From ea0e71d9aec276f0f41cbd157f47f6fd8c8b0e4f Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@stud.unibas.ch>
Date: Wed, 22 Feb 2012 12:22:08 +0100
Subject: [PATCH] Added RenumberAllResidue functionality
---
modules/mol/base/pymod/export_editors.cc | 1 +
modules/mol/base/src/editor_base.cc | 5 +++++
modules/mol/base/src/editor_base.hh | 11 +++++++++++
modules/mol/base/src/impl/chain_impl.cc | 22 ++++++++++++++++++++++
modules/mol/base/src/impl/chain_impl.hh | 2 ++
modules/mol/base/src/impl/entity_impl.cc | 8 ++++++++
modules/mol/base/src/impl/entity_impl.hh | 2 ++
modules/mol/base/src/residue_prop.hh | 10 ++++++++++
8 files changed, 61 insertions(+)
diff --git a/modules/mol/base/pymod/export_editors.cc b/modules/mol/base/pymod/export_editors.cc
index eb1720a1d..6cee09765 100644
--- a/modules/mol/base/pymod/export_editors.cc
+++ b/modules/mol/base/pymod/export_editors.cc
@@ -220,6 +220,7 @@ void export_Editors()
.def("AddTorsion", &EditorBase::AddTorsion)
.def("ReorderResidues",&EditorBase::ReorderResidues)
.def("ReorderAllResidues",&EditorBase::ReorderAllResidues)
+ .def("RenumberAllResidues",&EditorBase::RenumberAllResidues)
;
class_<XCSEditor, bases<EditorBase> >("XCSEditor", no_init)
diff --git a/modules/mol/base/src/editor_base.cc b/modules/mol/base/src/editor_base.cc
index e9fed6874..ba822f0f5 100644
--- a/modules/mol/base/src/editor_base.cc
+++ b/modules/mol/base/src/editor_base.cc
@@ -165,6 +165,11 @@ void EditorBase::ReorderAllResidues()
ent_.Impl()->ReorderAllResidues();
}
+void EditorBase::RenumberAllResidues(int start, bool keep_spacing)
+{
+ ent_.Impl()->RenumberAllResidues(start, keep_spacing);
+}
+
void EditorBase::RenameAtom(AtomHandle atom, const String& new_name)
{
CheckHandleValidity(atom);
diff --git a/modules/mol/base/src/editor_base.hh b/modules/mol/base/src/editor_base.hh
index 0527a0a7b..c6309cce3 100644
--- a/modules/mol/base/src/editor_base.hh
+++ b/modules/mol/base/src/editor_base.hh
@@ -205,6 +205,17 @@ public:
/// \brief reorder residues of all chains based on their residue number
void ReorderAllResidues();
+
+ /// \brief renumber residues of all chains
+ ///
+ /// \param start
+ /// Residues of every chain will be renumbered, whereas the first
+ /// residue gets the residue number start.
+ ///
+ /// \param keep_spacing
+ /// If set to false, residues will continously be renumbered ongoing from start.
+ /// Otherwise the spacings between the residues are kept.
+ void RenumberAllResidues(int start, bool keep_spacing);
/// \brief Get edit mode of editor
EditMode GetMode() const {return mode_;}
diff --git a/modules/mol/base/src/impl/chain_impl.cc b/modules/mol/base/src/impl/chain_impl.cc
index 5ac2b91ab..009f436a5 100644
--- a/modules/mol/base/src/impl/chain_impl.cc
+++ b/modules/mol/base/src/impl/chain_impl.cc
@@ -484,6 +484,28 @@ void ChainImpl::ReorderResidues()
UpdateShifts();
}
+void ChainImpl::RenumberAllResidues(int start, bool keep_spacing)
+{
+ ResNum actual_num=ResNum(start);
+ ResNum original_start_num=residue_list_[0]->GetNumber();
+ ResNum start_diff=ResNum(start)-original_start_num;
+
+
+ for (ResidueImplList::const_iterator i=residue_list_.begin();
+ i!=residue_list_.end(); ++i) {
+
+ if(keep_spacing){
+ ResNum temp=(*i)->GetNumber();
+ (*i)->SetNumber(temp+start_diff);
+ continue;
+ }
+
+ (*i)->SetNumber(actual_num);
+ actual_num++;
+ }
+ UpdateShifts();
+}
+
void ChainImpl::SetInSequence(const int index)
{
ResNum num=residue_list_[index]->GetNumber();
diff --git a/modules/mol/base/src/impl/chain_impl.hh b/modules/mol/base/src/impl/chain_impl.hh
index 8e99792dd..bcb3436e2 100644
--- a/modules/mol/base/src/impl/chain_impl.hh
+++ b/modules/mol/base/src/impl/chain_impl.hh
@@ -169,6 +169,8 @@ public:
void DeleteAllResidues();
void ReorderResidues();
+
+ void RenumberAllResidues(int start, bool keep_spacing);
int GetIndex(const ResidueImplPtr& res) const;
void AssignSecondaryStructure(SecStructure ss,
diff --git a/modules/mol/base/src/impl/entity_impl.cc b/modules/mol/base/src/impl/entity_impl.cc
index bc3fba841..daf9c7c1f 100644
--- a/modules/mol/base/src/impl/entity_impl.cc
+++ b/modules/mol/base/src/impl/entity_impl.cc
@@ -1210,4 +1210,12 @@ void EntityImpl::ReorderAllResidues()
}
}
+void EntityImpl::RenumberAllResidues(int start, bool keep_spacing)
+{
+ for(ChainImplList::iterator cit=chain_list_.begin();cit!=chain_list_.end();++cit) {
+ (*cit)->RenumberAllResidues(start, keep_spacing);
+ }
+
+}
+
}}} // ns
diff --git a/modules/mol/base/src/impl/entity_impl.hh b/modules/mol/base/src/impl/entity_impl.hh
index 3c5000920..dd88fb325 100644
--- a/modules/mol/base/src/impl/entity_impl.hh
+++ b/modules/mol/base/src/impl/entity_impl.hh
@@ -254,6 +254,8 @@ public:
void ReorderAllResidues();
+ void RenumberAllResidues(int start, bool keep_spacing);
+
private:
void DoCopy(EntityImplPtr dest);
diff --git a/modules/mol/base/src/residue_prop.hh b/modules/mol/base/src/residue_prop.hh
index 19bccc98e..168c9744c 100644
--- a/modules/mol/base/src/residue_prop.hh
+++ b/modules/mol/base/src/residue_prop.hh
@@ -75,6 +75,16 @@ public:
return num_;
}
+ ResNum operator+(const ResNum& r)
+ {
+ return ResNum(num_+r.num_);
+ }
+
+ ResNum operator-(const ResNum& r)
+ {
+ return ResNum(num_-r.num_);
+ }
+
ResNum& operator++()
{
++num_;
--
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