rna_denovo.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
/// @brief
/// @author Rhiju Das

// libRosetta headers
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/sequence/util.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.hh>
#include <basic/options/option.hh>
#include <basic/database/open.hh>
#include <basic/options/option_macros.hh>
#include <protocols/viewer/viewers.hh>
#include <core/pose/Pose.hh>
#include <core/init/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/io/rna/RNA_DataReader.hh>
#include <utility/vector1.hh>
#include <ObjexxFCL/string.functions.hh>

//RNA stuff.
#include <protocols/farna/RNA_DeNovoProtocol.hh>
#include <protocols/farna/options/RNA_DeNovoProtocolOptions.hh>
#include <protocols/farna/util.hh>
//#include <protocols/moves/PyMolMover.hh>

// C++ headers
#include <iostream>
#include <string>

// option key includes
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/chemical.OptionKeys.gen.hh>
#include <basic/options/keys/rna.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>

#include <core/import_pose/import_pose.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/sequence/Sequence.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/excn/Exceptions.hh>


using namespace core;
using namespace protocols;
using namespace basic::options::OptionKeys;
using utility::vector1;

vector1<pose::PoseOP> get_refine_pose_list( std::string const & input_silent_file,
  std::pair< utility::vector1< int >, utility::vector1< char > > const & output_res_and_chain,
  core::chemical::ResidueTypeSetCOP rsd_set );

///////////////////////////////////////////////////////////////////////////////
void
rna_denovo_test()
{

  using namespace basic::options;
  using namespace basic::options::OptionKeys;
  using namespace core::chemical;
  using namespace core::scoring;
  using namespace core::scoring::constraints;
  using namespace protocols::farna;

  /////////////////////////////////////////////////////////////////////////////////////////////
  /////////////////////////////////////////////////////////////////////////////////////////////
  // Some initialization
  /////////////////////////////////////////////////////////////////////////////////////////////
  /////////////////////////////////////////////////////////////////////////////////////////////
  ResidueTypeSetCOP rsd_set;
  rsd_set = core::chemical::ChemicalManager::get_instance()->residue_type_set( FA_STANDARD );

  pose::PoseOP native_pose_OP( new pose::Pose );
  pose::Pose & native_pose = *native_pose_OP;

  pose::Pose extended_pose;

  std::string const in_path = option[ in::path::path ]()[1];

  bool native_exists = false;
  //Read in native if it exists.
  if ( option[ in::file::native ].user() ) {
    native_exists = true;
    //Read in native if it exists.
    std::string native_pdb_file  = option[ in::file::native ];
    core::import_pose::pose_from_file( native_pose, *rsd_set, in_path + native_pdb_file , core::import_pose::PDB_file);
  } else {
    runtime_assert( !option[ OptionKeys::rna::farna::refine_native ]() );
  }

  //Prepare starting structure from scratch --> read from fasta.
  if ( option[ OptionKeys::rna::farna::refine_native ]() ) {
    extended_pose = native_pose;
  } else {
    std::string const sequence = core::sequence::read_fasta_file_return_str( option[ in::file::fasta ]()[1] );
    core::pose::make_pose_from_sequence( extended_pose, sequence, *rsd_set );
  }
  set_output_res_and_chain( extended_pose, option[ OptionKeys::rna::farna::output_res_num ].resnum_and_chain() );

  // Silent file input for fine refinement
  vector1<pose::PoseOP> refine_pose_list = get_refine_pose_list( option[ OptionKeys::rna::farna::refine_silent_file ](), option[ OptionKeys::rna::farna::output_res_num ].resnum_and_chain(), rsd_set );

  //Score these suckers.
  pose::Pose pose( extended_pose );
  ScoreFunctionOP scorefxn = ScoreFunctionFactory::create_score_function( RNA_LORES_WTS );

  RNA_DeNovoProtocolOptionsOP options( new RNA_DeNovoProtocolOptions);
  options->initialize_from_command_line();
  if ( option[ OptionKeys::rna::farna::refine_native ]() ) options->set_refine_pose( true );

  protocols::farna::RNA_DeNovoProtocol rna_de_novo_protocol( options );
  if ( native_exists ) rna_de_novo_protocol.set_native_pose( native_pose_OP );
  rna_de_novo_protocol.set_refine_pose_list( refine_pose_list );

  if ( option[ OptionKeys::constraints::cst_file ].user() ) {
    ConstraintSetOP cst_set = ConstraintIO::get_instance()->read_constraints( option[ OptionKeys::constraints::cst_file ](1), ConstraintSetOP( new ConstraintSet ), pose );
    pose.constraint_set( cst_set );
    for ( Size i = 1; i <= refine_pose_list.size(); ++i ) refine_pose_list[i]->constraint_set( cst_set );
  }

  if ( option[ OptionKeys::rna::data_file].user() ) {
    core::io::rna::RNA_DataReader rna_data_reader( in_path + option[ OptionKeys::rna::data_file ]  );
    rna_data_reader.fill_rna_data_info( pose );
  }

  protocols::viewer::add_conformation_viewer( pose.conformation(), "current", 600, 600 );

  // protocols::moves::AddPyMolObserver( pose, false, 0.01);

  rna_de_novo_protocol.apply( pose );

}

///////////////////////////////////////////////////////////////
vector1<pose::PoseOP>
get_refine_pose_list( std::string const & input_silent_file,
  std::pair< utility::vector1< int >, utility::vector1< char > > const & output_res_and_chain,
  core::chemical::ResidueTypeSetCOP rsd_set )
{

  vector1<pose::PoseOP> refine_pose_list;
  if ( input_silent_file.size() > 0 ) {
    core::import_pose::pose_stream::SilentFilePoseInputStream input( input_silent_file );
    input.set_order_by_energy( true );
    while ( input.has_another_pose() ) {
      pose::PoseOP new_pose( new pose::Pose );
      input.fill_pose( *new_pose, *rsd_set );
      protocols::farna::set_output_res_and_chain( *new_pose, output_res_and_chain );
      refine_pose_list.push_back( new_pose );
    }
  }
  return refine_pose_list;
}

///////////////////////////////////////////////////////////////
void*
my_main( void* )
{
  rna_denovo_test();
  protocols::viewer::clear_conformation_viewers();
  exit( 0 );
}


///////////////////////////////////////////////////////////////////////////////
int
main( int argc, char * argv [] )
{
  try {
    using namespace basic::options;

    std::cout << std::endl << "Basic usage:  " << argv[0] << "  -fasta <fasta file with sequence>  [ -native <native pdb file> ] " << std::endl;
    std::cout << std::endl << " Type -help for full slate of options." << std::endl << std::endl;

    option.add_relevant( in::file::fasta );
    option.add_relevant( in::file::input_res );
    option.add_relevant( in::file::native );
    option.add_relevant( out::file::silent );
    option.add_relevant( out::nstruct );
    option.add_relevant( score::weights );
    option.add_relevant( constraints::cst_file );
    option.add_relevant( rna::farna::minimize_rna );
    option.add_relevant( rna::farna::relax_rna );
    option.add_relevant( rna::farna::simple_relax );
    option.add_relevant( rna::farna::ignore_secstruct );
    option.add_relevant( rna::farna::lores_scorefxn );
    option.add_relevant( rna::farna::filter_lores_base_pairs );
    option.add_relevant( rna::farna::filter_lores_base_pairs_early );
    option.add_relevant( rna::farna::filter_chain_closure );
    option.add_relevant( rna::farna::filter_chain_closure_halfway );
    option.add_relevant( rna::farna::filter_chain_closure_distance );
    option.add_relevant( rna::farna::cycles );
    option.add_relevant( rna::farna::temperature );
    option.add_relevant( rna::farna::jump_change_frequency );
    option.add_relevant( rna::farna::close_loops );
    option.add_relevant( rna::farna::close_loops_after_each_move );
    option.add_relevant( rna::farna::output_lores_silent_file );
    option.add_relevant( rna::farna::heat );
    option.add_relevant( rna::farna::dump );
    option.add_relevant( rna::farna::staged_constraints );
    option.add_relevant( rna::farna::jump_library_file );
    option.add_relevant( rna::farna::params_file );
    option.add_relevant( basic::options::OptionKeys::rna::farna::vall_torsions );
    option.add_relevant( rna::farna::use_1jj2_torsions );
    option.add_relevant( rna::farna::rna_lores_chainbreak_weight );
    option.add_relevant( rna::farna::rna_lores_linear_chainbreak_weight );
    option.add_relevant( rna::farna::allow_bulge  );
    option.add_relevant( rna::farna::allowed_bulge_res );
    option.add_relevant( rna::farna::allow_consecutive_bulges );
    option.add_relevant( rna::farna::binary_output );
    option.add_relevant( rna::farna::move_first_rigid_body );
    option.add_relevant( rna::farna::root_at_first_rigid_body );
    option.add_relevant( rna::farna::suppress_bp_constraint );
    option.add_relevant( rna::farna::output_filters );
    option.add_relevant( rna::farna::autofilter );
    option.add_relevant( rna::farna::output_res_num );
    option.add_relevant( rna::farna::refine_silent_file );
    option.add_relevant( rna::farna::refine_native );
    option.add_relevant( rna::farna::bps_moves );
    option.add_relevant( rna::vary_geometry );
    option.add_relevant( basic::options::OptionKeys::rna::data_file );
    option.add_relevant( rna::farna::minimize::minimizer_use_coordinate_constraints );
    option.add_relevant( rna::farna::minimize::extra_minimize_res );
    option.add_relevant( rna::farna::minimize::extra_minimize_chi_res );
    option.add_relevant( rna::farna::minimize::minimize_bps );

    option.add_relevant( constraints::cst_file );

    ////////////////////////////////////////////////////////////////////////////
    // setup
    ////////////////////////////////////////////////////////////////////////////
    core::init::init(argc, argv);

    ////////////////////////////////////////////////////////////////////////////
    // end of setup
    ////////////////////////////////////////////////////////////////////////////

    protocols::viewer::viewer_main( my_main );
  } catch ( utility::excn::EXCN_Base const & e ) {
    std::cout << "caught exception " << e.msg() << std::endl;
    return -1;
  }
}