stepwise.cc File Reference

#include <utility/json_utilities.hh>
#include <core/types.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreFunction.hh>
#include <devel/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/import_pose/import_pose.hh>
#include <core/io/rna/RNA_DataReader.hh>
#include <core/io/silent/util.hh>
#include <protocols/scoring/VDW_CachedRepScreenInfo.hh>
#include <protocols/rna/setup/RNA_JobDistributor.hh>
#include <protocols/rna/setup/RNA_CSA_JobDistributor.hh>
#include <protocols/rna/setup/RNA_MonteCarloJobDistributor.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/rna/util.hh>
#include <protocols/stepwise/monte_carlo/submotif/SubMotifLibrary.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/jd3/full_model/FullModelJobQueen.hh>
#include <protocols/jd3/full_model_inputters/PDBFullModelInputter.hh>
#include <protocols/jd3/jobs/MoverJob.hh>
#include <protocols/jd3/JobDistributor.hh>
#include <protocols/jd3/JobDistributorFactory.hh>
#include <protocols/jd3/Job.fwd.hh>
#include <protocols/jd3/LarvalJob.fwd.hh>
#include <protocols/jd3/JobResult.fwd.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.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/run.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 <protocols/moves/PyMOLMover.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>

Classes
class	StepWiseJobQueen

Functions
core::scoring::ScoreFunctionOP	get_stepwise_score_function (OptionCollection const &option)
void	stepwise_monte_carlo ()
void	stepwise_monte_carlo_legacy ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.public.stepwise.stepwise")

Detailed Description

Author

Rhiju Das (rhiju.nosp@m.@sta.nosp@m.nford.nosp@m..edu)

Andrew Watkins (amw57.nosp@m.9@st.nosp@m.anfor.nosp@m.d.ed.nosp@m.u)

Function Documentation

core::scoring::ScoreFunctionOP get_stepwise_score_function

(

OptionCollection const &

option

)

References pyrosetta::create_score_function, basic::options::OptionKeys::cluster::energy_based_clustering::cst_file, basic::options::OptionKeys::stepwise::lores, basic::options::OptionKeys::rna::denovo::minimize_rna, basic::options::OptionKeys::DisulfideInsertion::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and score::weights().

Referenced by StepWiseJobQueen::complete_larval_job_maturation(), and stepwise_monte_carlo_legacy().

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::monte_carlo::csa::annealing, 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, test.T009_Exceptions::e, basic::options::OptionKeys::stepwise::enumerate, basic::options::OptionKeys::rna::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::options::OptionKeys::full_model::global_seq_file, devel::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::Exception::msg(), my_main(), in::file::native(), basic::options::OptionKeys::stepwise::new_move_selector, NEW_OPT, 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::score::fiber_diffraction::p, pyrosetta.distributed.io::pose_from_pdbstring(), 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, local::temperature, basic::options::OptionKeys::full_model::rna::terminal_res, basic::options::OptionKeys::inout::dbms::user, 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, option, out::file::silent(), stepwise_monte_carlo(), stepwise_monte_carlo_legacy(), utility_exit_with_message, and value.

Referenced by main().

void stepwise_monte_carlo

(

)

References demo.D060_Folding::jd.

Referenced by StepWiseJobQueen::complete_larval_job_maturation(), my_main(), and stepwise_monte_carlo_legacy().

void stepwise_monte_carlo_legacy

(

)

References basic::options::OptionKeys::stepwise::monte_carlo::csa::annealing, basic::options::OptionKeys::chemical::chemical, 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::rna::data_file, basic::options::OptionKeys::in::file::file, get_stepwise_score_function(), 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, demo.D010_Pose_structure::pose, basic::options::OptionKeys::DisulfideInsertion::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::broker::setup, run::show_simulation_in_pymol(), out::file::silent(), basic::options::OptionKeys::stepwise::stepwise, stepwise_monte_carlo(), basic::options::OptionKeys::stepwise::superimpose_over_all, and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

Variable Documentation

basic::Tracer TR("apps.public.stepwise.stepwise")

static