fast_gap.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:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (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
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file full_length_model.cc
/// @brief
/// @author James Thompson

#include <core/types.hh>
#include <core/init/init.hh>
#include <basic/Tracer.hh>
#include <core/chemical/util.hh>

#include <basic/options/option.hh>

#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/sequence/NWAligner.hh>
#include <core/sequence/ScoringScheme.fwd.hh>
#include <core/sequence/SimpleScoringScheme.hh>

#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/MoveMap.fwd.hh>

#include <core/import_pose/pose_stream/util.hh>
#include <core/import_pose/pose_stream/MetaPoseInputStream.hh>
#include <core/import_pose/PDBSilentStruct.hh>

#include <core/io/pdb/pose_io.hh>
#include <core/conformation/Conformation.hh>
#include <core/scoring/ScoreFunction.hh>

#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pack/task/TaskFactory.hh>

#include <core/fragment/FragSet.hh>
#include <core/fragment/FragSet.fwd.hh>

#include <protocols/relax/MiniRelax.cc>

#include <protocols/loophash/FastGapMover.hh>
#include <protocols/comparative_modeling/ThreadingMover.hh>

#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/excn/Exceptions.hh>

// C++ headers
#include <string>

// option key includes
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/relax.OptionKeys.gen.hh>

#include <core/pose/annotated_sequence.hh>
#include <utility/vector0.hh>


void restore_hack( core::pose::Pose & pose ) {
  core::import_pose::PDBSilentStruct ss;

  ss.fill_struct( pose );
  ss.fill_pose( pose, *(core::chemical::rsd_set_from_cmd_line()) );
}

int
main( int argc, char* argv [] ) {
  try {

  using namespace basic::options;
  using namespace basic::options::OptionKeys;
  using namespace core::chemical;
  using namespace core::sequence;
  using namespace core::fragment;
  using namespace core::import_pose::pose_stream;
  using namespace protocols::comparative_modeling;
  using namespace core::scoring;
  using namespace core::pack;
  using namespace core::kinematics;
  using core::Size;
  using utility::vector1;

  basic::Tracer tr( "full_length_model" );

  // options, random initialization
  core::init::init( argc, argv );

  protocols::loophash::FastGapMover fast_gap;
  ResidueTypeSetCAP rsd_set = rsd_set_from_cmd_line();
  MetaPoseInputStream input = streams_from_cmd_line();
  std::string sequence = core::sequence::read_fasta_file(
    option[ in::file::fasta ]()[1]
  )[1]->sequence();
  NWAligner nw_align;

  while ( input.has_another_pose() ) {
    core::pose::Pose start_pose;
    input.fill_pose( start_pose, *rsd_set );

    // make an alignment from the input pose to the full-length fasta
    ScoringSchemeOP ss( new SimpleScoringScheme( 6, 1, -4, -1 ) );
    SequenceOP full_length( new Sequence(
      sequence, "full_length", 1
    ) );
    SequenceOP pdb_seq( new Sequence(
      start_pose.sequence(), "pdb", 1
    ) );
    SequenceAlignment aln = nw_align.align( full_length, pdb_seq, ss );
    tr.Debug << "rebuilding pose with alignment: " << std::endl;
    tr.Debug << aln << std::endl;
    tr.flush();

    // build a model using threading (copy aligned regions)
    ThreadingMover threader(aln,start_pose);
    threader.build_loops(false);
    core::pose::Pose full_length_pose;
    core::pose::make_pose_from_sequence( full_length_pose, sequence, *rsd_set );
    threader.apply(full_length_pose);

    full_length_pose.dump_pdb("here.pdb");

    fast_gap.apply(full_length_pose);

    std::string output_prefix( core::pose::tag_from_pose(start_pose) );
    // output PDB
    alignment_into_pose( aln, full_length_pose );
    utility::io::ozstream output( output_prefix + "_full_length.pdb" );
    output << "REMARK REBUILT_RESIDUES";
    output << std::endl;
    output << "REMARK query_aln    " << aln.sequence(1)->to_string() << std::endl;
    output << "REMARK template_aln " << aln.sequence(2)->to_string()<< std::endl;
    output << std::endl;
    core::io::pdb::dump_pdb( full_length_pose, output );
    output.close();
    //full_length_pose.dump_pdb( output_prefix + "_full_length.pdb" );
  } // has_another_pose()
   } catch ( utility::excn::EXCN_Base const & e ) {
    std::cout << "caught exception " << e.msg() << std::endl;
    return -1;
  }
} // int main( int argc, char * argv [] )