PDB: new methods to get all the atoms in a residue

src/tools/PDB.cpp

@@ -243,6 +243,17 @@ AtomNumber PDB::getNamedAtomFromResidueAndChain( const std::string& aname, const
   return numbers[0]; // This is to stop compiler errors
 }
 
+std::vector<AtomNumber> PDB::getAtomsInResidue(const unsigned& resnum,const std::string& chainid)const {
+  std::vector<AtomNumber> tmp;
+  for(unsigned i=0;i<size();++i){
+     if( residue[i]==resnum && ( chainid=="*" || chain[i]==chainid) ) tmp.push_back(numbers[i]);
+  }
+  if(tmp.size()==0) {
+    std::string num; Tools::convert( resnum, num );
+    plumed_merror("Cannot find residue " + num + " from chain " + chainid  );
+  }
+  return tmp;
+}
 
 std::string PDB::getChainID(const unsigned& resnumber) const {
   for(unsigned i=0;i<size();++i){

src/tools/PDB.h

@@ -98,6 +98,8 @@ public:
 /// Return the atom named aname from residue number resnum and chain.
 /// Chain=="*" matches any chain and makes it equivalent to getNamedAtomFromResidue.
   AtomNumber getNamedAtomFromResidueAndChain( const std::string& aname, const unsigned& resnum, const std::string& chain ) const;
+/// Access to the atoms of a residue 
+  std::vector<AtomNumber> getAtomsInResidue(const unsigned& resnum,const std::string& chainid)const;
 /// Get the extents of the blocks containing the atoms
   const std::vector<unsigned> & getAtomBlockEnds() const ;
 /// Get the number of blocks of atoms in the pdb