From 39592e192108d9a4359bbd294b8dd8eb236d76dd Mon Sep 17 00:00:00 2001
From: marco <marco@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Tue, 21 Sep 2010 12:34:40 +0000
Subject: [PATCH] remove some const-weirdness
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2712 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/conop/src/builder.cc | 20 ++++++++++----------
modules/conop/src/builder.hh | 20 ++++++++++----------
modules/conop/src/heuristic_builder.cc | 17 +++++++++--------
modules/conop/src/heuristic_builder.hh | 12 +++++++-----
modules/conop/src/rule_based_builder.cc | 23 +++++++++++++----------
modules/conop/src/rule_based_builder.hh | 16 ++++++++--------
6 files changed, 57 insertions(+), 51 deletions(-)
diff --git a/modules/conop/src/builder.cc b/modules/conop/src/builder.cc
index 14c103e55..b53a14644 100644
--- a/modules/conop/src/builder.cc
+++ b/modules/conop/src/builder.cc
@@ -26,7 +26,7 @@ namespace ost { namespace conop {
Builder::~Builder() {}
-void Builder::CompleteAtoms(const mol::ResidueHandle& rh) {}
+void Builder::CompleteAtoms(mol::ResidueHandle rh) {}
void Builder::CheckResidueCompleteness(const mol::ResidueHandle& rh) {}
@@ -34,10 +34,10 @@ mol::ResidueKey Builder::IdentifyResidue(const mol::ResidueHandle& rh) {
return mol::ResidueKey();
}
void Builder::FillResidueProps(mol::ResidueHandle residue){};
-void Builder::ConnectAtomsOfResidue(const mol::ResidueHandle& rh) {}
+void Builder::ConnectAtomsOfResidue(mol::ResidueHandle rh) {}
-void Builder::ConnectResidueToPrev(const mol::ResidueHandle& rh,
- const mol::ResidueHandle& p) {
+void Builder::ConnectResidueToPrev(mol::ResidueHandle rh,
+ mol::ResidueHandle p) {
this->ConnectResidueToNext(p, rh);
}
@@ -46,11 +46,11 @@ bool Builder::IsResidueComplete(const mol::ResidueHandle& rh)
return true;
}
-void Builder::ConnectResidueToNext(const mol::ResidueHandle& rh,
- const mol::ResidueHandle& n) {}
+void Builder::ConnectResidueToNext(mol::ResidueHandle rh,
+ mol::ResidueHandle n) {}
-void Builder::AssignTorsions(const mol::ChainHandle& ch) {}
-void Builder::AssignTorsionsToResidue(const mol::ResidueHandle& rh) {}
+void Builder::AssignTorsions(mol::ChainHandle ch) {}
+void Builder::AssignTorsionsToResidue(mol::ResidueHandle rh) {}
void Builder::FillAtomProps(mol::AtomHandle atom) {}
@@ -159,7 +159,7 @@ bool Builder::AreResiduesConsecutive(const mol::ResidueHandle& r1,
r2.GetNumber().GetInsCode()==r1.GetNumber().NextInsertionCode().GetInsCode();
}
-void Builder::AssignBackBoneTorsionsToResidue(const mol::ResidueHandle& res)
+void Builder::AssignBackBoneTorsionsToResidue(mol::ResidueHandle res)
{
mol::ResidueHandle prev=res.GetPrev();
@@ -202,7 +202,7 @@ void Builder::AssignBackBoneTorsionsToResidue(const mol::ResidueHandle& res)
-void Builder::DistanceBasedConnect(const mol::AtomHandle& atom)
+void Builder::DistanceBasedConnect(mol::AtomHandle atom)
{
mol::EntityHandle ent=atom.GetEntity();
mol::XCSEditor editor=ent.RequestXCSEditor(mol::BUFFERED_EDIT);
diff --git a/modules/conop/src/builder.hh b/modules/conop/src/builder.hh
index b47e432ac..9ece21a63 100644
--- a/modules/conop/src/builder.hh
+++ b/modules/conop/src/builder.hh
@@ -54,7 +54,7 @@ public:
/// \brief add any missing atoms to the residue based on its key,
/// with coordinates set to zero
- virtual void CompleteAtoms(const mol::ResidueHandle& rh);
+ virtual void CompleteAtoms(mol::ResidueHandle rh);
/// \brief verify that the given residue has all atoms it
@@ -80,27 +80,27 @@ public:
/// Connects atoms of residue based on residue and atom name. This method does
/// not establish inter-residue bonds. To connect atoms that belong to
/// different residues, use ConnectResidueToPrev(), or ConnectResidueToNext().
- virtual void ConnectAtomsOfResidue(const mol::ResidueHandle& rh);
+ virtual void ConnectAtomsOfResidue(mol::ResidueHandle rh);
/// \brief connect atoms of residue to previous
///
/// The order of the parameters is important. In case of a polypeptide chain,
/// the residues are thought to be ordered from N- to C- terminus.
///
/// \sa ConnectResidueToNext
- virtual void ConnectResidueToPrev(const mol::ResidueHandle& rh,
- const mol::ResidueHandle& prev);
+ virtual void ConnectResidueToPrev(mol::ResidueHandle rh,
+ mol::ResidueHandle prev);
/// \sa ConnectResidueToPrev
- virtual void ConnectResidueToNext(const mol::ResidueHandle& rh,
- const mol::ResidueHandle& next);
+ virtual void ConnectResidueToNext(mol::ResidueHandle rh,
+ mol::ResidueHandle next);
/// \brief assign named torsions to a complete chain
- virtual void AssignTorsions(const mol::ChainHandle& ch);
+ virtual void AssignTorsions(mol::ChainHandle ch);
/// \brief assign named torsions to single residue
- virtual void AssignTorsionsToResidue(const mol::ResidueHandle& residue);
+ virtual void AssignTorsionsToResidue(mol::ResidueHandle residue);
/// \brief assign Backbone torsions to single residue
- void AssignBackBoneTorsionsToResidue(const mol::ResidueHandle& res);
+ void AssignBackBoneTorsionsToResidue(mol::ResidueHandle res);
/// \brief Check if peptide bond is formed between the two atoms.
///
@@ -130,7 +130,7 @@ public:
/// |brief Connect \p atom with all atoms for whith IsBondFeasible() and
/// AreResiduesConsecutive() returns true
- void DistanceBasedConnect(const mol::AtomHandle& atom);
+ void DistanceBasedConnect(mol::AtomHandle atom);
};
diff --git a/modules/conop/src/heuristic_builder.cc b/modules/conop/src/heuristic_builder.cc
index 03398956f..5429a5697 100644
--- a/modules/conop/src/heuristic_builder.cc
+++ b/modules/conop/src/heuristic_builder.cc
@@ -221,7 +221,7 @@ void HeuristicBuilder::ConnectivityFromAtomNames(const mol::ResidueHandle& res,
}
}
-void HeuristicBuilder::ConnectAtomsOfResidue(const mol::ResidueHandle& res)
+void HeuristicBuilder::ConnectAtomsOfResidue(mol::ResidueHandle res)
{
LOG_DEBUG("HeuristicBuilder: ConnectAtomsOfResidue on " << res.GetKey() << " " << res.GetNumber());
@@ -288,7 +288,8 @@ void ConnectPrevNext(HeuristicBuilder* builder,mol::ResidueHandle res0,
}
if(!res1) return; // ignore if prev/next residue is invalid
- LOG_DEBUG(fname << " found second residue " << res1.GetKey() << " " << res1.GetNumber());
+ LOG_DEBUG(fname << " found second residue " << res1.GetKey()
+ << " " << res1.GetNumber());
std::pair<detail::ConnResEntry,bool> res0_ret = builder->LookupResEntry(res0.GetKey());
std::pair<detail::ConnResEntry,bool> res1_ret = builder->LookupResEntry(res1.GetKey());
@@ -322,7 +323,7 @@ void ConnectPrevNext(HeuristicBuilder* builder,mol::ResidueHandle res0,
}
-void HeuristicBuilder::AssignTorsionsToResidue(const mol::ResidueHandle& res)
+void HeuristicBuilder::AssignTorsionsToResidue(mol::ResidueHandle res)
{
mol::XCSEditor editor=res.GetEntity().RequestXCSEditor(mol::BUFFERED_EDIT);
@@ -390,7 +391,7 @@ void HeuristicBuilder::AssignTorsionsToResidue(const mol::ResidueHandle& res)
}
}
-void HeuristicBuilder::AssignTorsions(const mol::ChainHandle& chain)
+void HeuristicBuilder::AssignTorsions(mol::ChainHandle chain)
{
if (chain.GetResidueCount()==0)
return;
@@ -405,13 +406,13 @@ void HeuristicBuilder::AssignTorsions(const mol::ChainHandle& chain)
}
}
-void HeuristicBuilder::ConnectResidueToPrev(const mol::ResidueHandle& rh,
- const mol::ResidueHandle& prev) {
+void HeuristicBuilder::ConnectResidueToPrev(mol::ResidueHandle rh,
+ mol::ResidueHandle prev) {
ConnectPrevNext<false>(this, rh, prev);
}
-void HeuristicBuilder::ConnectResidueToNext(const mol::ResidueHandle& rh,
- const mol::ResidueHandle& next) {
+void HeuristicBuilder::ConnectResidueToNext(mol::ResidueHandle rh,
+ mol::ResidueHandle next) {
ConnectPrevNext<true>(this, rh, next);
}
diff --git a/modules/conop/src/heuristic_builder.hh b/modules/conop/src/heuristic_builder.hh
index d251e53bf..bcfccdbb1 100644
--- a/modules/conop/src/heuristic_builder.hh
+++ b/modules/conop/src/heuristic_builder.hh
@@ -79,26 +79,28 @@ public:
HeuristicBuilder();
virtual ~HeuristicBuilder();
- virtual void AssignTorsions(const mol::ChainHandle& ch);
+ virtual void AssignTorsions(mol::ChainHandle ch);
//! \brief connect by using information in the heuristic connectivity table.
//
// This does not make any assumption on the correctness of internal or external
// coordinates. Only the atom names and residue need to be known.
- virtual void ConnectAtomsOfResidue(const mol::ResidueHandle& rh);
+ virtual void ConnectAtomsOfResidue(mol::ResidueHandle rh);
virtual bool IsResidueComplete(const mol::ResidueHandle& rh);
// virtual char GetOneLetterCode(const mol::ResidueKey& residue) const;
//!\brief connect to previous residue in chain.
- virtual void ConnectResidueToPrev(const mol::ResidueHandle& rh, const mol::ResidueHandle& prev);
+ virtual void ConnectResidueToPrev(mol::ResidueHandle rh,
+ mol::ResidueHandle prev);
//!
- virtual void AssignTorsionsToResidue(const mol::ResidueHandle& residue);
+ virtual void AssignTorsionsToResidue(mol::ResidueHandle residue);
virtual void FillResidueProps(mol::ResidueHandle residue);
//!\brief connect to next residue in chain.
- virtual void ConnectResidueToNext(const mol::ResidueHandle& rh, const mol::ResidueHandle& next);
+ virtual void ConnectResidueToNext(mol::ResidueHandle rh,
+ mol::ResidueHandle next);
//!\brief get connectivity table for residues
// Retrieve connectiviy information based on residue key. The returned
diff --git a/modules/conop/src/rule_based_builder.cc b/modules/conop/src/rule_based_builder.cc
index f2a8fd18f..755d03dd5 100644
--- a/modules/conop/src/rule_based_builder.cc
+++ b/modules/conop/src/rule_based_builder.cc
@@ -31,7 +31,7 @@
namespace ost { namespace conop {
-void RuleBasedBuilder::CompleteAtoms(const mol::ResidueHandle& rh) {}
+void RuleBasedBuilder::CompleteAtoms(mol::ResidueHandle rh) {}
void RuleBasedBuilder::CheckResidueCompleteness(const mol::ResidueHandle& rh) {
LookupCompound(rh);
@@ -91,7 +91,8 @@ struct OrdinalComp {
};
-void RuleBasedBuilder::LookupCompound(const mol::ResidueHandle& rh) {
+void RuleBasedBuilder::LookupCompound(const mol::ResidueHandle& rh)
+{
if ((last_compound_) && (rh.GetName()==last_compound_->GetID())) {
return;
} else {
@@ -99,8 +100,9 @@ void RuleBasedBuilder::LookupCompound(const mol::ResidueHandle& rh) {
}
}
-void RuleBasedBuilder::ReorderAtoms(const mol::ResidueHandle& residue,
- CompoundPtr compound) {
+void RuleBasedBuilder::ReorderAtoms(mol::ResidueHandle residue,
+ CompoundPtr compound)
+{
mol::impl::ResidueImplPtr impl=residue.Impl();
mol::impl::AtomImplList::iterator i=impl->GetAtomList().begin();
for (; i!=impl->GetAtomList().end(); ++i) {
@@ -146,7 +148,7 @@ mol::AtomHandle RuleBasedBuilder::LocateAtom(const mol::AtomHandleList& ahl, int
return not_found ? mol::AtomHandle() : *r_it;
}
-void RuleBasedBuilder::ConnectAtomsOfResidue(const mol::ResidueHandle& rh) {
+void RuleBasedBuilder::ConnectAtomsOfResidue(mol::ResidueHandle rh) {
LookupCompound(rh);
if (!last_compound_) {
mol::AtomHandleList atoms=rh.GetAtomList();
@@ -175,8 +177,8 @@ void RuleBasedBuilder::ConnectAtomsOfResidue(const mol::ResidueHandle& rh) {
}
}
-void RuleBasedBuilder::ConnectResidueToNext(const mol::ResidueHandle& rh,
- const mol::ResidueHandle& next) {
+void RuleBasedBuilder::ConnectResidueToNext(mol::ResidueHandle rh,
+ mol::ResidueHandle next) {
if (!next.IsValid()) {
return;
}
@@ -204,7 +206,7 @@ void RuleBasedBuilder::ConnectResidueToNext(const mol::ResidueHandle& rh,
}
-void RuleBasedBuilder::AssignTorsions(const mol::ChainHandle& chain) {
+void RuleBasedBuilder::AssignTorsions(mol::ChainHandle chain) {
if (chain.GetResidueCount()==0)
return;
std::vector<mol::ResidueHandle> rlist = chain.GetResidueList();
@@ -215,11 +217,12 @@ void RuleBasedBuilder::AssignTorsions(const mol::ChainHandle& chain) {
}
}
-void RuleBasedBuilder::AssignTorsionsToResidue(const mol::ResidueHandle& residue) {
+void RuleBasedBuilder::AssignTorsionsToResidue(mol::ResidueHandle residue) {
/// The only components having named torsions are the standard set of amino
/// acids, plus some of compounds derived from them such as selenium
/// methionine. Things are simplified a lot by only storing the torsions
- /// of the side chains in the database. PHI, PSI and OMEGA torsions are checked without a lookup in the database.
+ /// of the side chains in the database. PHI, PSI and OMEGA torsions are
+ /// checked without a lookup in the database.
LookupCompound(residue);
if (!last_compound_)
return;
diff --git a/modules/conop/src/rule_based_builder.hh b/modules/conop/src/rule_based_builder.hh
index bd1af72f5..0ab392b24 100644
--- a/modules/conop/src/rule_based_builder.hh
+++ b/modules/conop/src/rule_based_builder.hh
@@ -46,7 +46,7 @@ public:
/// \brief fill atom properties such as element and radius
virtual void FillAtomProps(mol::AtomHandle atom);
- virtual void CompleteAtoms(const mol::ResidueHandle& rh);
+ virtual void CompleteAtoms(mol::ResidueHandle rh);
/// \brief Check residue completeness
///
@@ -68,7 +68,7 @@ public:
virtual mol::ResidueKey IdentifyResidue(const mol::ResidueHandle& rh);
- virtual void ConnectAtomsOfResidue(const mol::ResidueHandle& rh);
+ virtual void ConnectAtomsOfResidue(mol::ResidueHandle rh);
/// \brief Connects the two residues together.
///
@@ -79,11 +79,11 @@ public:
/// bond.
/// \param next
/// is the C-terminal partner, donating the nitrogen to the bond.
- virtual void ConnectResidueToNext(const mol::ResidueHandle& rh,
- const mol::ResidueHandle& next);
+ virtual void ConnectResidueToNext(mol::ResidueHandle rh,
+ mol::ResidueHandle next);
/// \brief requires chemical types
- virtual void AssignTorsions(const mol::ChainHandle& ch);
- virtual void AssignTorsionsToResidue(const mol::ResidueHandle& residue);
+ virtual void AssignTorsions(mol::ChainHandle ch);
+ virtual void AssignTorsionsToResidue(mol::ResidueHandle residue);
/// \brief Invoked whenever an unkknown atom has been encountered during a
/// residue completeness check.
///
@@ -118,11 +118,11 @@ private:
CompoundPtr last_compound_;
void LookupCompound(const mol::ResidueHandle& rh);
/// Change internal order of atoms in residue to the order given by compound
- void ReorderAtoms(const mol::ResidueHandle& residue, CompoundPtr compound);
+ void ReorderAtoms(mol::ResidueHandle residue, CompoundPtr compound);
mol::AtomHandle LocateAtom(const mol::AtomHandleList& ahl, int ordinal);
- void AssignBackBoneTorsionsToResidue(const mol::ResidueHandle& residue);
+ void AssignBackBoneTorsionsToResidue(mol::ResidueHandle residue);
};
--
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