FragData.cc

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// (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/fragments/FragData.cc
/// @brief  a collection classes of the FragData and SingleResidueFragData class hirachy
/// @author Oliver Lange (olange@u.washington.edu)
/// @date   Wed Oct 20 12:08:31 2007
///

// Unit Headers
#include <core/fragment/FragData.hh>

// Package Headers
#include <core/fragment/Frame.hh>

// Project Headers
#include <core/pose/Pose.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
// ObjexxFCL Headers
#include <ObjexxFCL/format.hh>

// Utility headers
#include <utility/vector1.fwd.hh>

#include <utility/vector1.hh>



namespace core {
namespace fragment {

using namespace kinematics;


//helper function
void
make_pose_from_sequence_(
  std::string sequence,
  chemical::ResidueTypeSet residue_set,
  pose::Pose& pose
) {
  using namespace chemical;
  // clear all of the old data in the pose
  pose.clear();

  // setup the pose by appending the appropriate residues residues
  for ( Size seqpos = 1; seqpos <= sequence.length(); ++seqpos ) {
    char aa = sequence[seqpos-1]; // string indexing is zero-based!
    AA my_aa = aa_from_oneletter_code( aa );
    ResidueTypeCOPs const & rsd_type_list( residue_set.aa_map( my_aa ) );
    Size best_index = 1;
    ResidueType const & rsd_type( *(rsd_type_list[ best_index ]) );
    conformation::ResidueOP new_rsd( conformation::ResidueFactory::create_residue( rsd_type ) );
  } // for seqpos
    // pose.conformation().insert_chain_ending( pose.total_residue() - 1 );    probably not necessary
} // make_pose_match_sequence_

FragData::FragData( SingleResidueFragDataOP SRFD, Size n) : valid_( false ), score_( 0.0 ) {
  for ( Size i = 1; i<=n; i++ ) {
    data_.push_back( SRFD->clone() );
  }
}


FragDataOP FragData::clone() const {
  FragDataOP fd = new FragData( size() );
  for ( Size pos = 1; pos<=size(); pos++ ) {
    fd->data_[pos] = data_[pos]->clone();
  };
  return fd;
}

Size FragData::apply( MoveMap const& mm, pose::Pose& pose, Size start, Size end ) const {
  if ( !is_valid() ) return 0;
  Size pos = start;
  Size ct( 0 );
  for ( SRFD_List::const_iterator it= data_.begin(), eit=data_.end(); it!=eit; ++it, ++pos ) {
    //success = success && data_[ pos-start+1 ]->apply( pose, pos );
    if ( pos > end ) break;
    if ( pos > pose.total_residue() ) break;
    if ( !(*it)->is_applicable( mm, pos ) ) continue; //don't apply for this residue
    if ( !(*it)->apply( mm, pose, pos ) ) continue; //don't apply for this residue
    ct++;
  }
  return ct;
}

Size FragData::apply( pose::Pose& pose, Size start, Size end ) const {
  Size pos = start;
  Size ct ( 0 );
  if ( !is_valid() ) return 0;
  for ( SRFD_List::const_iterator it= data_.begin(), eit=data_.end(); it!=eit; ++it, ++pos ) {
    if ( pos > end ) break;
    if ( !(*it)->apply( pose, pos ) ) continue;
    ++ct;
  }
  return ct;
}

Size FragData::apply( MoveMap const& mm, pose::Pose& pose, Frame const& frame ) const {
  runtime_assert( size() == frame.length() );
  if ( !is_valid() ) return 0;
  if ( frame.is_continuous() ) {
    return apply( mm, pose, frame.start(), frame.end() );
  }
  Size ct ( 0 );
  Size ipos( 1 );
  for ( SRFD_List::const_iterator it= data_.begin(), eit=data_.end(); it!=eit; ++it, ++ipos ) {
    if ( frame.seqpos( ipos ) > pose.total_residue() ) continue;
    if ( !(*it)->is_applicable( mm, ipos, frame ) ) continue;
    if ( !(*it)->apply( mm, pose, ipos, frame ) ) continue;
    ++ct;
  }
  return ct;
}

Size FragData::apply( pose::Pose& pose, Frame const& frame ) const {
  runtime_assert( size() == frame.length() );
  if ( !is_valid() ) return 0;
  Size ipos( 1 );
  Size ct ( 0 );
  for ( SRFD_List::const_iterator it= data_.begin(), eit=data_.end(); it!=eit; ++it, ++ipos ) {
    if ( frame.seqpos( ipos ) > pose.total_residue() ) continue;
    if ( !(*it)->apply( pose, ipos, frame ) ) continue;
    ++ct;
  }
  return ct;
}

Size FragData::apply_ss( MoveMap const& mm, std::string& ss, Frame const& frame ) const {
  Size ipos ( 1 );
  Size ct( 0 );
  if ( !is_valid() ) return 0;
  for ( SRFD_List::const_iterator it= data_.begin(), eit=data_.end(); it!=eit; ++it, ++ipos ) {
    if ( !(*it)->is_applicable( mm, ipos, frame ) ) continue;
    if ( !(*it)->apply_ss( ss, ipos, frame ) ) continue;
    ++ct;
  }
  return ct;
}


Size FragData::is_applicable( kinematics::MoveMap const& mm, Size start, Size end ) const {
  Size insert_size( 0 );
  //  if ( !is_valid() ) return 0; //this might be necessary to have!!!
  for (Size pos=start; pos<=end; pos++ ) {
    if ( !data_[ pos-start+1 ]->is_applicable( mm, pos ) ) continue;
    ++insert_size;
  }
  return insert_size;
}

Size FragData::is_applicable( kinematics::MoveMap const& mm, Frame const& frame ) const {
  runtime_assert( size() == frame.length() );
  // if ( !is_valid() ) return 0;
  if ( frame.is_continuous() ) {
    return is_applicable( mm, frame.start(), frame.end() );
  }
  Size insert_size( 0 );
  for (Size j=1; j<=size(); j++ ) {
    if ( !data_[ j ]->is_applicable( mm, j, frame ) ) continue;
    ++insert_size;
  }
  return insert_size;
}

bool FragData::steal( pose::Pose const& pose, Size start, Size end ) {
  bool success( true );
  for (Size pos=start; pos<=end; pos++) {
    runtime_assert( start > 0 );
    if ( pos > pose.total_residue() ) return false;
    success = success && data_[ pos-start+1 ]->steal( pose, pos );
  }
  if ( success ) set_valid();
  return success;
}


bool FragData::steal( pose::Pose const& pose, Frame const& frame ) {
  runtime_assert( size() == frame.length() );
  if ( frame.is_continuous() ) {
    return steal( pose, frame.start(), frame.end() );
  }
  bool success( true );
  for (Size j=1; j<=size(); j++ ) {
    runtime_assert( frame.seqpos( j ) > 0 );
    if ( frame.seqpos( j ) > pose.total_residue() ) return false;
    success = success && data_[ j ]->steal( pose, j, frame );
  }
  if ( success ) set_valid();
  return success;
}

FragDataOP FragData::generate_sub_fragment( Size start, Size stop ) {
  runtime_assert( stop >= start );
  runtime_assert( stop <= size() );
  FragDataOP new_frag = new FragData;
  for ( Size pos = start; pos<=stop; pos++ ) {
    new_frag->add_residue( data_[ pos ] ); //reuse of data
  }
  new_frag->set_valid();
  return new_frag;
}

bool FragData::is_compatible( FragData const& frag_data ) const {
  if ( frag_data.size() != size() ) return false;
  for ( SRFD_List::const_iterator it1= data_.begin(), it2=frag_data.data_.begin(), eit1=data_.end(); it1!=eit1; ++it1,++it2 ) {
    //    if ( typeid( *it1 ) != typeid( *it2 ) ) return false;
    if ( ! (*it1)->is_compatible( **it2 ) ) return false;
  }
  return true;
}

void FragData::show( std::ostream &os, Frame const& frame ) const {
  Size i = 1;
  if ( is_valid() ) {
    for ( SRFD_List::const_iterator it= data_.begin(), eit=data_.end(); it!=eit; ++it ) {
      os << ObjexxFCL::fmt::RJ( 10, frame.seqpos( i++ ) ) << " " << ObjexxFCL::fmt::RJ( 5, pdbpos() ) << " " << pdbid() <<" ";
      //      std::cerr << "FragData::show " << i-1 << std::endl;
      (*it)->show( os );
      os << std::endl;
      //      std::cerr << "FragData:show -- done" << std::endl;
    }
  } else {
    os << "EMPTY TEMPLATE" << std::endl;
  }
}

void FragData::show( std::ostream &os ) const {
  Size i = 1;
  if ( is_valid() ) {
    for ( SRFD_List::const_iterator it= data_.begin(), eit=data_.end(); it!=eit; ++it ) {
      os << ObjexxFCL::fmt::RJ( 10, i++ ) << " " << ObjexxFCL::fmt::RJ( 5, pdbpos() ) << " " << pdbid() << " " ;
      (*it)->show( os );
      os << std::endl;
    }
  } else {
    os << "EMPTY_TEMPLATE" << std::endl;
  }
}

void FragData::show_classic( std::ostream &os ) const {
  for ( SRFD_List::const_iterator it= data_.begin(), eit=data_.end(); it!=eit; ++it ) {
    os << " 1xxx X   111 ";
    (*it)->show( os );
    os << std::endl;
  }
}

FragDataOP AnnotatedFragData::clone() const {
  return new AnnotatedFragData( pdbid_, startpos_, *Parent::clone() );
}


} // fragment
} // core