PDB: new method to get all the atoms in a chain

src/tools/PDB.cpp

@@ -255,6 +255,17 @@ std::vector<AtomNumber> PDB::getAtomsInResidue(const unsigned& resnum,const std:
   return tmp;
 }
 
+std::vector<AtomNumber> PDB::getAtomsInChain(const std::string& chainid)const {
+  std::vector<AtomNumber> tmp;
+  for(unsigned i=0;i<size();++i){
+     if( chainid=="*" || chain[i]==chainid ) tmp.push_back(numbers[i]);
+  }
+  if(tmp.size()==0) {
+    plumed_merror("Cannot find atoms from chain " + chainid  );
+  }
+  return tmp;
+}
+
 std::string PDB::getChainID(const unsigned& resnumber) const {
   for(unsigned i=0;i<size();++i){
      if(resnumber==residue[i]) return chain[i];

src/tools/PDB.h

@@ -100,6 +100,8 @@ public:
   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;
+/// Access to the atoms of a chain 
+  std::vector<AtomNumber> getAtomsInChain(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