swa_protein_main.cc File Reference

#include <core/types.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/conformation/Conformation.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/Sequence.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/stepwise/modeler/StepWiseModeler.hh>
#include <protocols/stepwise/modeler/options/StepWiseModelerOptions.hh>
#include <protocols/stepwise/modeler/align/StepWiseLegacyClustererSilentBased.hh>
#include <protocols/stepwise/legacy/modeler/protein/StepWiseProteinPoseSetup.hh>
#include <protocols/stepwise/legacy/modeler/protein/util.hh>
#include <protocols/stepwise/modeler/working_parameters/StepWiseWorkingParameters.hh>
#include <protocols/stepwise/modeler/protein/InputStreamWithResidueInfo.hh>
#include <protocols/stepwise/modeler/util.hh>
#include <protocols/stepwise/sampler/protein/util.hh>
#include <core/io/silent/SilentFileData.fwd.hh>
#include <core/io/silent/util.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <core/pose/Pose.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/util.hh>
#include <core/pose/subpose_manipulation_util.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.hh>
#include <devel/init.hh>
#include <utility/vector1.hh>
#include <basic/Tracer.hh>
#include <core/io/silent/SilentStruct.hh>
#include <basic/options/keys/full_model.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/stepwise.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/cluster.OptionKeys.gen.hh>
#include <basic/options/keys/edensity.OptionKeys.gen.hh>

Typedefs
using	Matrix = numeric::xyzMatrix< Real >

Functions
void	initialize_native_pose (core::pose::PoseOP &native_pose, core::chemical::ResidueTypeSetCAP &rsd_set)
void	rebuild_test ()
void	cluster_outfile_test ()
void	calc_rms_test ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("swa_protein_main")

Typedef Documentation

Matrix

using Matrix = numeric::xyzMatrix<Real>

Function Documentation

calc_rms_test()

void calc_rms_test

(

)

References basic::options::OptionKeys::full_model::calc_rms_res, basic::options::OptionKeys::chemical::chemical, gaussian-sampling::input, in::file::native(), docking::native_pose, option, pdbslice(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::in::file::silent, in::file::silent(), out::file::silent(), basic::options::OptionKeys::inout::dbms::user, and basic::options::OptionKeys::full_model::working_res.

Referenced by my_main().

cluster_outfile_test()

void cluster_outfile_test

(

)

References basic::options::OptionKeys::cluster::auto_tune, basic::options::OptionKeys::full_model::calc_rms_res, basic::options::OptionKeys::stepwise::protein::cluster_by_all_atom_rmsd, basic::options::OptionKeys::cluster::energy_based_clustering::cluster_radius, out::nstruct(), option, basic::options::OptionKeys::cluster::radius, basic::options::OptionKeys::stepwise::protein::score_diff_cut, in::file::silent(), out::file::silent(), basic::options::OptionKeys::inout::dbms::user, and basic::options::OptionKeys::full_model::working_res.

Referenced by my_main().

initialize_native_pose()

void initialize_native_pose	(	core::pose::PoseOP &	native_pose,
		core::chemical::ResidueTypeSetCAP &	rsd_set
	)

References basic::options::OptionKeys::stepwise::protein::disulfide_file, basic::options::OptionKeys::stepwise::dump, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, in::file::native(), docking::native_pose, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by rebuild_test().

main()

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

References basic::options::OptionKeys::stepwise::align_pdb, basic::options::OptionKeys::stepwise::protein::allow_virtual_side_chains, argv, basic::options::OptionKeys::stepwise::atr_rep_screen, basic::options::OptionKeys::cluster::auto_tune, basic::options::OptionKeys::stepwise::protein::bridge_res, numeric::model_quality::calc_rms(), basic::options::OptionKeys::stepwise::protein::cart_min, basic::options::OptionKeys::stepwise::protein::ccd_close, basic::options::OptionKeys::in::file::centroid, basic::options::OptionKeys::stepwise::protein::centroid_output, basic::options::OptionKeys::stepwise::rna::centroid_screen, basic::options::OptionKeys::stepwise::protein::centroid_weights, basic::options::OptionKeys::stepwise::protein::cluster_by_all_atom_rmsd, cluster_test(), basic::options::OptionKeys::cluster::energy_based_clustering::cst_file, basic::options::OptionKeys::full_model::cutpoint_closed, basic::options::OptionKeys::full_model::cutpoint_open, basic::options::OptionKeys::stepwise::protein::disable_sampling_of_loop_takeoff, basic::options::OptionKeys::stepwise::protein::disulfide_file, basic::options::OptionKeys::magnesium::montecarlo::dump, test.T009_Exceptions::e, utility::options::OptionKeys::options::exit, basic::options::OptionKeys::stepwise::protein::filter_native_big_bins, basic::options::OptionKeys::rna::erraser::fixed_res, basic::options::OptionKeys::dna::specificity::frag_files, basic::options::OptionKeys::stepwise::protein::ghost_loops, basic::options::OptionKeys::stepwise::protein::global_optimize, basic::init(), basic::options::OptionKeys::full_model::jump_res, basic::options::OptionKeys::relax::min_tolerance, basic::options::OptionKeys::dna::specificity::min_type, basic::options::OptionKeys::stepwise::protein::move_jumps_between_chains, my_main(), basic::options::OptionKeys::stepwise::protein::n_sample, NEW_OPT, basic::options::OptionKeys::stepwise::protein::nstruct_centroid, option, basic::options::OptionKeys::stepwise::protein::protein_prepack, rebuild(), basic::options::OptionKeys::stepwise::rmsd_screen, basic::options::OptionKeys::stepwise::protein::sample_beta, basic::options::OptionKeys::full_model::sample_res, basic::options::OptionKeys::cluster::score_diff_cut, secstruct(), basic::options::OptionKeys::rna::erraser::skip_minimize, basic::options::OptionKeys::stepwise::use_green_packer, basic::options::OptionKeys::stepwise::protein::use_packer_instead_of_rotamer_trials, viewer_main(), basic::options::OptionKeys::full_model::virtual_res, and basic::options::OptionKeys::full_model::working_res.

my_main()

void* my_main

(

void *

)

References numeric::model_quality::calc_rms(), calc_rms_test(), cluster_outfile_test(), cluster_test(), utility::options::OptionKeys::options::exit, option, rebuild_test(), and utility_exit_with_message.

Referenced by main().

rebuild_test()

void rebuild_test

(

)

References basic::options::OptionKeys::stepwise::align_pdb, basic::options::OptionKeys::stepwise::protein::allow_virtual_side_chains, basic::options::OptionKeys::stepwise::atr_rep_screen, basic::options::OptionKeys::stepwise::protein::bridge_res, basic::options::OptionKeys::full_model::calc_rms_res, basic::options::OptionKeys::in::file::centroid, basic::options::OptionKeys::relax::centroid_mode, basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::constraints, pyrosetta::create_score_function, basic::options::OptionKeys::cluster::energy_based_clustering::cst_file, basic::options::OptionKeys::full_model::cutpoint_closed, basic::options::OptionKeys::full_model::cutpoint_open, basic::options::OptionKeys::stepwise::protein::disulfide_file, basic::options::OptionKeys::magnesium::montecarlo::dump, in::file::fasta(), basic::options::OptionKeys::rna::erraser::fixed_res, initialize_native_pose(), basic::options::OptionKeys::full_model::jump_res, edensity::mapfile(), docking::native_pose, option, beta_nonlocal::pose, basic::options::OptionKeys::stepwise::protein::protein_prepack, runtime_assert, basic::options::OptionKeys::full_model::sample_res, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, secstruct(), basic::options::OptionKeys::in::file::silent, out::file::silent(), basic::options::OptionKeys::stepwise::test_encapsulation, basic::options::OptionKeys::inout::dbms::user, basic::options::OptionKeys::full_model::virtual_res, and score::weights().

Referenced by my_main().

Variable Documentation

TR

basic::Tracer TR("swa_protein_main") ( "swa_protein_main"  )

static