Residue.functions.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   src/core/conformation/Residue.functions.cc
/// @brief  Implementation of non-member functions that operate on Residue objects
/// @author Andrew Leaver-Fay

// Unit headers
#include <core/conformation/Residue.functions.hh>

// Package headers
#include <core/conformation/Residue.hh>
// AUTO-REMOVED #include <core/conformation/Conformation.hh>

// Project headers
#include <core/chemical/AtomICoor.hh>
#include <core/types.hh>

#include <core/kinematics/Jump.hh>
#include <utility/vector1.hh>
#include <numeric/xyz.functions.hh>


namespace core {
namespace conformation {


void
idealize_hydrogens(
  Residue & res,
  Conformation const & conf
)
{
//  assert( res.seqpos() != -1 ); // commented out: seqpos is Size, so can number be negative
  utility::vector1< bool > atoms_placed( res.natoms(), false );
  for ( Size ii = 1; ii <= res.nheavyatoms(); ++ii ) atoms_placed[ ii ] = true;
  int n_remaining = res.natoms() - res.nheavyatoms();

  /// Some hydrogen atom locations are calculated as a function of
  /// other hydrogen atom locations.  2HB on phe depends on 1HB, e.g.
  /// There must be some hydrogen whose coordinates are determined
  /// entirely by heavy atoms.  Usually, this hydrogen appears first
  /// in a list of hydrogens, but this isn't guaranteed by the ResidueType
  /// atom ordering, so this function makes several passes over the set of
  /// hydrogens (at most 3 passes assuming we never work with methane)

  while ( n_remaining > 0 ) {
    Size n_placed_this_iteration = 0;
    for ( Size ii = res.nheavyatoms() + 1; ii <= res.natoms(); ++ii ) {
      bool all_stubs_placed = true;
      for ( Size jj = 1; jj <= 3; ++jj ) {
        // assume that all atoms on neighboring residues have been placed
        // but check for all internal atoms whether they have been placed.
        if ( res.icoor( ii ).stub_atom( jj ).is_internal() &&
          ! atoms_placed[ res.icoor( ii ).stub_atom( jj ).atomno() ] ) {
          all_stubs_placed = false;
          break;
        }
      }
      if ( all_stubs_placed ) {
        Vector iixyz = res.icoor( ii ).build( res, conf );
        res.set_xyz( ii, iixyz );
        ++n_placed_this_iteration;
        atoms_placed[ ii ] = true;
        --n_remaining;
      }
    }
    if ( n_placed_this_iteration == 0 ) {
      std::cerr << "Error from core::conformation::Residue.functions.cc.";
      std::cerr << "Could not place the following hydrogens: ";
      for ( Size ii = 1; ii <= res.natoms(); ++ii ) {
        if ( ! atoms_placed[ ii ] ) {
          std::cerr << res.atom_name( ii ) << " with atom stubs: ";
          std::cerr << res.atom_name( res.icoor( ii ).stub_atom(1).atomno() ) << ", ";
          std::cerr << res.atom_name( res.icoor( ii ).stub_atom(2).atomno() ) << ", & ";
          std::cerr << res.atom_name( res.icoor( ii ).stub_atom(3).atomno() ) << std::endl;
        }
      }
      utility_exit_with_message( "Failed to place ideal hydrogen positions" );
    }
  }

}

/// @details hokey "update chi from coordinates" useful for when
/// the coordinates are known for a rotamer (specifically, a residue
/// living outside of a conformation object); after the coordinates are
/// set, the chis have to be updated -- that won't happen automatically.
void set_chi_according_to_coordinates(
  conformation::Residue & rotamer
)
{
  for ( Size ii = 1; ii <= rotamer.nchi(); ++ii ) {
    chemical::AtomIndices const & ii_chi_atoms( rotamer.chi_atoms( ii ) );
    Real const ii_chi = numeric::dihedral(
      rotamer.xyz( ii_chi_atoms[ 1 ]),
      rotamer.xyz( ii_chi_atoms[ 2 ]),
      rotamer.xyz( ii_chi_atoms[ 3 ]),
      rotamer.xyz( ii_chi_atoms[ 4 ]) );
    rotamer.chi()[ ii ] = ii_chi;
  }
  if ( rotamer.is_protein() ) {

  }
}

}
}