RNA_SWA_MonteCarloUtil.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 RNA_DeleteMover
/// @brief Torsions an RNA residue from a chain terminus.
/// @detailed
/// @author Rhiju Das

#include <protocols/swa/monte_carlo/RNA_SWA_MonteCarloUtil.hh>
#include <protocols/swa/monte_carlo/types.hh>
#include <protocols/swa/monte_carlo/SubToFullInfo.hh>

// libRosetta headers
#include <core/types.hh>
#include <core/chemical/VariantType.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>

#include <protocols/moves/MonteCarlo.hh>

#include <basic/Tracer.hh>

#include <map>

#include <numeric/random/random.hh>

static numeric::random::RandomGenerator RG(239111);  // <- Magic number, do not change it!

using namespace core;
using core::Real;

namespace protocols {
namespace swa {
namespace monte_carlo {

  //////////////////////////////////////////////////////////////////////////////////////////////////////////////////
  MovingResidueCase
  get_moving_residue_case( pose::Pose const & pose, Size const i ) {

    MovingResidueCase moving_residue_case( NO_CASE );

    Size const & nres( pose.total_residue() );
    kinematics::FoldTree const & fold_tree( pose.fold_tree() );
    if ( i == nres || fold_tree.is_cutpoint( i ) ){ // could be a 5' chain terminus
      if ( i == 1 || fold_tree.is_cutpoint( i-1 ) ){
        moving_residue_case = FLOATING_BASE; // don't know how to handle this yet.
      } else {
        moving_residue_case = CHAIN_TERMINUS_3PRIME;
      }
    } else if ( i == 1 || fold_tree.is_cutpoint( i-1 ) ){
      moving_residue_case = CHAIN_TERMINUS_5PRIME;
    } else {
      moving_residue_case = INTERNAL;
    }

    return moving_residue_case;
  }



  //////////////////////////////////////////////////////////////////////////////////////////////////////////////////
  void
  get_potential_delete_residues( pose::Pose & pose,
                                 utility::vector1< Size > & possible_res,
                                 utility::vector1< MovingResidueCase > & moving_residue_cases,
                                 utility::vector1< AddOrDeleteChoice > & add_or_delete_choices ) {


    Size const & nres( pose.total_residue() );
    kinematics::FoldTree const & fold_tree( pose.fold_tree() );

    SubToFullInfo & sub_to_full_info = nonconst_sub_to_full_info_from_pose( pose );
    utility::vector1< Size > const & moving_res_list = sub_to_full_info.moving_res_list();

    for ( Size n = 1; n <= moving_res_list.size(); n++ ){

      Size const i = moving_res_list[ n ];

      if ( i == nres || fold_tree.is_cutpoint( i ) ){ // could be a 3' chain terminus

        possible_res.push_back( i );
        moving_residue_cases.push_back( CHAIN_TERMINUS_3PRIME );
        add_or_delete_choices.push_back( DELETE );

      } else if ( i == 1 || fold_tree.is_cutpoint( i-1 ) ) {

        possible_res.push_back( i );
        moving_residue_cases.push_back( CHAIN_TERMINUS_5PRIME );
        add_or_delete_choices.push_back( DELETE );

      }


    }

  }

  //////////////////////////////////////////////////////////////////////////////////////////////////////////////////
  void
  get_potential_add_residues( pose::Pose & pose,
                              utility::vector1< Size > & possible_res,
                              utility::vector1< MovingResidueCase > & moving_residue_cases,
                              utility::vector1< AddOrDeleteChoice > & add_or_delete_choices ) {

    Size const & nres( pose.total_residue() );
    kinematics::FoldTree const & fold_tree( pose.fold_tree() );

    SubToFullInfo & sub_to_full_info = nonconst_sub_to_full_info_from_pose( pose );
    std::map< Size, Size > sub_to_full = sub_to_full_info.sub_to_full();
    utility::vector1< Size > cutpoints_in_full_pose = sub_to_full_info.cutpoints_in_full_pose();
    Size nres_full = sub_to_full_info.full_sequence().size();

    utility::vector1< bool > is_cutpoint_in_full_pose;
    for ( Size i = 1; i <= nres_full; i++ ) is_cutpoint_in_full_pose.push_back( false );
    for ( Size n = 1; n <= cutpoints_in_full_pose.size(); n++ ) is_cutpoint_in_full_pose[ cutpoints_in_full_pose[n] ] = true;

    for ( Size i = 1; i <= nres; i++ ){

      if ( ( i == nres ) ||
           ( fold_tree.is_cutpoint( i ) && (sub_to_full[ i ]+1 < sub_to_full[ i+1 ]) ) ) { // could be a 3' chain terminus

        Size const i_full = sub_to_full[ i ] ;
        if ( !is_cutpoint_in_full_pose[ i_full ] && i_full < nres_full ){ // good, there's still a gap!

          possible_res.push_back( i );
          moving_residue_cases.push_back( CHAIN_TERMINUS_3PRIME );
          add_or_delete_choices.push_back( ADD );

        }
      }
    }

    for ( Size i = 1; i <= nres; i++ ){

      if ( ( i == 1 ) ||
           ( fold_tree.is_cutpoint( i-1 ) && (sub_to_full[ i ]-1 > sub_to_full[ i-1 ]) ) ) { // could be a 5' chain terminus

        Size const i_full = sub_to_full[ i ];
        if ( i_full > 1 && !is_cutpoint_in_full_pose[ i_full-1 ] ) { // good, there's still a gap!

          possible_res.push_back( i );
          moving_residue_cases.push_back( CHAIN_TERMINUS_5PRIME );
          add_or_delete_choices.push_back( ADD );
        }
      }
    }

  }

  //////////////////////////////////////////////////////////////////////////////////////////////////////////////////
  void
  get_random_residue_at_chain_terminus( pose::Pose & pose,
                                        Size & residue_at_chain_terminus,
                                        MovingResidueCase & moving_residue_case,
                                        AddOrDeleteChoice & add_or_delete_choice,
                                        bool const disallow_delete ) {


    utility::vector1< Size >  possible_res;
    utility::vector1< MovingResidueCase > moving_residue_cases;
    utility::vector1< AddOrDeleteChoice > add_or_delete_choices;

    if ( !disallow_delete ){
      get_potential_delete_residues( pose,  possible_res, moving_residue_cases, add_or_delete_choices );
    }

    get_potential_add_residues( pose, possible_res, moving_residue_cases, add_or_delete_choices );

    Size const res_idx =  int( RG.uniform() * possible_res.size() ) + 1;

    residue_at_chain_terminus = possible_res[ res_idx ];
    moving_residue_case       = moving_residue_cases[ res_idx ];
    add_or_delete_choice      = add_or_delete_choices[ res_idx ];

  }


}
}
}