stepwise.cc File Reference

#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.hh>
#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>
#include <basic/options/keys/full_model.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#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>
#include <fstream>
#include <iostream>
#include <sstream>
#include <string>
#include <list>

Functions
static THREAD_LOCAL basic::Tracer	TR ("apps.pilot.rhiju.stepwise_monte_carlo")
void	stepwise_monte_carlo ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Function Documentation

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

References basic::options::OptionKeys::magnesium::montecarlo::add_delete_frequency, basic::options::OptionKeys::stepwise::align_pdb, basic::options::OptionKeys::stepwise::monte_carlo::allow_internal_hinge_moves, basic::options::OptionKeys::stepwise::monte_carlo::allow_internal_local_moves, basic::options::OptionKeys::stepwise::monte_carlo::allow_skip_bulge, basic::options::OptionKeys::stepwise::monte_carlo::allow_variable_bond_geometry, basic::options::OptionKeys::stepwise::protein::allow_virtual_side_chains, basic::options::OptionKeys::stepwise::atr_rep_screen, basic::options::OptionKeys::full_model::rna::block_stack_above_res, basic::options::OptionKeys::full_model::rna::block_stack_below_res, basic::options::OptionKeys::full_model::rna::bulge_res, basic::options::OptionKeys::rna::corrected_geo, utility::io::oc::cout, basic::options::OptionKeys::stepwise::monte_carlo::csa::csa_bank_size, basic::options::OptionKeys::stepwise::monte_carlo::csa::csa_output_rounds, basic::options::OptionKeys::stepwise::monte_carlo::csa::csa_rmsd, constraints::cst_file(), basic::options::OptionKeys::full_model::cutpoint_closed, basic::options::OptionKeys::full_model::cutpoint_open, basic::options::OptionKeys::magnesium::montecarlo::cycles, basic::options::OptionKeys::motifs::data_file, basic::options::OptionKeys::stepwise::enumerate, basic::options::OptionKeys::rna::farna::erraser::erraser, basic::options::OptionKeys::full_model::extra_min_res, in::file::fasta(), basic::options::OptionKeys::full_model::rna::force_anti_chi_res_list, basic::options::OptionKeys::stepwise::rna::force_centroid_interaction, basic::options::OptionKeys::full_model::rna::force_north_sugar_list, basic::options::OptionKeys::full_model::rna::force_south_sugar_list, basic::options::OptionKeys::full_model::rna::force_syn_chi_res_list, basic::init(), in::file::input_res(), basic::options::OptionKeys::magnesium::integration_test, basic::options::OptionKeys::full_model::jump_res, basic::options::OptionKeys::stepwise::monte_carlo::just_min_after_mutation_frequency, basic::options::OptionKeys::stepwise::monte_carlo::make_movie, basic::options::OptionKeys::relax::min_tolerance, basic::options::OptionKeys::dna::specificity::min_type, basic::options::OptionKeys::stepwise::monte_carlo::minimize_single_res_frequency, basic::options::OptionKeys::full_model::motif_mode, basic::options::OptionKeys::stepwise::move, utility::excn::EXCN_Base::msg(), my_main(), in::file::native(), basic::options::OptionKeys::stepwise::new_move_selector, out::nstruct(), basic::options::OptionKeys::stepwise::num_pose_minimize, basic::options::OptionKeys::stepwise::num_random_samples, option, basic::options::OptionKeys::full_model::other_poses, out::overwrite(), basic::options::OptionKeys::stepwise::preminimize, basic::options::OptionKeys::stepwise::rna::rebuild_bulge_mode, basic::options::OptionKeys::full_model::root_res, basic::options::OptionKeys::full_model::sample_res, out::file::silent(), basic::options::OptionKeys::stepwise::monte_carlo::skip_deletions, basic::options::OptionKeys::stepwise::monte_carlo::submotif_frequency, basic::options::OptionKeys::stepwise::superimpose_over_all, basic::options::OptionKeys::stepwise::monte_carlo::switch_focus_frequency, basic::options::OptionKeys::abinitio::temperature, basic::options::OptionKeys::full_model::rna::terminal_res, basic::options::OptionKeys::full_model::virtual_sugar_res, basic::options::OptionKeys::stepwise::virtualize_free_moieties_in_native, and score::weights().

void* my_main

(

void *

)

References utility::io::oc::cout, utility::options::OptionKeys::options::exit, and stepwise_monte_carlo().

Referenced by main().

void stepwise_monte_carlo

(

)

References basic::options::OptionKeys::chemical::chemical, pyrosetta::create_score_function, basic::options::OptionKeys::stepwise::monte_carlo::csa::csa_bank_size, basic::options::OptionKeys::stepwise::monte_carlo::csa::csa_output_rounds, basic::options::OptionKeys::stepwise::monte_carlo::csa::csa_rmsd, basic::options::OptionKeys::constraints::cst_file, basic::options::OptionKeys::rna::data_file, in::file::fasta(), basic::options::OptionKeys::in::file::file, pyrosetta::get_score_function, basic::options::OptionKeys::stepwise::lores, basic::options::OptionKeys::rna::farna::minimize_rna, basic::options::OptionKeys::magnesium::monte_carlo, basic::options::OptionKeys::stepwise::move, test.Workshop7test::native_pose, out::nstruct(), option, options, out::overwrite(), basic::options::OptionKeys::in::path::path, app.surface_docking.surface_docking::pose, PyMOL_demo::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::broker::setup, out::file::silent(), basic::options::OptionKeys::stepwise::stepwise, basic::options::OptionKeys::stepwise::superimpose_over_all, basic::options::OptionKeys::inout::dbms::user, and score::weights().

Referenced by my_main().

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

static