place_fragments_into_density.cc File Reference

#include <devel/init.hh>
#include <core/pose/Pose.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/util.hh>
#include <core/import_pose/import_pose.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <protocols/electron_density/util.hh>
#include <protocols/electron_density/SetupForDensityScoringMover.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/rigid/RB_geometry.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/scoring/electron_density/ElectronDensity.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/fragment/util.hh>
#include <core/fragment/FragmentIO.hh>
#include <core/fragment/FragSet.hh>
#include <core/fragment/Frame.hh>
#include <core/fragment/FrameIterator.hh>
#include <core/fragment/FragData.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/edensity.OptionKeys.gen.hh>
#include <ObjexxFCL/format.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyzVector.io.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <basic/Tracer.hh>
#include <iostream>
#include <string>
#include <list>
#include <algorithm>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <apps/pilot/rayyrw/min_pack_min.hh>
#include <apps/pilot/rayyrw/util.hh>

Classes
class	ThisApplication
class	Results_Keeper

Functions
core::Size	get_radius (core::pose::Pose &pose)
core::Size	get_median (utility::vector1< core::Size > &v)
core::Size	get_radius_in_frag_set (core::fragment::FragSetCOP fragments, std::string &sequence, core::Size given_seq_pos)
void	density_grid_search (core::Real const &no_density_score, core::scoring::electron_density::ElectronDensity &density, core::pose::Pose &pose, core::Size nRsteps, double &map_s, double &map_s2, double &pose_s, double &pose_s2, core::Size list_size, core::Real movestep, core::Size edge, std::list< Results_Keeper > &keeper_list)
void	move_it (core::pose::Pose &pose, numeric::xyzVector< core::Real > &pre_trans, numeric::xyzVector< core::Real > &translation, numeric::xyzMatrix< core::Real > &rotation)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("place_fragment_into_density")
static basic::Tracer	func ("density_grid_search_func")

Function Documentation

density_grid_search()

void density_grid_search	(	core::Real const &	no_density_score,
		core::scoring::electron_density::ElectronDensity &	density,
		core::pose::Pose &	pose,
		core::Size	nRsteps,
		double &	map_s,
		double &	map_s2,
		double &	pose_s,
		double &	pose_s2,
		core::Size	list_size,
		core::Real	movestep,
		core::Size	edge,
		std::list< Results_Keeper > &	keeper_list
	)

References score_vs_rmsd::density, func, basic::options::OptionKeys::docking::ligand::grid::grid, create_a3b_hbs::i, subloop_histogram::iterator, create_a3b_hbs::j, create_a3b_hbs::k, beta_nonlocal::pose, PyMOL_demo::pose_s, and 3d_histogram::rotation.

Referenced by main().

get_median()

core::Size get_median

(

utility::vector1< core::Size > &

v

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

Referenced by get_radius_in_frag_set().

get_radius()

core::Size get_radius

(

core::pose::Pose &

pose

)

References val2thr::atom, basic::options::OptionKeys::edensity::atom_mask, numeric::xyzVector< T >::distance_squared(), create_a3b_hbs::i, enumerate_junctions::int, create_a3b_hbs::j, max(), min(), basic::options::option, and beta_nonlocal::pose.

Referenced by get_radius_in_frag_set(), and main().

get_radius_in_frag_set()

core::Size get_radius_in_frag_set	(	core::fragment::FragSetCOP	fragments,
		std::string &	sequence,
		core::Size	given_seq_pos
	)

References basic::options::OptionKeys::in::path::fragments, numeric::kinematic_closure::frame(), get_median(), get_radius(), create_a3b_hbs::j, basic::options::OptionKeys::cluster::radius, basic::options::OptionKeys::in::file::residue_type_set, ObjexxFCL::format::RJ(), basic::options::OptionKeys::relax::sequence, and TR.

Referenced by main().

main()

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

References argv, MinPackMin::backbone_minimization(), basic::options::OptionKeys::cycles, basic::options::OptionKeys::msd::debug, score_vs_rmsd::density, density_grid_search(), test.T009_Exceptions::e, ObjexxFCL::format::F(), in::file::fasta(), utility::file::file_exists(), detail::find(), basic::options::OptionKeys::in::file::fold_tree, basic::options::OptionKeys::in::path::fragments, numeric::kinematic_closure::frame(), get_radius(), get_radius_in_frag_set(), basic::options::OptionKeys::docking::ligand::grid::grid, create_a3b_hbs::i, basic::init(), int2str(), subloop_histogram::iterator, create_a3b_hbs::j, move_it(), in::file::native(), docking::native_pose, basic::options::OptionKeys::loodo::num_frags, basic::options::option, option, erraser_single_res_analysis::out, MinPackMin::pack_sidechains(), make_symmdef_file_denovo::pos, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, PyMOL_demo::pose_s, ThisApplication::register_options(), remove_all_virtual_residues(), basic::options::OptionKeys::in::file::residue_type_set, MinPackMin::rigid_body_minimization(), ObjexxFCL::format::RJ(), 3d_histogram::rotation, out::file::scorefile(), basic::options::OptionKeys::relax::sequence, out::file::silent(), tag, TR, basic::options::OptionKeys::rigid::translation, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

move_it()

void move_it	(	core::pose::Pose &	pose,
		numeric::xyzVector< core::Real > &	pre_trans,
		numeric::xyzVector< core::Real > &	translation,
		numeric::xyzMatrix< core::Real > &	rotation
	)

References natoms(), beta_nonlocal::pose, 3d_histogram::rotation, and basic::options::OptionKeys::rigid::translation.

Referenced by main().

Variable Documentation

func

basic::Tracer func("density_grid_search_func") ( "density_grid_search_func"  )

static

Referenced by add_coordinate_constraints(), add_dna_states(), add_triazole_constraints(), addcyclicconstraints(), InteractionDistMinimizer::apply(), A3BPeptideBuilder::apply(), CovalentPeptidomimeticDockDesign::apply(), CovalentPeptidomimeticCreator::apply(), MikeLinkerMover::apply(), TriazoleCreator::apply(), constrain_loop_ends(), create_dihedral_constraint(), density_grid_search(), utility::graph::depth_first_search_sort(), utility::graph::depth_first_visit(), utility::graph::depth_first_visit_sort_impl(), basic::thread_manager::RosettaThreadManager::do_work_vector_in_threads_no_locking(), enforce_atoms_coplanar(), enforce_triazole_distance(), ga_main(), get_gaussian_chain_func(), main(), numeric::expression_parser::ArithmeticASTFactor::parse(), apps::pilot::momeara::HBondConformation::relax_pose_around_hbond(), detail::report_error(), rotamerize_rna_test(), sequence_tolerance_main(), sequence_tolerance_mf_main(), setup_rna_base_pair_constraints(), setup_rna_chainbreak_constraints(), and vary_bond_length().

TR

basic::Tracer TR("place_fragment_into_density") ( "place_fragment_into_density"  )

static

Referenced by get_radius_in_frag_set(), and main().