From 45895eaca341388041e91f9bbeafb2c4aa81e2d2 Mon Sep 17 00:00:00 2001
From: Carlo Camilloni <carlo.camilloni@gmail.com>
Date: Fri, 20 Dec 2013 22:43:55 +0100
Subject: [PATCH] added omega as additional symbol for atom selection in
proteins
---
src/tools/MolDataClass.cpp | 10 ++++++++++
src/tools/MolDataClass.h | 2 +-
2 files changed, 11 insertions(+), 1 deletion(-)
diff --git a/src/tools/MolDataClass.cpp b/src/tools/MolDataClass.cpp
index a080268d5..c29f13820 100644
--- a/src/tools/MolDataClass.cpp
+++ b/src/tools/MolDataClass.cpp
@@ -124,6 +124,16 @@ void MolDataClass::specialSymbol( const std::string& type, const std::string& sy
numbers[1]=mypdb.getNamedAtomFromResidue("CA",resnum);
numbers[2]=mypdb.getNamedAtomFromResidue("C",resnum);
numbers[3]=mypdb.getNamedAtomFromResidue("N",resnum+1);
+ } else if( symbol.find("omega")!=std::string::npos ){
+ std::size_t dash=symbol.find_first_of('-');
+ unsigned resnum; Tools::convert( symbol.substr(dash+1), resnum );
+ std::string resname = mypdb.getResidueName(resnum);
+ if( !allowedResidue( type, resname ) || isTerminalGroup( type, resname ) ) return ;
+ numbers.resize(4);
+ numbers[0]=mypdb.getNamedAtomFromResidue("CA",resnum);
+ numbers[1]=mypdb.getNamedAtomFromResidue("C",resnum);
+ numbers[2]=mypdb.getNamedAtomFromResidue("N",resnum+1);
+ numbers[3]=mypdb.getNamedAtomFromResidue("CA",resnum+1);
}
} else {
plumed_merror(type + " is not a valid molecule type");
diff --git a/src/tools/MolDataClass.h b/src/tools/MolDataClass.h
index 6247795da..8e2804f12 100644
--- a/src/tools/MolDataClass.h
+++ b/src/tools/MolDataClass.h
@@ -43,7 +43,7 @@ public:
static void getBackboneForResidue( const std::string& type, const unsigned& residuenum, const PDB& mypdb, std::vector<AtomNumber>& atoms );
/// Return true if the residue is a terminal group e.g. ACE, NME for proteins
static bool isTerminalGroup( const std::string& type, const std::string& residuename );
-/// Used to interpret special symbols - currently phi and psi
+/// Used to interpret special symbols - currently phi and psi and omega
static void specialSymbol( const std::string& type, const std::string& symbol, const PDB& mypdb, std::vector<AtomNumber>& numbers );
};
--
GitLab