentList::const_iterator it=aln.begin();
+ for(seq::AlignmentList::const_iterator it=aln.begin();
it!=aln.end(); ++it, ++chain_name_idx) {
if(chain_name_idx >= chain_names.size()) {
throw promod3::Error("running out of chain names");
@@ -890,7 +889,7 @@ ModellingHandle BuildRawModel(const ost::seq::AlignmentList& aln,
StructuralGapList gap_list;
BuildRawChain(*it, edi, gap_list, chain_names[chain_name_idx], spdbv_style);
result.gaps.insert(result.gaps.end(), gap_list.begin(), gap_list.end());
- ost::seq::SequenceHandle seqres = ost::seq::CreateSequence(
+ seq::SequenceHandle seqres = seq::CreateSequence(
chain_names.substr(chain_name_idx, 1),
it->GetSequence(0).GetGaplessString());
result.seqres.AddSequence(seqres);
@@ -914,7 +913,7 @@ ModellingHandle BuildRawModel(const ost::seq::AlignmentList& aln,
return result;
}
-void AddLigands(const ost::seq::AlignmentList& aln, XCSEditor& edi,
+void AddLigands(const seq::AlignmentList& aln, XCSEditor& edi,
EntityHandle& model)
{
@@ -924,7 +923,7 @@ void AddLigands(const ost::seq::AlignmentList& aln, XCSEditor& edi,
// make sure we handle duplicates
std::set<mol::EntityHandle> unique_handles;
std::vector<mol::ResidueViewList> ligand_views;
- for(ost::seq::AlignmentList::const_iterator it = aln.begin();
+ for(seq::AlignmentList::const_iterator it = aln.begin();
it != aln.end(); ++it) {
mol::EntityHandle handle = it->GetSequence(1).GetAttachedView().GetHandle();
// did we already do that?
@@ -978,7 +977,7 @@ void AddLigands(const ost::seq::AlignmentList& aln, XCSEditor& edi,
}
}
-void BuildRawChain(const ost::seq::AlignmentHandle& aln,
+void BuildRawChain(const seq::AlignmentHandle& aln,
XCSEditor& edi,
StructuralGapList& gap_list,
char chain_name,
@@ -1073,9 +1072,9 @@ void BuildRawChain(const ost::seq::AlignmentHandle& aln,
// insert Cbeta, unless dst residue is glycine.
if (!has_cbeta && !(trg_olc == 'G' || trg_olc == 'g')) {
- ost::mol::AtomHandle ca = dst_res.FindAtom("CA");
- ost::mol::AtomHandle n = dst_res.FindAtom("N");
- ost::mol::AtomHandle c = dst_res.FindAtom("C");
+ mol::AtomHandle ca = dst_res.FindAtom("CA");
+ mol::AtomHandle n = dst_res.FindAtom("N");
+ mol::AtomHandle c = dst_res.FindAtom("C");
geom::Vec3 cbeta_pos;
promod3::core::ConstructCBetaPos(n.GetPos(), ca.GetPos(), c.GetPos(),
cbeta_pos);
@@ -1088,7 +1087,7 @@ void BuildRawChain(const ost::seq::AlignmentHandle& aln,
if (consecutive_residues && before.IsValid()) {
AtomHandle c_before = before.FindAtom("C");
AtomHandle n_this = dst_res.FindAtom("N");
- if(ost::conop::IsBondFeasible(c_before, n_this)) {
+ if(conop::IsBondFeasible(c_before, n_this)) {
edi.Connect(c_before, n_this);
} else {
// not possible to generate feasible peptide bond