RNA_AtomVDW.cc

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file   core/scoring/methods/AtomVDW.hh
/// @brief
/// @author Rhiju Das


// Unit Headers
#include <core/scoring/rna/RNA_AtomVDW.hh>

// Package headers

// Project headers
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ResidueTypeSet.hh>

#include <basic/database/open.hh>

// Utility headers
#include <utility/io/izstream.hh>

#include <core/chemical/ResidueType.hh>
#include <utility/vector1.hh>
#include <basic/Tracer.hh>


static basic::Tracer tr("core.scoring.rna.RNA_AtomVDW");

namespace core {
namespace scoring {
namespace rna {

Size
rna_residue_name_to_num( char const c )
{
  if ( c == 'a') return 1;
  if ( c == 'c') return 2;
  if ( c == 'g') return 3;
  if ( c == 'u') return 4;
  if ( c == 'Z') return 5; // Mg(2+)
  tr << "What is this? " << c << std::endl;
  utility_exit_with_message( "Asked for rna_residue_name_to_num for unknown residue_name" );
  return 0;
}

//Why doesn't this helper function already exist in vector class?
Size
get_position_in_vector( utility::vector1< std::string> & vec, std::string const element )
{
  Size count( 1 );
  for ( utility::vector1<std::string>::iterator iter = vec.begin(); iter < vec.end(); iter++ )  {
    if (*iter == element) return count;
    count++;
  }
  vec.push_back( element );
  return count;
}


/// @details ctor, reads data file. Need to configure to allow alternate tables/atom_sets
RNA_AtomVDW::RNA_AtomVDW()
{
  //Read in data file, and fill in private data.
  utility::io::izstream stream;
  basic::database::open( stream, "chemical/rna/rna_atom_vdw.txt" );

  rna_vdw_parameter_.dimension( 9, 9, 5, 5 );  // 5 = a,c,g,u,Z (Mg2+)
  rna_vdw_parameter_ = 0.0; // zero everything out.

  if ( !stream.good() ) utility_exit_with_message( "Unable to open rna_scoring/AtomVDW/atom_vdw.txt!" );

  // read the entire file and figure out what atom_types are present and in what order
  utility::vector1< std::string > lines;

  std::string line;
  std::string atom_name1, atom_name2;
  char which_residue1, which_residue2;
  Real input_bump_parameter;
  while ( getline( stream, line ) ) {
    lines.push_back(line);
    std::istringstream l(line);
    l >> which_residue1 >> which_residue2 >> atom_name1 >> atom_name2 >> input_bump_parameter;

    Size const pos1 = get_position_in_vector( rna_vdw_atom_[which_residue1], atom_name1 );
    Size const pos2 = get_position_in_vector( rna_vdw_atom_[which_residue2], atom_name2 );

    runtime_assert( pos1 <= rna_vdw_parameter_.size1() );
    runtime_assert( pos1 <= rna_vdw_parameter_.size2() );

    rna_vdw_parameter_( pos1,
                        pos2,
                        rna_residue_name_to_num( which_residue1 ),
                        rna_residue_name_to_num( which_residue2 ) ) = input_bump_parameter;
    //perhaps we should explicitly force symmetry here?

  }

  //  for ( Size i = 1; i <= 9; i++ ) {
  //    for ( Size j = 1; j <= 9; j++ ) {
  //      for ( Size m = 1; m <= 5; m++ ) {
  //        for ( Size n = 1; n <= 5; n++ ) {
          //          std::cout << "BUMP PARAM: " << i << " " << j << " " << m << " " << n << " " << rna_vdw_parameter_( i, j, m, n ) << std::endl;
  //        }
  //      }
  //    }
  //  }

}

//////////////////////////////////////////////
utility::vector1 < std::string > const
RNA_AtomVDW::vdw_atom_list( char const which_nucleotide ) const
{
  AtomList::const_iterator iter = rna_vdw_atom_.find( which_nucleotide );

  if ( iter == rna_vdw_atom_.end() ) {
    tr << "WARNING! Asked for vdw_atom_list for " << which_nucleotide << " and it did not exist! " << std::endl;
    utility::vector1< std::string > blank_vector;
    return blank_vector;
  }

  return (iter->second);
}

Real
RNA_AtomVDW::bump_parameter( Size const atom1, Size const atom2,
                             char const which_residue1, char const which_residue2 ) const
{
  return rna_vdw_parameter_( atom1, atom2,
                             rna_residue_name_to_num( which_residue1 ),
                             rna_residue_name_to_num( which_residue2 ) );
}



} // namespace rna
} // namespace scoring
} // namespace core