stepwise.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 swa_monte_carlo.cc
/// @author Rhiju Das (rhiju@stanford.edu)

// libRosetta headers
#include <core/types.hh>
#include <core/chemical/util.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/init/init.hh>
#include <core/pose/Pose.hh>
#include <core/pose/full_model_info/FullModelInfo.hh>
#include <core/pose/full_model_info/util.hh>
#include <core/pose/util.hh>
#include <core/io/rna/RNA_DataReader.cc> // temporary, for scoring RNA chemical mapping data. Move into core?
#include <protocols/stepwise/setup/FullModelInfoSetupFromCommandLine.hh>
#include <protocols/stepwise/setup/StepWiseJobDistributor.hh>
#include <protocols/stepwise/setup/StepWiseCSA_JobDistributor.hh>
#include <protocols/stepwise/setup/StepWiseMonteCarloJobDistributor.hh>
#include <protocols/stepwise/monte_carlo/StepWiseMonteCarlo.hh>
#include <protocols/stepwise/monte_carlo/options/StepWiseMonteCarloOptions.hh>
#include <protocols/stepwise/monte_carlo/util.hh>
#include <protocols/stepwise/modeler/util.hh>
#include <protocols/stepwise/modeler/file_util.hh>
#include <protocols/stepwise/modeler/rna/util.hh>
#include <protocols/stepwise/monte_carlo/submotif/SubMotifLibrary.hh>
#include <protocols/viewer/viewers.hh>

//////////////////////////////////////////////////
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/chemical.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh> // for option[ in::file::tags ] and etc.
#include <basic/options/keys/full_model.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh> // for option[ out::file::silent  ] and etc.
#include <basic/options/keys/rna.OptionKeys.gen.hh>
#include <basic/options/keys/stepwise.OptionKeys.gen.hh>

#include <basic/Tracer.hh>
#include <utility/vector1.hh>
#include <utility/file/FileName.hh>

//////////////////////////////////////////////////////////
#include <ObjexxFCL/string.functions.hh>
#include <ObjexxFCL/format.hh>

// C++ headers
#include <fstream>
#include <iostream>
#include <sstream>
#include <string>
#include <list>

using namespace protocols;
using namespace basic::options;
using namespace basic::options::OptionKeys;
using namespace basic::options::OptionKeys::stepwise::monte_carlo;
using utility::vector1;

static THREAD_LOCAL basic::Tracer TR( "apps.pilot.rhiju.stepwise_monte_carlo" );

//////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void
stepwise_monte_carlo()
{
  using namespace core::pose;
  using namespace core::scoring;
  using namespace core::chemical;
  using namespace core::pose::full_model_info;
  using namespace protocols::stepwise;
  using namespace protocols::stepwise::modeler;
  using namespace protocols::stepwise::monte_carlo::submotif;
  using namespace protocols::stepwise::setup;
  using namespace protocols::stepwise::monte_carlo;
  using namespace protocols::stepwise::monte_carlo::mover;
  using namespace protocols::stepwise::monte_carlo::options;
  using namespace utility::file;

  bool const just_RNA = just_modeling_RNA( option[ in::file::fasta ]() );
  ResidueTypeSetCAP rsd_set = core::chemical::ChemicalManager::get_instance()->residue_type_set( FA_STANDARD );

  ScoreFunctionOP scorefxn;
  if ( option[ score::weights ].user() ) scorefxn = get_score_function();
  else if ( option[ OptionKeys::stepwise::lores ]() && !option[ OptionKeys::rna::farna::minimize_rna ]() ) {
    scorefxn = ScoreFunctionFactory::create_score_function( "stepwise/rna/rna_lores_for_stepwise.wts" );
  } else if ( just_RNA ) scorefxn = ScoreFunctionFactory::create_score_function( "stepwise/rna/rna_res_level_energy.wts" );
  else scorefxn = ScoreFunctionFactory::create_score_function( "stepwise/stepwise_res_level_energy.wts" ); // RNA/protein.
  if ( option[ OptionKeys::constraints::cst_file ].user() && !scorefxn->has_nonzero_weight( atom_pair_constraint ) ) scorefxn->set_weight( atom_pair_constraint, 1.0 );

  PoseOP native_pose, align_pose;
  PoseOP pose_op = initialize_pose_and_other_poses_from_command_line( rsd_set );
  pose::Pose & pose = *pose_op;
  initialize_native_and_align_pose( native_pose, align_pose, rsd_set, pose_op );
  // temporary, for scoring RNA chemical mapping data. Move into initalize_pose?
  core::io::rna::get_rna_data_info( pose, option[ basic::options::OptionKeys::rna::data_file ](), scorefxn );

  // Get rid of this commented code when it is incorporated into a unit test.
  // test_merge_and_slice_with_two_helix_test_case( input_poses, scorefxn ); exit( 0 );

  // setup test move specified via -stepwise:move option
  StepWiseMove const test_move( option[ OptionKeys::stepwise::move ](), const_full_model_info( pose ).full_model_parameters() );

  // actual pose to be sampled... do not score pose is user has specified a move
  if ( pose.total_residue() > 0 && test_move.move_type() == NO_MOVE ) ( *scorefxn )( pose );
  Vector center_vector = ( align_pose != 0 ) ? get_center_of_mass( *align_pose ) : Vector( 0.0 );
  protocols::viewer::add_conformation_viewer ( pose.conformation(), "current", 500, 500, false, ( align_pose != 0 ), center_vector );

  StepWiseMonteCarloOP stepwise_monte_carlo( new StepWiseMonteCarlo( scorefxn ) );
  stepwise_monte_carlo->set_native_pose( align_pose ); //allows for alignment to be to non-native
  stepwise_monte_carlo->set_move( test_move );

  StepWiseMonteCarloOptionsOP options( new StepWiseMonteCarloOptions );
  options->initialize_from_command_line();
  stepwise_monte_carlo->set_options( options );
  if ( ( options->from_scratch_frequency() > 0.0 || const_full_model_info( *pose_op ).other_pose_list().size() > 0 ) && !scorefxn->has_nonzero_weight( other_pose ) ) scorefxn->set_weight( other_pose, 1.0 ); // critical if more than one pose shows up and focus switches...

  std::string const silent_file = option[ out::file::silent ]();
  if ( option[ out::overwrite ]() ) remove_silent_file_if_it_exists( silent_file );
  stepwise_monte_carlo->set_out_path( FileName( silent_file ).path() );
  stepwise_monte_carlo->set_submotif_library( SubMotifLibraryCOP( new SubMotifLibrary( rsd_set, options->lores() /*include_submotifs_from_jump_library*/, options->use_first_jump_for_submotif() ) ) );

  // main loop
  StepWiseJobDistributorOP stepwise_job_distributor( new StepWiseMonteCarloJobDistributor( stepwise_monte_carlo, silent_file, option[ out::nstruct ]() ) );
  if ( option[ csa::csa_bank_size ].user() ) {
    stepwise_job_distributor = StepWiseJobDistributorOP( new StepWiseCSA_JobDistributor( stepwise_monte_carlo, silent_file, option[ out::nstruct ](), option[ csa::csa_bank_size ](), option[ csa::csa_rmsd ](), option[ csa::csa_output_rounds ]() ) );
  }
  stepwise_job_distributor->set_native_pose( native_pose );
  stepwise_job_distributor->set_superimpose_over_all( option[ OptionKeys::stepwise::superimpose_over_all ]() );
  stepwise_job_distributor->initialize( pose );

  while ( stepwise_job_distributor->has_another_job() ) {
    stepwise_job_distributor->apply( pose );
  }

}

///////////////////////////////////////////////////////////////
void*
my_main( void* )
{
  clock_t const my_main_time_start( clock() );
  stepwise_monte_carlo();
  protocols::viewer::clear_conformation_viewers();
  std::cout << "Total time to run " << static_cast<Real>( clock() - my_main_time_start ) / CLOCKS_PER_SEC << " seconds." << std::endl;
  exit( 0 );
}


///////////////////////////////////////////////////////////////////////////////
int
main( int argc, char * argv [] )
{
  try {
    std::cout << std::endl << "Basic usage:  " << argv[0] << "  -fasta <fasta file with sequence> -s <start pdb> -input_res <input pdb1> [ -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::overwrite );
    option.add_relevant( out::nstruct );
    option.add_relevant( score::weights );
    option.add_relevant( constraints::cst_file );
    option.add_relevant( OptionKeys::full_model::other_poses );
    option.add_relevant( OptionKeys::full_model::jump_res );
    option.add_relevant( OptionKeys::full_model::root_res );
    option.add_relevant( OptionKeys::full_model::virtual_sugar_res );
    option.add_relevant( OptionKeys::full_model::cutpoint_open );
    option.add_relevant( OptionKeys::full_model::cutpoint_closed );
    option.add_relevant( OptionKeys::full_model::sample_res );
    option.add_relevant( OptionKeys::full_model::motif_mode );
    option.add_relevant( OptionKeys::full_model::rna::force_syn_chi_res_list );
    option.add_relevant( OptionKeys::full_model::rna::bulge_res );
    option.add_relevant( OptionKeys::full_model::extra_min_res );
    option.add_relevant( OptionKeys::full_model::rna::terminal_res );
    option.add_relevant( OptionKeys::full_model::rna::block_stack_above_res );
    option.add_relevant( OptionKeys::full_model::rna::block_stack_below_res );
    option.add_relevant( OptionKeys::stepwise::monte_carlo::cycles );
    option.add_relevant( OptionKeys::stepwise::monte_carlo::skip_deletions );
    option.add_relevant( OptionKeys::stepwise::monte_carlo::add_delete_frequency );
    option.add_relevant( OptionKeys::stepwise::monte_carlo::minimize_single_res_frequency );
    option.add_relevant( OptionKeys::stepwise::monte_carlo::switch_focus_frequency );
    option.add_relevant( OptionKeys::stepwise::monte_carlo::just_min_after_mutation_frequency );
    option.add_relevant( OptionKeys::stepwise::monte_carlo::submotif_frequency );
    option.add_relevant( OptionKeys::stepwise::monte_carlo::allow_internal_hinge_moves );
    option.add_relevant( OptionKeys::stepwise::monte_carlo::allow_internal_local_moves );
    option.add_relevant( OptionKeys::stepwise::monte_carlo::allow_skip_bulge );
    option.add_relevant( OptionKeys::stepwise::monte_carlo::temperature );
    option.add_relevant( OptionKeys::stepwise::monte_carlo::allow_variable_bond_geometry );
    option.add_relevant( OptionKeys::stepwise::monte_carlo::csa::csa_bank_size );
    option.add_relevant( OptionKeys::stepwise::monte_carlo::csa::csa_rmsd );
    option.add_relevant( OptionKeys::stepwise::monte_carlo::csa::csa_output_rounds );
    option.add_relevant( OptionKeys::stepwise::superimpose_over_all );
    option.add_relevant( OptionKeys::stepwise::move );
    option.add_relevant( OptionKeys::stepwise::num_random_samples );
    option.add_relevant( OptionKeys::stepwise::num_pose_minimize );
    option.add_relevant( OptionKeys::stepwise::align_pdb );
    option.add_relevant( OptionKeys::stepwise::enumerate );
    option.add_relevant( OptionKeys::stepwise::preminimize );
    option.add_relevant( OptionKeys::stepwise::atr_rep_screen );
    option.add_relevant( OptionKeys::stepwise::min_type );
    option.add_relevant( OptionKeys::stepwise::min_tolerance );
    option.add_relevant( OptionKeys::stepwise::virtualize_free_moieties_in_native );
    option.add_relevant( OptionKeys::stepwise::new_move_selector );
    option.add_relevant( OptionKeys::stepwise::rna::erraser );
    option.add_relevant( OptionKeys::stepwise::rna::force_centroid_interaction );
    option.add_relevant( OptionKeys::stepwise::rna::rebuild_bulge_mode );
    option.add_relevant( OptionKeys::stepwise::rna::integration_test );
    option.add_relevant( OptionKeys::stepwise::protein::allow_virtual_side_chains );
    option.add_relevant( OptionKeys::rna::corrected_geo );
    option.add_relevant( OptionKeys::rna::data_file );

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

    protocols::viewer::viewer_main( my_main );

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