BB_Pos.cc

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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/// @file ./src/protocols/fldsgn/topology/BB_Pos.cc
/// @brief
/// @author Andrew Leaver-Fay (leaverfa@email.unc.edu), Nobuyasu Koga ( nobuyasu@u.washington.edu )

/// Unit headers
#include <protocols/fldsgn/topology/BB_Pos.hh>

/// Package headers
#include <core/conformation/Residue.hh>
#include <core/pose/Pose.hh>

#include <utility/vector1.hh>


namespace protocols {
namespace fldsgn {
namespace topology {

/// @details.  After a change in size, the residue types and the integer indices are all wrong.
/// Erase the old information.
void
BB_Pos::resize( Size const nres )
{
  if ( N_.size() == (Size) nres ) return;

  N_.resize( nres );
  CA_.resize( nres );
  C_.resize( nres );
  O_.resize( nres );
  CB_.resize( nres );

  residue_types_.resize( nres ); std::fill( residue_types_.begin(), residue_types_.end(), static_cast< core::chemical::ResidueType const * > (0) );
  N_index_.resize( nres );       std::fill( N_index_.begin(), N_index_.end(), 0 );
  CA_index_.resize( nres );      std::fill( CA_index_.begin(), CA_index_.end(), 0 );
  CB_index_.resize( nres );      std::fill( CB_index_.begin(), CB_index_.end(), 0 );
  C_index_.resize( nres );       std::fill( C_index_.begin(), C_index_.end(), 0 );
  O_index_.resize( nres );       std::fill( O_index_.begin(), O_index_.end(), 0 );

}

/// @details.  After a change in size, the residue types and the integer indices are all wrong.
/// Erase the old information.
void
BB_Pos::clear()
{
  N_.clear();
  CA_.clear();
  C_.clear();
  O_.clear();
  CB_.clear();
  residue_types_.clear();
  N_index_.clear();
  CA_index_.clear();
  CB_index_.clear();
  C_index_.clear();
  O_index_.clear();
}

/// @details: Optimize the common case where the sequence of the pose is not changing from
/// score function evaluation to evaluation (e.g. abinitio!)
void
BB_Pos::take_coordinates_from_pose( Pose const & pose )
{
  if ( ! bbindices_up_to_date( pose ) ) {
    update_indices( pose );
  }

  for ( Size i=1; i<= pose.total_residue(); ++i ) {
    core::conformation::Residue const & rsd( pose.residue(i) );
    if ( rsd.is_protein() ) {
      assert( N_index_[ i ]  );
      assert( CA_index_[ i ] );
      assert( C_index_[ i ]  );
      assert( O_index_[ i ]  );

      N_ [i] = rsd.xyz( N_index_[ i ]  );
      CA_[i] = rsd.xyz( CA_index_[ i ] );
      C_ [i] = rsd.xyz( C_index_[ i ]  );
      O_ [i] = rsd.xyz( O_index_[ i ]  );
      if ( rsd.aa() == core::chemical::aa_gly ) {
        CB_[i] = 0.0;
      } else {
        CB_[i] = rsd.xyz( CB_index_[ i ] );
      }
    } else {
      N_ [i] = 0.0;
      CA_[i] = 0.0;
      C_ [i] = 0.0;
      O_ [i] = 0.0;
      CB_[i] = 0.0;
    }
  }

}

bool
BB_Pos::bbindices_up_to_date( Pose const & pose ) const
{
  if ( N_.size() != pose.total_residue() ) return false;

  for ( Size ii = 1; ii <= pose.total_residue(); ++ii ) {
    if ( residue_types_[ ii ] != & ( pose.residue_type( ii ) ) ) return false;
  }
  return true;
}

void
BB_Pos::update_indices( Pose const & pose )
{
  resize( pose.total_residue() );

  static std::string const bbN("N");
  static std::string const bbCA("CA");
  static std::string const bbC("C");
  static std::string const bbO("O");
  static std::string const scCB("CB");

  for ( Size i = 1; i <= pose.total_residue(); ++i ) {
    core::conformation::Residue const & rsd( pose.residue(i) );
    residue_types_[ i ] = & ( rsd.type() );
    if ( rsd.is_protein() ) {

      N_index_[  i ] = rsd.atom_index( bbN );
      CA_index_[ i ] = rsd.atom_index( bbCA );
      C_index_[  i ] = rsd.atom_index( bbC );
      O_index_[  i ] = rsd.atom_index( bbO );

      if ( rsd.aa() == core::chemical::aa_gly ) {
        CB_index_[ i ] = 0;
      } else {
        CB_index_[ i ] = rsd.atom_index( scCB );
      }
    } else {
      N_index_[  i ] = 0;
      CA_index_[ i ] = 0;
      C_index_[  i ] = 0;
      O_index_[  i ] = 0;
      CB_index_[ i ] = 0;
    }
  }

}


} // ns topology
} // ns fldsgn
} // ns protocols