From 54decf4b6c0098a71978f6b6364c2456767c4326 Mon Sep 17 00:00:00 2001
From: Niklaus Johner <nij2003@med.cornell.edu>
Date: Fri, 13 Jan 2012 17:17:18 -0500
Subject: [PATCH] Corrected the function to set the residue number of a residue
in the editor to check for breaking of the in_sequence property. Added an
SetInSequence() function to the ChainHandle to check and update the
in_sequence property
---
CMakeLists.txt | 2 +-
modules/io/pymod/wrap_io.cc | 1 -
modules/mol/base/src/chain_handle.cc | 6 ++++++
modules/mol/base/src/chain_handle.hh | 4 +++-
modules/mol/base/src/editor_base.cc | 2 ++
modules/mol/base/src/impl/chain_impl.cc | 15 +++++++++++++++
modules/mol/base/src/impl/chain_impl.hh | 5 ++++-
7 files changed, 31 insertions(+), 4 deletions(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 306445073..e438e4cb4 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -242,4 +242,4 @@ message(STATUS
" Compound Lib (-DCOMPOUND_LIB) : ${_COMP_LIB}\n"
" TMAlign and TMScore (-DCOMPILE_TMTOOLS) : ${_TM_TOOLS}\n"
" Static Libraries (-DENABLE_STATIC) : ${ENABLE_STATIC}\n"
- " Debian-style 'libexec' (-DDEBIAN_STYLE_LIBEXEC) : ${_DEBIAN_STYLE_LIBEXEC}")
\ No newline at end of file
+ " Debian-style 'libexec' (-DDEBIAN_STYLE_LIBEXEC) : ${_DEBIAN_STYLE_LIBEXEC}")
diff --git a/modules/io/pymod/wrap_io.cc b/modules/io/pymod/wrap_io.cc
index 53ba11f7c..bc10f6f6a 100644
--- a/modules/io/pymod/wrap_io.cc
+++ b/modules/io/pymod/wrap_io.cc
@@ -113,7 +113,6 @@ BOOST_PYTHON_MODULE(_ost_io)
def("LoadCRD", &LoadCRD);
def("LoadCHARMMTraj_", &LoadCHARMMTraj, (arg("ent"), arg("trj_filename"),
arg("stride")=1, arg("lazy_load")=false));
-
def("LoadMAE", &LoadMAE);
export_pdb_io();
diff --git a/modules/mol/base/src/chain_handle.cc b/modules/mol/base/src/chain_handle.cc
index 9ff209e35..c1e745f2c 100644
--- a/modules/mol/base/src/chain_handle.cc
+++ b/modules/mol/base/src/chain_handle.cc
@@ -251,5 +251,11 @@ EntityView ChainHandle::Select(const String& q, QueryFlags flags) const {
else return this->GetEntity().Select(Query("cname='"+Impl()->GetName()+"'"), flags);
}
+void ChainHandle::SetInSequence(const int index)
+{
+ this->CheckValidity();
+ Impl()->SetInSequence(index);
+}
+
}}
diff --git a/modules/mol/base/src/chain_handle.hh b/modules/mol/base/src/chain_handle.hh
index 576c4b671..8f88c6e37 100644
--- a/modules/mol/base/src/chain_handle.hh
+++ b/modules/mol/base/src/chain_handle.hh
@@ -193,7 +193,9 @@ public:
bool operator==(const ChainHandle& ref) const;
bool operator!=(const ChainHandle& ref) const;
-
+ /// \brief checks whether res breaks the in sequence property
+ /// and updates it accordingly
+ void SetInSequence(const int index);
};
}} // ns
diff --git a/modules/mol/base/src/editor_base.cc b/modules/mol/base/src/editor_base.cc
index 6757c2af6..e9fed6874 100644
--- a/modules/mol/base/src/editor_base.cc
+++ b/modules/mol/base/src/editor_base.cc
@@ -79,7 +79,9 @@ void EditorBase::RenameResidue(ResidueHandle res, const String& new_name)
void EditorBase::SetResidueNumber(ResidueHandle res, const ResNum& new_num)
{
CheckHandleValidity(res);
+ int index=res.GetIndex();
res.Impl()->SetNumber(new_num);
+ res.GetChain().SetInSequence(index);
}
void EditorBase::RenameChain(ChainHandle chain, const String& new_name)
diff --git a/modules/mol/base/src/impl/chain_impl.cc b/modules/mol/base/src/impl/chain_impl.cc
index 460269020..5ac2b91ab 100644
--- a/modules/mol/base/src/impl/chain_impl.cc
+++ b/modules/mol/base/src/impl/chain_impl.cc
@@ -484,4 +484,19 @@ void ChainImpl::ReorderResidues()
UpdateShifts();
}
+void ChainImpl::SetInSequence(const int index)
+{
+ ResNum num=residue_list_[index]->GetNumber();
+ //Check if rp is in sequence
+ if (in_sequence_) {
+ if (index>0 && residue_list_[index-1]->GetNumber()>=num)
+ in_sequence_=false;
+ if (index<static_cast<int>(residue_list_.size())-1 && residue_list_[index+1]->GetNumber()<=num)
+ in_sequence_=false;
+ }
+ if (in_sequence_) {
+ this->UpdateShifts();
+ }
+}
+
}}} // ns
diff --git a/modules/mol/base/src/impl/chain_impl.hh b/modules/mol/base/src/impl/chain_impl.hh
index 1f871d504..8e99792dd 100644
--- a/modules/mol/base/src/impl/chain_impl.hh
+++ b/modules/mol/base/src/impl/chain_impl.hh
@@ -175,7 +175,10 @@ public:
const ResNum& start,
const ResNum& end);
int GetIndexForResNum(const ResNum& number) const;
-
+ ///\brief checks if the residue with that index breaks the in_sequence
+ /// property and updates it accordingly
+ void SetInSequence(int index);
+
private:
int GetIndexForResNumInSequence(const ResNum& number) const;
void UpdateShifts();
--
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