swa_protein_main.cc File Reference

#include <core/scoring/rms_util.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/AtomICoor.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueMatcher.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/conformation/Conformation.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/RT.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID.hh>
#include <core/id/NamedAtomID.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/Sequence.fwd.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/ScoreFunction.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/util.hh>
#include <protocols/stepwise/modeler/protein/InputStreamWithResidueInfo.hh>
#include <protocols/stepwise/modeler/file_util.hh>
#include <protocols/stepwise/modeler/util.hh>
#include <protocols/stepwise/modeler/rna/util.hh>
#include <protocols/stepwise/sampler/NoOpStepWiseSampler.hh>
#include <protocols/stepwise/sampler/protein/util.hh>
#include <protocols/cluster/cluster.hh>
#include <core/io/silent/ProteinSilentStruct.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/optimizeH.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <basic/options/option.hh>
#include <basic/options/after_opts.hh>
#include <basic/options/util.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/datacache/CacheableDataType.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/import_pose/pose_stream/ExtendedPoseInputStream.hh>
#include <core/import_pose/pose_stream/PoseInputStream.fwd.hh>
#include <core/import_pose/pose_stream/PDBPoseInputStream.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <basic/datacache/CacheableString.hh>
#include <basic/basic.hh>
#include <basic/database/open.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <utility/vector1.hh>
#include <numeric/xyzVector.hh>
#include <numeric/conversions.hh>
#include <numeric/random/random.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/angle.functions.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <fstream>
#include <iostream>
#include <basic/Tracer.hh>
#include <basic/options/keys/full_model.OptionKeys.gen.hh>
#include <basic/options/keys/chemical.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
typedef numeric::xyzMatrix< Real >	Matrix

Functions
static THREAD_LOCAL basic::Tracer	TR ("swa_protein_main")
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[])

Typedef Documentation

typedef numeric::xyzMatrix< Real > Matrix

Function Documentation

void calc_rms_test

(

)

References basic::options::OptionKeys::full_model::calc_rms_res, basic::options::OptionKeys::chemical::chemical, app.surface_docking.surface_docking::input, in::file::native(), test.Workshop7test::native_pose, option, options, app.surface_docking.surface_docking::pose, in::file::silent(), basic::options::OptionKeys::in::file::silent, out::file::silent(), basic::options::OptionKeys::inout::dbms::user, and basic::options::OptionKeys::full_model::working_res.

Referenced by my_main().

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::remodel::cluster_radius, out::nstruct(), option, options, 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().

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, in::file::native(), option, options, app.surface_docking.surface_docking::pose, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by rebuild_test().

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

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::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(), utility::io::oc::cout, basic::options::OptionKeys::constraints::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, utility::options::OptionKeys::options::exit, basic::options::OptionKeys::stepwise::protein::filter_native_big_bins, basic::options::OptionKeys::rna::farna::erraser::fixed_res, basic::options::OptionKeys::dna::specificity::frag_files, basic::options::OptionKeys::stepwise::protein::ghost_loops, basic::options::OptionKeys::stepwise::protein::global_optimize, devel::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, utility::excn::EXCN_Base::msg(), my_main(), basic::options::OptionKeys::stepwise::protein::n_sample, NEW_OPT, basic::options::OptionKeys::stepwise::protein::nstruct_centroid, option, options, basic::options::OptionKeys::stepwise::protein::protein_prepack, 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, basic::options::OptionKeys::mp::secstruct, basic::options::OptionKeys::rna::farna::erraser::skip_minimize, basic::options::OptionKeys::stepwise::use_green_packer, basic::options::OptionKeys::stepwise::protein::use_packer_instead_of_rotamer_trials, basic::options::OptionKeys::full_model::virtual_res, and basic::options::OptionKeys::full_model::working_res.

void* my_main

(

void *

)

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

Referenced by main().

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::constraints::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::farna::erraser::fixed_res, pyrosetta::get_score_function, initialize_native_pose(), basic::options::OptionKeys::full_model::jump_res, edensity::mapfile(), test.Workshop7test::native_pose, option, options, loops::pack, app.surface_docking.surface_docking::pose, basic::options::OptionKeys::stepwise::protein::protein_prepack, runtime_assert, basic::options::OptionKeys::full_model::sample_res, PyMOL_demo::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::mp::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().

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

static