rna_denovo.cc File Reference

#include <core/types.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <protocols/viewer/viewers.hh>
#include <core/pose/Pose.hh>
#include <devel/init.hh>
#include <utility/vector1.hh>
#include <protocols/rna/denovo/RNA_DeNovoProtocol.hh>
#include <core/import_pose/RNA_DeNovoSetup.hh>
#include <core/import_pose/options/RNA_DeNovoProtocolOptions.hh>
#include <protocols/rna/denovo/RNA_FragmentMonteCarlo.hh>
#include <core/fragment/rna/FullAtomRNA_Fragments.hh>
#include <protocols/rna/movers/RNA_LoopCloser.hh>
#include <core/import_pose/RNA_BasePairHandler.hh>
#include <protocols/rna/denovo/movers/RNA_Minimizer.hh>
#include <core/import_pose/RNA_DeNovoParameters.hh>
#include <protocols/rna/denovo/movers/RNA_Relaxer.hh>
#include <protocols/rna/denovo/RNA_DeNovoPoseInitializer.hh>
#include <core/import_pose/libraries/RNA_ChunkLibrary.hh>
#include <protocols/rna/setup/RNA_MonteCarloJobDistributor.hh>
#include <protocols/rna/setup/RNA_CSA_JobDistributor.hh>
#include <core/pose/rna/RNA_BasePairClassifier.hh>
#include <protocols/rna/denovo/util.hh>
#include <protocols/stepwise/modeler/rna/checker/RNA_VDW_BinChecker.hh>
#include <protocols/scoring/VDW_CachedRepScreenInfo.hh>
#include <core/conformation/Residue.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/rna/RNA_ScoringInfo.hh>
#include <core/chemical/rna/util.hh>
#include <core/scoring/rna/chemical_shift/RNA_ChemicalShiftPotential.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID.hh>
#include <core/id/DOF_ID.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pose/util.hh>
#include <core/io/silent/RNA_SilentStruct.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentFileOptions.hh>
#include <core/io/silent/util.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/pose/rna/RNA_BaseDoubletClasses.hh>
#include <core/pose/rna/util.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <protocols/jd3/chunk_library/ChunkLibraryJobQueen.hh>
#include <protocols/jd3/chunk_library/MoverAndChunkLibraryJob.hh>
#include <protocols/jd3/LarvalJob.hh>
#include <protocols/jd3/JobDistributor.hh>
#include <protocols/jd3/JobDistributorFactory.hh>
#include <protocols/jd3/JobQueen.hh>
#include <core/scoring/Energies.hh>
#include <iostream>
#include <string>
#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/stepwise.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/full_model.OptionKeys.gen.hh>
#include <basic/options/keys/edensity.OptionKeys.gen.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/full_model_info/FullModelInfo.hh>
#include <core/sequence/Sequence.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/options/keys/OptionKeyList.hh>

Classes
class	RNA_DeNovoJobQueen

Functions
void	rna_denovo ()
void	rna_denovo_legacy ()
void *	my_main (void *)
int	main (int argc, char *argv[])

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

Detailed Description

Author

Rhiju Das

Function Documentation

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

References basic::options::OptionKeys::rna::denovo::allow_bulge, basic::options::OptionKeys::rna::denovo::allow_consecutive_bulges, basic::options::OptionKeys::rna::denovo::allowed_bulge_res, basic::options::OptionKeys::rna::denovo::autofilter, basic::options::OptionKeys::rna::denovo::out::binary_output, full_model::rna::block_stack_above_res(), full_model::rna::block_stack_below_res(), basic::options::OptionKeys::rna::denovo::bps_moves, basic::options::OptionKeys::rna::denovo::close_loops, basic::options::OptionKeys::rna::denovo::close_loops_after_each_move, utility::io::oc::cout, constraints::cst_file(), full_model::cutpoint_closed(), full_model::cutpoint_open(), basic::options::OptionKeys::rna::denovo::cycles, full_model::cyclize(), basic::options::OptionKeys::rna::data_file, basic::options::OptionKeys::rna::denovo::out::dump, test.T009_Exceptions::e, basic::options::OptionKeys::rna::denovo::minimize::extra_minimize_chi_res, basic::options::OptionKeys::rna::denovo::minimize::extra_minimize_res, in::file::fasta(), basic::options::OptionKeys::rna::denovo::filter_chain_closure, basic::options::OptionKeys::rna::denovo::filter_chain_closure_distance, basic::options::OptionKeys::rna::denovo::filter_chain_closure_halfway, basic::options::OptionKeys::rna::denovo::filter_lores_base_pairs, basic::options::OptionKeys::rna::denovo::filter_lores_base_pairs_early, basic::options::OptionKeys::rna::denovo::fixed_stems, basic::options::OptionKeys::rna::denovo::heat, devel::init(), in::file::input_res(), basic::options::OptionKeys::rna::denovo::jump_change_frequency, basic::options::OptionKeys::rna::denovo::lores_scorefxn, basic::options::OptionKeys::edensity::mapfile, basic::options::OptionKeys::rna::denovo::minimize::minimize_bps, basic::options::OptionKeys::rna::denovo::minimize_rna, basic::options::OptionKeys::rna::denovo::minimize::minimizer_use_coordinate_constraints, basic::options::OptionKeys::rna::denovo::move_first_rigid_body, utility::excn::Exception::msg(), my_main(), in::file::native(), NEW_OPT, basic::options::OptionKeys::rna::denovo::no_filters, out::nstruct(), basic::options::OptionKeys::rna::denovo::obligate_pair, basic::options::OptionKeys::rna::denovo::obligate_pair_explicit, basic::options::OptionKeys::rna::denovo::offset, option, options, basic::options::OptionKeys::rna::denovo::output_filters, basic::options::OptionKeys::rna::denovo::out::output_lores_silent_file, basic::options::OptionKeys::rna::denovo::output_res_num, out::overwrite(), basic::options::OptionKeys::rna::denovo::params_file, basic::options::OptionKeys::chemical::patch_selectors, basic::options::OptionKeys::rna::denovo::refine_native, basic::options::OptionKeys::rna::denovo::refine_silent_file, basic::options::OptionKeys::rna::denovo::rna_lores_chainbreak_weight, basic::options::OptionKeys::rna::denovo::rna_lores_linear_chainbreak_weight, basic::options::OptionKeys::rna::denovo::root_at_first_rigid_body, basic::options::OptionKeys::rna::denovo::rounds, basic::options::OptionKeys::rna::denovo::secstruct, basic::options::OptionKeys::rna::denovo::secstruct_file, basic::options::OptionKeys::rna::denovo::sequence, basic::options::OptionKeys::rna::denovo::set_lores_weights, score::set_weights(), out::file::silent(), basic::options::OptionKeys::rna::denovo::staged_constraints, basic::options::OptionKeys::rna::denovo::suppress_bp_constraint, basic::options::OptionKeys::rna::denovo::tag, basic::options::OptionKeys::rna::denovo::temperature, basic::options::OptionKeys::rna::denovo::use_1jj2_torsions, basic::options::OptionKeys::rna::denovo::vall_torsions, basic::options::OptionKeys::rna::vary_geometry, and score::weights().

void* my_main

(

void *

)

References utility::options::OptionKeys::options::exit, option, options, rna_denovo(), rna_denovo_legacy(), and value.

Referenced by main().

void rna_denovo

(

)

References utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::denovo, demo.D060_Folding::jd, option, options, demo.D010_Pose_structure::pose, basic::options::OptionKeys::stepwise::superimpose_over_all, and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

void rna_denovo_legacy

(

)

References utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::denovo, basic::options::option, option, options, demo.D010_Pose_structure::pose, 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.rna.denovo")

static

Referenced by RNA_DeNovoJobQueen::calc_rmsds(), RNA_DeNovoJobQueen::output_silent_struct(), and RNA_DeNovoJobQueen::output_to_silent_file().