StepWiseRNA_Base_Sugar_Rotamer.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 StepWiseRNA_Base_Sugar_Rotamer
/// @brief Parameters to be passed between different modules of stepwise RNA building.
/// @detailed
/// @author Parin Sripakdeevong


//////////////////////////////////
#include <protocols/swa/rna/StepWiseRNA_Base_Sugar_Rotamer.hh>
#include <core/id/TorsionID.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/rna/RNA_FittedTorsionInfo.hh>
#include <core/scoring/rna/RNA_Util.hh>
#include <basic/Tracer.hh>

#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <numeric/angle.functions.hh> 

#include <string>

using namespace core;
using core::Real;
using ObjexxFCL::fmt::F;

static basic::Tracer TR( "protocols.swa.rna.stepwise_rna_base_sugar_rotamer" );

namespace protocols {
namespace swa {
namespace rna {

  //////////////////////////////////////////////////////////////////////////////////////////
  // Constructor
  StepWiseRNA_Base_Sugar_Rotamer::StepWiseRNA_Base_Sugar_Rotamer(
                      BaseState const & base_state, 
                      PuckerState const & pucker_state, 
                      core::scoring::rna::RNA_FittedTorsionInfo const & rna_fitted_torsion_info,
                      core::Size const bin_size): //This is to determine the bin value for chi
    base_state_(base_state),
    pucker_state_(pucker_state),
    rna_fitted_torsion_info_(rna_fitted_torsion_info),
    inputted_bin_size_( bin_size ), // must be 20, 10, or 5
    extra_anti_chi_(false), 
    extra_syn_chi_(false) 
  {
    reset();

//    num_base_std_ID_act_= (1 + 40/bin_size_) 


    base_state_list_.clear(); //April 30, 2011
    if(base_state_== BOTH){
      base_state_list_.push_back(ANTI); 
      base_state_list_.push_back(SYN); 
    }else if(base_state_== ANTI){
      base_state_list_.push_back(ANTI); 
    }else if(base_state == SYN){
      base_state_list_.push_back(SYN); 
    }else if(base_state == NONE){
      //std::cout << "BLAH: base_state == NONE" << std::endl;
    }else{
      utility_exit_with_message( "Invalid base_state_=" + ObjexxFCL::string_of(base_state_) );
    }

    //WARNING..DO NOT TRY TO INTRODUCE "NONE" value. pucker_state needs alway be defined even if not sampled, since EPSILON (in Rotamer Generator) depends on value of pucker_state! April 30, 2011
    pucker_state_list_.clear();
    if(pucker_state_ == ALL){
      pucker_state_list_.push_back(NORTH);
      pucker_state_list_.push_back(SOUTH);
    }else if(pucker_state_ == NORTH){
      pucker_state_list_.push_back(NORTH);
    }else if(pucker_state_ == SOUTH ){
      pucker_state_list_.push_back(SOUTH);
    }else{
      utility_exit_with_message( "Invalid pucker_state_=" + ObjexxFCL::string_of(pucker_state_) );
    }

  }

  //////////////////////////////////////////////////////////////////////////
  //destructor
  StepWiseRNA_Base_Sugar_Rotamer::~StepWiseRNA_Base_Sugar_Rotamer()
  {}

  //////////////////////////////////////////////////////////////////////////
  bool
  StepWiseRNA_Base_Sugar_Rotamer::get_next_rotamer(){

    if(pucker_ID_ > pucker_state_list_.size()) return false;

    //old_ID is always consistent the stored chi_/delta_ value
    pucker_ID_old_=pucker_ID_;
    base_ID_old_=base_ID_;
    base_std_ID_old_=base_std_ID_;

    PuckerState const & curr_pucker_state=current_pucker_state();


    Size base_center_ID=99;
    if(base_state_list_.size()!=0){
      if( ( extra_anti_chi_ && (base_state_list_[base_ID_]==ANTI) ) || ( extra_syn_chi_ && (base_state_list_[base_ID_]==SYN) ) ){ 
  //      total_variation_=60; //+-30 Aug_29 to Sept 15 2010 //Mod out on May 06, 2011
  //      total_variation_=100; //+-50 //testing on Sept 15 2010
  //      bin_size_= std::min(int(inputted_bin_size_), 10); // Aug_29 to Sept 15 2010 //Mod out on May 06, 2011

        total_variation_=120;
        bin_size_=inputted_bin_size_;       
        num_base_std_ID_= Size(1 + (total_variation_/bin_size_) ); //-40,-20,0,20,40
      }else{
        total_variation_=40;  //+-20
        bin_size_=inputted_bin_size_;
        num_base_std_ID_= Size(1 + (total_variation_/bin_size_) ); //-20,0,20
      }

      if(base_state_list_[base_ID_]==ANTI){
        base_center_ID=1;
      }else if(base_state_list_[base_ID_]==SYN){
        base_center_ID=2;
      }else{
        utility_exit_with_message( "Invalid current_base_state" + ObjexxFCL::string_of(base_state_list_[base_ID_] ) );
      }
    }

    if (curr_pucker_state == NORTH) {

      if(base_state_list_.size()!=0){
        chi_ = rna_fitted_torsion_info_.gaussian_parameter_set_chi_north()[ base_center_ID ].center + bin_size_*(base_std_ID_-1) - (total_variation_/2);
      }

      delta_ = rna_fitted_torsion_info_.ideal_delta_north();
      nu2_ = rna_fitted_torsion_info_.ideal_nu2_north();
      nu1_ = rna_fitted_torsion_info_.ideal_nu1_north();
    } else if(curr_pucker_state == SOUTH) {

      if(base_state_list_.size()!=0){
        chi_ = rna_fitted_torsion_info_.gaussian_parameter_set_chi_south()[ base_center_ID ].center + bin_size_*(base_std_ID_-1) - (total_variation_/2);
      }

      delta_ = rna_fitted_torsion_info_.ideal_delta_south(); //default
      nu2_ = rna_fitted_torsion_info_.ideal_nu2_south(); //default
      nu1_ = rna_fitted_torsion_info_.ideal_nu1_south(); //default

//      delta_ =rna_fitted_torsion_info_.gaussian_parameter_set_delta_south()[ 1 ].center;
//      nu2_ = rna_fitted_torsion_info_.gaussian_parameter_set_nu2_south()[ 1 ].center;
//      nu1_ = rna_fitted_torsion_info_.gaussian_parameter_set_nu1_south()[ 1 ].center;
//      nu2_ = -38.9; //2eew res A_19 torsion value
//      nu1_ = 161.8; //2eew res A_19 torsion value
//      delta_= 146.8; //1q9a res G_9 torsion value
//      nu2_ = -41.6; //1q9a res G_9 torsion value
//      nu1_ = 167.2; //1q9a res G_9 torsion value

    }else{
      utility_exit_with_message( "Invalid current_pucker_state!" + ObjexxFCL::string_of(curr_pucker_state) );
    }

    base_std_ID_++;

    if(base_state_list_.size()!=0){
      if(base_std_ID_ > num_base_std_ID_){
        base_std_ID_=1;
        base_ID_++;
      }
    }

    if(base_ID_ > base_state_list_.size()){
      base_ID_ = 1;
      pucker_ID_++;
    }

    return true;
  }

  //////////////////////////////////////////////////////////////////////////
  PuckerState const & 
  StepWiseRNA_Base_Sugar_Rotamer::current_pucker_state() const { 

//    std::cout << "pucker_ID_old_= " << pucker_ID_old_ << std::endl;   
//    std::cout << "pucker_state_list_.size()= " << pucker_state_list_.size() << std::endl;   

    PuckerState const & pucker_state=pucker_state_list_[pucker_ID_old_];

    if(pucker_state!=NORTH && pucker_state!=SOUTH) utility_exit_with_message( "pucker_state should equal NORTH or SOUTH!" );

    return pucker_state;
  }

  //////////////////////////////////////////////////////////////////////////

  std::string const 
  StepWiseRNA_Base_Sugar_Rotamer::current_base_state() const { 

    using namespace ObjexxFCL;
    
    Real const principal_chi=numeric::principal_angle_degrees(chi_);
    std::string base_state_string;

    if(base_state_list_.size()==0){
      base_state_string="ZZ";
    }else{

      if(principal_chi>0.0){
        if(base_state_list_[base_ID_old_]!=ANTI) utility_exit_with_message( "principal_chi>0 but base_state_list_(base_ID_old_)!=ANTI" );
        base_state_string="A"; //anti   
      }else{
        if(base_state_list_[base_ID_old_]!=SYN ) utility_exit_with_message( "principal_chi<=0 but base_state_list_(base_ID_old_)!=SYN" );
        base_state_string="S"; //syn  
      }

      base_state_string+=string_of(base_std_ID_old_);
    }

    return base_state_string;
  }

  //////////////////////////////////////////////////////////////////////////
  std::string const
  StepWiseRNA_Base_Sugar_Rotamer::current_tag() const { 

    std::string tag=current_base_state();

    if(current_pucker_state()==NORTH){
      tag+="N";
    }else if(current_pucker_state()==SOUTH){
      tag+="S";
    }else{
      utility_exit_with_message( "Invalid current_pucker_state!" );
    }

    return tag;

  }
  //////////////////////////////////////////////////////////////////////////
  void
  StepWiseRNA_Base_Sugar_Rotamer::reset() { 

    pucker_ID_=1;
    base_ID_=1;
    base_std_ID_=1;

    pucker_ID_old_=pucker_ID_;
    base_ID_old_=base_ID_;
    base_std_ID_old_=base_std_ID_;


    chi_=0.0;
    delta_=0.0;
    nu2_=0.0;
    nu1_=0.0;

  }

  //////////////////////////////////////////////////////////////////////////



}
}
}