trie.functions.hh

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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// (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   core/scoring/trie/trie.functions.hh
/// @brief
/// @author Andrew Leaver-Fay (aleaverfay@gmail.com)


#ifndef INCLUDED_core_scoring_trie_trie_functions_hh
#define INCLUDED_core_scoring_trie_trie_functions_hh

// Unit Headers
#include <core/scoring/trie/trie.functions.fwd.hh>

// Package Headers
#include <core/scoring/trie/CPDataCorrespondence.hh>
#include <core/scoring/trie/RotamerDescriptor.hh>
// AUTO-REMOVED #include <core/scoring/trie/RotamerTrie.hh>
#include <core/scoring/trie/RotamerTrieBase.hh>

// Project Headers
#include <core/conformation/Residue.hh>
#include <core/conformation/RotamerSetBase.hh>
#include <core/scoring/etable/count_pair/types.hh>

#include <utility/vector1.hh>


namespace core {
namespace scoring {
namespace trie {

/// @details
/// Class AT must define a constructor that takes a residue const & and an atom index.
template < class AT, class CPDAT >
RotamerTrieBaseOP
create_trie(
  conformation::RotamerSetBase const & rotset,
  AT    const & /* dummy variable for type identification */,
  CPDAT const & /* dummy variable for type identification */,
  CPDataCorrespondence const & cpdata_map,
  Distance atomic_interaction_cutoff
)
{

  utility::vector1< RotamerDescriptor< AT, CPDAT > > rotamer_descriptors( rotset.num_rotamers() );

  for ( Size ii = 1; ii <= rotset.num_rotamers(); ++ii ) {
    conformation::ResidueCOP ii_rotamer( rotset.rotamer( ii ) );
    rotamer_descriptors[ ii ].natoms( ii_rotamer->natoms() );
    Size count_added_atoms = 0;
    for ( Size jj = 1; jj <= ii_rotamer->nheavyatoms(); ++jj ) {

      AT newatom( *ii_rotamer, jj );
      newatom.is_hydrogen( false );

      CPDAT cpdata;
      initialize_cpdata_for_atom( cpdata, jj, *ii_rotamer, cpdata_map );


      RotamerDescriptorAtom< AT, CPDAT > rdatom( newatom, cpdata );
      rotamer_descriptors[ ii ].atom( ++count_added_atoms, rdatom );

      for ( Size kk = ii_rotamer->attached_H_begin( jj ),
          kk_end = ii_rotamer->attached_H_end( jj );
          kk <= kk_end; ++kk ) {

        AT newhatom( *ii_rotamer, kk );
        newhatom.is_hydrogen( true );

        CPDAT cpdata;
        initialize_cpdata_for_atom( cpdata, kk, *ii_rotamer, cpdata_map );

        RotamerDescriptorAtom< AT, CPDAT > rdatom( newhatom, cpdata );
        rotamer_descriptors[ ii ].atom( ++count_added_atoms, rdatom );

      }
    }
    rotamer_descriptors[ ii ].rotamer_id( ii );
  }

  sort( rotamer_descriptors.begin(), rotamer_descriptors.end() );

  RotamerTrieBaseOP newtrie = new RotamerTrie< AT, CPDAT >( rotamer_descriptors, atomic_interaction_cutoff );
  for ( Size ii = 1; ii <= cpdata_map.n_entries(); ++ii ) {
    newtrie->set_resid_2_connection_entry( cpdata_map.resid_for_entry( ii ), ii );
  }
  return newtrie;
}

/// @details
/// Creates a rotamer trie given a single residue -- a one-residue trie.
/// Class AT must define a constructor that takes a residue const & and an atom index.
template < class AT, class CPDAT >
RotamerTrieBaseOP
create_trie(
  conformation::Residue const & res,
  AT    const & /* dummy variable for type identification */,
  CPDAT const & /* dummy variable for type identification */,
  CPDataCorrespondence const & cpdata_map,
  Distance atomic_interaction_cutoff
)
{

  utility::vector1< RotamerDescriptor< AT, CPDAT > > rotamer_descriptor( 1 );

  rotamer_descriptor[ 1 ].natoms( res.natoms() );
  Size count_added_atoms = 0;
  for ( Size jj = 1; jj <= res.nheavyatoms(); ++jj ) {

    AT newatom( res, jj );
    newatom.is_hydrogen( false );

    CPDAT cpdata;
    initialize_cpdata_for_atom( cpdata, jj, res, cpdata_map );


    RotamerDescriptorAtom< AT, CPDAT > rdatom( newatom, cpdata );
    rotamer_descriptor[ 1 ].atom( ++count_added_atoms, rdatom );

    for ( Size kk = res.attached_H_begin( jj ), kk_end = res.attached_H_end( jj );
        kk <= kk_end; ++kk ) {

      AT newhatom( res, kk );
      newhatom.is_hydrogen( true );

      CPDAT cpdata;
      initialize_cpdata_for_atom( cpdata, kk, res, cpdata_map );

      RotamerDescriptorAtom< AT, CPDAT > rdatom( newhatom, cpdata );
      rotamer_descriptor[ 1 ].atom( ++count_added_atoms, rdatom );
    }
  }
  rotamer_descriptor[ 1 ].rotamer_id( 1 );

  RotamerTrieBaseOP newtrie = new RotamerTrie< AT, CPDAT >( rotamer_descriptor, atomic_interaction_cutoff );
  for ( Size ii = 1; ii <= cpdata_map.n_entries(); ++ii ) {
    newtrie->set_resid_2_connection_entry( cpdata_map.resid_for_entry( ii ), ii );
  }
  return newtrie;
}


template < class CPDAT >
void
initialize_cpdata_for_atom(
  CPDAT & cp_data,
  Size atom_index,
  conformation::Residue const & res,
  CPDataCorrespondence const & cpdata_map
)
{
  for ( Size ii = 1; ii <= cpdata_map.n_entries(); ++ii ) {
    if ( res.is_bonded( cpdata_map.resid_for_entry( ii ) ) ) {
      for ( Size jj = 1; jj <= cpdata_map.n_connpoints_for_entry( ii ); ++jj ) {
        Size const connection_atom(
          res.residue_connect_atom_index( cpdata_map.connid_for_entry_connpoint( ii, jj ) ));
        cp_data.set_dist_to_connect_point(
          ii, jj, res.path_distance( atom_index, connection_atom ));
      }
    } else {
      for ( Size jj = 1; jj <= cpdata_map.n_connpoints_for_entry( ii ); ++jj ) {
        cp_data.set_dist_to_connect_point( ii, jj, etable::count_pair::INFINITE_SEPARATION );
      }
    }
  }
}

} // namespace trie
} // namespace scoring
} // namespace core

#endif