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

// Unit Headers
#include <protocols/simple_moves/oop/OopMover.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>
// 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 basic::Tracer TR( "protocols.simple_moves.oop.OopMover" );


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

namespace protocols {
namespace simple_moves {
namespace oop {

/*
kdrew: the helper function moves a single oop with the given move
pose: pose to make change to
oop_pre_pos: position of first residue of oop to make change to
phi_angle: value to change phi angle to
psi_angle: value to change psi angle to
*/
void OopMover::apply( core::pose::Pose & pose )
{
  using numeric::conversions::radians;
  using numeric::conversions::degrees;

  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 );

  //kdrew: first residue is a special case, no phi torsion
  if( pose.residue_type( oop_pre_pos_ ).is_lower_terminus() )
  {
    //kdrew: no phi angle, adjust CYP-N-Ca-C torsion
    Real offset = 180 + phi_angle_ ;

    AtomID aidCYP( pose.residue(oop_pre_pos_).atom_index("CYP"), oop_pre_pos_ );
    AtomID aidN( pose.residue(oop_pre_pos_).atom_index("N"), oop_pre_pos_ );
    AtomID aidCA( pose.residue(oop_pre_pos_).atom_index("CA"), oop_pre_pos_ );
    AtomID aidC( pose.residue(oop_pre_pos_).atom_index("C"), oop_pre_pos_ );

    pose.conformation().set_torsion_angle( aidCYP, aidN, aidCA, aidC, radians( offset ) ); 
  }


  TR << "current oop_pre ("<< oop_pre_pos_<< ") PHI: " << pose.phi(oop_pre_pos_) << std::endl;
  pose.set_phi(oop_pre_pos_, phi_angle_);
  TR << "new oop_pre ("<< oop_pre_pos_<< ") PHI: " << pose.phi(oop_pre_pos_) << std::endl;
  //pose.dump_pdb( "rosetta_out_oop_pre.pdb" );
  TR << "current oop_pre ("<< oop_pre_pos_<< ") PSI: " << pose.psi(oop_pre_pos_) << std::endl;
  pose.set_psi(oop_pre_pos_, psi_angle_);
  TR << "new oop_pre ("<< oop_pre_pos_<< ") PSI: " << pose.psi(oop_pre_pos_) << std::endl;
  //pose.dump_pdb( "rosetta_out_oop_pre_pos_t.pdb" );

  update_hydrogens_( pose );

}

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

///@brief
OopMover::OopMover( 
    core::Size oop_seq_position 
  ): Mover(), oop_pre_pos_(oop_seq_position), oop_post_pos_(oop_seq_position+1)
{
  Mover::type( "OopMover" );
}

OopMover::OopMover( 
    core::Size oop_seq_position, 
    core::Real phi_angle,
    core::Real psi_angle
  ): Mover(), oop_pre_pos_(oop_seq_position), oop_post_pos_(oop_seq_position+1), phi_angle_(phi_angle), psi_angle_(psi_angle)
{
  Mover::type( "OopMover" );

}

OopMover::~OopMover(){}

void OopMover::update_hydrogens_( core::pose::Pose & pose )
{
  using numeric::conversions::radians;
  using numeric::conversions::degrees;

  AtomID aidVZP( pose.residue(oop_pre_pos_).atom_index("VZP"), oop_pre_pos_);
  AtomID aidCYP( pose.residue(oop_pre_pos_).atom_index("CYP"), oop_pre_pos_);
  AtomID aidN( pose.residue(oop_pre_pos_).atom_index("N"), oop_pre_pos_);
  AtomID aidCA( pose.residue(oop_pre_pos_).atom_index("CA"), oop_pre_pos_);
  AtomID aid1HYP( pose.residue(oop_pre_pos_).atom_index("1HYP"), oop_pre_pos_);
  AtomID aidVYP( pose.residue(oop_post_pos_).atom_index("VYP"), oop_post_pos_);
  AtomID aidCZP( pose.residue(oop_post_pos_).atom_index("CZP"), oop_post_pos_);
  AtomID aidN_Z( pose.residue(oop_post_pos_).atom_index("N"), oop_post_pos_);
  AtomID aidCA_Z( pose.residue(oop_post_pos_).atom_index("CA"), oop_post_pos_);
  AtomID aid1HZP( pose.residue(oop_post_pos_).atom_index("1HZP"), oop_post_pos_);

  //kdrew: definitions for xyz coordinates 
  Vector const& CA_xyz ( pose.residue(oop_pre_pos_).xyz("CA") );
  Vector const& N_xyz ( pose.residue(oop_pre_pos_).xyz("N") );
  Vector const& CYP_xyz ( pose.residue(oop_pre_pos_).xyz("CYP") );
  Vector const& CAZ_xyz ( pose.residue(oop_post_pos_).xyz("CA") );
  Vector const& NZ_xyz ( pose.residue(oop_post_pos_).xyz("N") );
  Vector const& CZP_xyz ( pose.residue(oop_post_pos_).xyz("CZP") );


  //kdrew: VZP and VYP are relative to the 1Hs, so move the 1Hs and VZP|VYP and 2H moves with it
  //kdrew: calculate the difference between the virtual atom VZP torsion and the torsion involving the real CZP atom (on the post residue)
  Real VZP_torsion_correction = numeric::dihedral_degrees( CZP_xyz, CYP_xyz, N_xyz, CA_xyz ) - degrees( pose.conformation().torsion_angle( aidVZP, aidCYP, aidN, aidCA ) );
  //kdrew: change the 1HYP torsion by the corrected amount
  Real torsion_1HYP = degrees(pose.conformation().torsion_angle(aid1HYP,aidCYP,aidN,aidCA)) + VZP_torsion_correction;
  pose.conformation().set_torsion_angle(aid1HYP,aidCYP,aidN,aidCA,radians(torsion_1HYP)); 
  //pose.dump_pdb( "rosetta_out_oop_pre_mvH.pdb" );

  //kdrew: calculate the difference between the virtual atom VYP torsion and the torsion involving the real CYP atom (on the pre residue)
  Real VYP_torsion_correction = numeric::dihedral_degrees( CYP_xyz, CZP_xyz, NZ_xyz, CAZ_xyz ) - degrees( pose.conformation().torsion_angle( aidVYP, aidCZP, aidN_Z, aidCA_Z ));
  //kdrew: change the 1HZP torsion by the corrected amount
  Real torsion_1HZP = degrees(pose.conformation().torsion_angle(aid1HZP,aidCZP,aidN_Z,aidCA_Z)) + VYP_torsion_correction;
  pose.conformation().set_torsion_angle(aid1HZP,aidCZP,aidN_Z,aidCA_Z,radians(torsion_1HZP)); 
  //pose.dump_pdb( "rosetta_out_oop_pre_pos_t_mvH.pdb" );

  //kdrew: possibly minimize pose here

  //kdrew: debug printing
  //kdrew: VZP CYP N CA
  TR<<"VZP-CYP-N-CA: "<< degrees(pose.conformation().torsion_angle(aidVZP,aidCYP,aidN,aidCA)) <<std::endl; 
  //kdrew: CZP CYP N CA
  TR<<"CZP-CYP-N-CA: "<< numeric::dihedral_degrees(CZP_xyz,CYP_xyz,N_xyz,CA_xyz) <<std::endl; 
  //kdrew: 1HYP CYP N CA
  TR<<"1HYP-CYP-N-CA: "<< degrees(pose.conformation().torsion_angle(aid1HYP,aidCYP,aidN,aidCA)) <<std::endl; 

  //kdrew: VYP CZP N_Z CA_Z
  TR<<"VYP-CZP-N-CA: "<< degrees(pose.conformation().torsion_angle(aidVYP,aidCZP,aidN_Z,aidCA_Z)) << std::endl; 
  //kdrew: CYP CZP N_Z CA_Z
  TR<<"CYP-CZP-N-CA: "<< numeric::dihedral_degrees(CYP_xyz,CZP_xyz,NZ_xyz,CAZ_xyz) <<std::endl; 
  //kdrew: 1HZP CZP N_Z CA_Z
  TR<<"1HZP-CZP-N-CA: "<< degrees(pose.conformation().torsion_angle(aid1HZP,aidCZP,aidN_Z,aidCA_Z)) << std::endl; 

}

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