1LetterCode

How to get the 1 letter code AS sequence out of a .pdb file?

	#include <BALL/KERNEL/chain.h>
	#include <BALL/KERNEL/protein.h>
	#include <BALL/KERNEL/system.h>
	#include <BALL/STRUCTURE/peptides.h>
	#include <BALL/FORMAT/PDBFile.h>

	using namespace BALL;

	//read in .pdb file containing protein
	PDBFile infile("system.pdb");
	System S;
	infile >> S;
	infile.close();

	// get the BALL sequence
	String ball_seq= "";

	// get the protein
	if (RTTI::isKindOf<Protein>(*(S.getMolecule(0))))
	{
	  //we take the first chain for illustration
	  Protein* protein = RTTI::castTo<Protein>(*(S.getMolecule(0)));
	  ChainIterator ch_it = protein->beginChain();
	  for (ResidueIterator r_it = ch_it->beginResidue(); +r_it; r_it++)
	  {
	    if ((r_it->isAminoAcid()) && (r_it->getName() != String("ACE")))
	    {
	      ball_seq += Peptides::OneLetterCode(r_it->getName());
	    }
	  }
	}
	cout << "One letter code: " << ball_seq << endl;

A possible alternative would look like this:

	#include <BALL/FORMAT/PDBFile.h>
	#include <BALL/KERNEL/system.h>
	#include <BALL/STRUCTURE/peptides.h>

	#include <iostream>

	using namespace BALL;

	int main(int argc, char* argv[])
	{
	  PDBFile in(argv[1]);
	  if(!in) {
	    return -1;
	  }

	  System sys;
	  in >> sys;
	  in.close();

	  for(ProteinIterator it = sys.beginProtein(); +it; ++it) {
	    String seq = Peptides::GetSequence(*it);
	    std::cout << "Sequence of protein "
	              << it->getName() << ": " << seq << std::endl;
	  }

	  return 0;
	}