libRosetta Users Guide

libRosetta Refold Demo

This is a demo program that reads a PDB file, tweaks the conformation of the protein, refolds the protein to update the tweaked atom positions, and writes the tweaked protein to a PDB file.

// libRosetta headers
#include <rosetta/conformation/protein/Protein.hh>
#include <rosetta/conformation/protein/io.hh>
#include <rosetta/conformation/TorsionAngle.hh>
#include <rosetta/conformation/builder/ProteinBuilder.hh>
#include <rosetta/io/pdb/read_pdb.hh>
#include <rosetta/options/option.hh>

// Numeric headers
#include <numeric/conversions.hh>

// Standard library headers
#include <cstdlib>
#include <fstream>
#include <iostream>
#include <string>


/// @brief Demo of reading, tweaking, refolding, and writing a protein
int
main( int argc, char * argv[] )
{
   using namespace rosetta;
   using namespace rosetta::conformation;
   using namespace rosetta::conformation::builder;
   using namespace rosetta::conformation::protein;
   using namespace rosetta::io::pdb;
   using namespace rosetta::options;
   using namespace std;
   using numeric::conversions::radians;
   typedef  ProteinBuilder::Proteins  Proteins;

   // Get command line options
   options::initialize().load( argc, argv, true );
   options::process();

   // Read the PDB
   Proteins proteins( read_pdb( argv[1] ) );

   // Grab the first protein
   Protein & protein( **proteins.begin() );

   // Tweak the conformation in 2 places just for the fun of it
   protein.phi( 20 ) += radians( +40.0 ); // +40 degrees
   protein.phi( 80 ) -= radians( -40.0 ); // -40 degrees

   // Refold the protein
   protein.refold_N2C(); // N2C direction fullatom refold

   // Write the PDB
   string const output_file( protein.id() + ".tweaked.pdb" );
   std::ofstream pdb_stream( output_file.c_str() );
   pdb_write( pdb_stream, protein );
}