OopRandomSmallMover.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:
//
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/// @file protocols/simple_moves/oop/OopRandomSmallMover.cc
/// @brief OopRandomSmallMover methods implemented
/// @author Kevin Drew, kdrew@nyu.edu

// Unit Headers
#include <protocols/simple_moves/oop/OopRandomSmallMover.fwd.hh>
#include <protocols/simple_moves/oop/OopRandomSmallMover.hh>
#include <protocols/simple_moves/oop/OopMover.hh>
#include <protocols/simple_moves/oop/OopPatcher.hh>
// Package Headers

// Project Headers
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/VariantType.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/util.hh>
#include <core/pose/Pose.hh>
#include <core/id/AtomID.hh>
// Random number generator
#include <numeric/random/random.hh>
// Utility Headers
#include <numeric/xyz.functions.hh>
#include <basic/Tracer.hh>
#include <basic/basic.hh>
#include <core/types.hh>

// C++ Headers

using basic::T;
using basic::Error;
using basic::Warning;

static numeric::random::RandomGenerator RG(956734);
static basic::Tracer TR( "protocols.simple_moves.oop.OopRandomSmallMover" );


using namespace core;
using namespace conformation;
using namespace chemical;
using namespace core::id;

namespace protocols {
namespace simple_moves {
namespace oop {

///@details
void OopRandomSmallMover::apply( core::pose::Pose & pose ){

  using numeric::conversions::radians;
  using numeric::conversions::degrees;
  
  TR<< "in OopRandomSmallMover::apply" << std::endl;
  //kdrew: for all positions in oop_seq_positions_, input assertion check
  for(Size i = 1; i <= oop_seq_positions_.size(); i++)
  {
    Size oop_pre_pos = oop_seq_positions_[i];
    Size oop_post_pos = oop_pre_pos+1;                   
    TR<< "oop_pre_pos:" << oop_pre_pos << " oop_post_pos:" << oop_post_pos << std::endl;

    runtime_assert ( pose.residue(oop_pre_pos).has_variant_type(chemical::OOP_PRE) == 1) ;
    runtime_assert ( pose.residue(oop_post_pos).has_variant_type(chemical::OOP_POST) == 1) ;
    //kdrew: an oop pre position cannot be last position
    runtime_assert ( oop_pre_pos != pose.total_residue() );
    //kdrew: an oop post position cannot be first position
    runtime_assert ( oop_post_pos != 1 );

  }//for


  //kdrew: randomly choose position from oop_seq_positions
  core::Size random_pos = oop_seq_positions_[int(RG.uniform()*oop_seq_positions_.size())+1];

  oop::OopMoverOP oop_mover ( new oop::OopMover( random_pos ) );
  Real small_angle = max_small_angle_/2.0; ///< this is max_angle/2, which is the deviation from the angle input
  Real phi_angle = basic::periodic_range( pose.phi( random_pos ) - small_angle + RG.uniform() * max_small_angle_, 360.0 );
  //kdrew: no phi angle for n-terms, angle that gets changed is CYP-N-Ca-C
  if( pose.residue_type( random_pos ).is_lower_terminus() )
  { 
    AtomID aidCYP( pose.residue(random_pos).atom_index("CYP"), random_pos );
    AtomID aidN( pose.residue(random_pos).atom_index("N"), random_pos );
    AtomID aidCA( pose.residue(random_pos).atom_index("CA"), random_pos );
    AtomID aidC( pose.residue(random_pos).atom_index("C"), random_pos );

    Real CYP_N_Ca_C_angle = degrees( pose.conformation().torsion_angle( aidCYP, aidN, aidCA, aidC ) ); 
        phi_angle = basic::periodic_range( CYP_N_Ca_C_angle - small_angle + RG.uniform() * max_small_angle_, 360.0 ) - 180.0; 
  }

  Real psi_angle = basic::periodic_range( pose.psi( random_pos ) - small_angle + RG.uniform() * max_small_angle_, 360.0 );
  oop_mover->set_phi( phi_angle );
  oop_mover->set_psi( psi_angle );
  oop_mover->apply( pose );
  //oop_puck_mover_helper( pose, random_pos, phi_angle, psi_angle );

}//apply

std::string
OopRandomSmallMover::get_name() const {
  return "OopRandomSmallMover";
}

///@brief
OopRandomSmallMover::OopRandomSmallMover(
) : Mover()
{
  Mover::type( "OopRandomSmallMover" );
}

OopRandomSmallMover::OopRandomSmallMover( utility::vector1< core::Size > oop_seq_positions ): Mover(), oop_seq_positions_(oop_seq_positions), max_small_angle_(0.0)
{
  Mover::type( "OopRandomSmallMover" );
}

OopRandomSmallMover::OopRandomSmallMover( utility::vector1< core::Size > oop_seq_positions, core::Real max_small_angle ): Mover(), oop_seq_positions_(oop_seq_positions), max_small_angle_( max_small_angle )
{
  Mover::type( "OopRandomSmallMover" );
}

OopRandomSmallMover::~OopRandomSmallMover(){}


}//oop
}//simple_moves
}//protocols