UpstreamResTypeGeometry.cc

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//
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/// @file   protocols/match/upstream/ProteinUpstreamBuilder.cc
/// @brief
/// @author Alex Zanghellini (zanghell@u.washington.edu)
/// @author Andrew Leaver-Fay (aleaverfay@gmail.com), porting to mini

// Unit headers
#include <protocols/match/upstream/UpstreamResTypeGeometry.hh>

// Package headers
// AUTO-REMOVED #include <protocols/match/upstream/OriginalScaffoldBuildPoint.hh>

// Project headers
#include <core/chemical/ResidueType.hh>
#include <core/chemical/Atom.hh>

// Utility headers
#include <utility/exit.hh>
// AUTO-REMOVED #include <utility/string_util.hh>

#include <utility/vector1.hh>


namespace protocols {
namespace match {
namespace upstream {

/// @details Auto-generated virtual destructor
UpstreamResTypeGeometry::~UpstreamResTypeGeometry() {}


UpstreamResTypeGeometry::UpstreamResTypeGeometry() :
  restype_name_( "UNINITIALIZED" ),
  N_atom_id_( 0 ),
  CA_atom_id_( 0 ),
  C_atom_id_( 0 ),
  O_atom_id_( 0 ),
  CB_atom_id_( 0 ),
  H_atom_id_( 0 ),
  HA_atom_id_( 0 )
{}

UpstreamResTypeGeometry::UpstreamResTypeGeometry( core::chemical::ResidueType const & res ) :
  restype_name_( res.name() ),
  N_atom_id_( 0 ),
  CA_atom_id_( 0 ),
  C_atom_id_( 0 ),
  O_atom_id_( 0 ),
  CB_atom_id_( 0 ),
  H_atom_id_( 0 ),
  HA_atom_id_( 0 )
{
  initialize_from_residue_type( res );
}

void
UpstreamResTypeGeometry::initialize_from_residue_type(
  core::chemical::ResidueType const & res
)
{
  if ( restype_name_ != res.name() ) {
    restype_name_ = res.name();
  }

  /// 1. Resize arrays that depend on the number of atoms
  Size const n_atoms = res.natoms();

  controlling_chi_for_atom_ =  res.last_controlling_chi();
  which_point_for_atom_.resize( n_atoms );
  std::fill( which_point_for_atom_.begin(), which_point_for_atom_.end(), 0 );
  restype_atom_id_2_nonchi_atom_id_.resize( n_atoms );
  std::fill( restype_atom_id_2_nonchi_atom_id_.begin(), restype_atom_id_2_nonchi_atom_id_.end(), 0 );
  nonchi_atom_id_2_restype_atom_id_.resize( 0 );
  nonchi_atoms_in_ideal_frame_.resize( 0 );

  /// 2. Resize arrays that depend on the number of chi
  Size const n_chi = res.nchi();

  chitip_atoms_.resize( n_chi );
  std::fill( chitip_atoms_.begin(), chitip_atoms_.end(), 0 );

  ht_for_chitip_atoms_.resize( n_chi );
  for ( Size ii = 1; ii <= n_chi; ++ii ) ht_for_chitip_atoms_[ ii ].set_identity();

  nonchitip_atoms_.resize( res.nchi() );
  for ( Size ii = 1; ii <= n_chi; ++ii ) nonchitip_atoms_[ ii ].clear();

  points_for_nonchitip_atoms_.resize( res.nchi() );
  for ( Size ii = 1; ii <= n_chi; ++ii ) points_for_nonchitip_atoms_[ ii ].clear();

  /// Quick atom indexing

  N_atom_id_  = ( res.has( "N"  ) ? res.atom_index("N")  : 0 );
  CA_atom_id_ = ( res.has( "CA" ) ? res.atom_index("CA") : 0 );
  C_atom_id_  = ( res.has( "C"  ) ? res.atom_index("C")  : 0 );
  O_atom_id_  = ( res.has( "O"  ) ? res.atom_index("O")  : 0 );
  CB_atom_id_ = ( res.has( "CB" ) ? res.atom_index("CB") : 0 );
  H_atom_id_  = ( res.has( "H"  ) ? res.atom_index("H")  : 0 );
  HA_atom_id_ = ( res.has( "HA" ) ? res.atom_index("HA") : 0 );

  if ( HA_atom_id_ == 0 && res.aa() == core::chemical::aa_gly ) {
    HA_atom_id_ = ( res.has( "2HA" ) ? res.atom_index( "2HA" ) : 0 );
  }

  if ( N_atom_id_ != 0 && CA_atom_id_ != 0 && C_atom_id_ != 0 ) {

    Vector halfpoint = 0.5 * ( res.atom( N_atom_id_ ).ideal_xyz() + res.atom( C_atom_id_ ).ideal_xyz() );
    HTReal ideal_frame( res.atom( N_atom_id_ ).ideal_xyz(), halfpoint, res.atom( CA_atom_id_ ).ideal_xyz() );

    /// backbone atoms, besides the cannonical 3
    for ( Size ii = 1; ii <= n_atoms; ++ii ) {
      if ( ii == N_atom_id_ || ii == CA_atom_id_ || ii == C_atom_id_ ) continue;
      if ( res.last_controlling_chi( ii ) != 0 ) continue;
      nonchi_atoms_in_ideal_frame_.push_back( ideal_frame.to_local_coordinate( res.atom( ii ).ideal_xyz() ));
      nonchi_atom_id_2_restype_atom_id_.push_back( ii );
      restype_atom_id_2_nonchi_atom_id_[ ii ] = nonchi_atoms_in_ideal_frame_.size();
    }
  }


  if ( nchi() == 0 ) return; // match from gly? can't see why you'd want to!


  for ( Size ii = 1; ii <= n_chi; ++ii ) {
    assert( res.chi_atoms( ii ).size() == 4 );

    Size const
      chiat2( res.chi_atoms( ii )[ 2 ] ),
      chiat3( res.chi_atoms( ii )[ 3 ] ),
      chiat4( res.chi_atoms( ii )[ 4 ] );

    chitip_atoms_[ ii ] = chiat4;


    ht_for_chitip_atoms_[ ii ].set_xaxis_rotation_rad( -1 * res.icoor( chiat4 ).theta() );
    ht_for_chitip_atoms_[ ii ].walk_along_z( res.icoor( chiat4 ).d() );

    HTReal chi_tip_frame(
      res.atom( chiat2 ).ideal_xyz(),
      res.atom( chiat3 ).ideal_xyz(),
      res.atom( chiat4 ).ideal_xyz() );

    Size const n_nontip_ats_for_chi = res.atoms_last_controlled_by_chi( ii ).size() - 1;

    nonchitip_atoms_[ ii ].reserve( n_nontip_ats_for_chi );
    points_for_nonchitip_atoms_[ ii ].reserve( n_nontip_ats_for_chi );

    for ( Size jj = 1; jj <= res.atoms_last_controlled_by_chi( ii ).size(); ++jj ) {
      Size const jjatom = res.atoms_last_controlled_by_chi( ii )[ jj ];
      if ( jjatom == chiat4 ) continue;

      Vector jjloc_in_chitip_frame = chi_tip_frame.to_local_coordinate( res.atom( jjatom ).ideal_xyz() );
      nonchitip_atoms_[ ii ].push_back( jjatom );
      points_for_nonchitip_atoms_[ ii ].push_back( jjloc_in_chitip_frame );
      which_point_for_atom_[ jjatom ] = points_for_nonchitip_atoms_[ ii ].size();
    }
  }

}

bool
UpstreamResTypeGeometry::atom_has_nonchi_coordinate( Size restype_atomid ) const
{
  return restype_atom_id_2_nonchi_atom_id_[ restype_atomid ] != 0;
}

UpstreamResTypeGeometry::Vector const &
UpstreamResTypeGeometry::coordinate_for_nonchi_atom_in_ideal_frame( Size restype_atomid ) const
{
  runtime_assert( restype_atom_id_2_nonchi_atom_id_[ restype_atomid ] != 0 );
  return nonchi_atoms_in_ideal_frame_[ restype_atom_id_2_nonchi_atom_id_[ restype_atomid ] ];
}


}
}
}