matdes_design_2comp.cc File Reference

#include <basic/database/open.hh>
#include <basic/options/keys/holes.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/symmetry.OptionKeys.gen.hh>
#include <basic/options/keys/matdes.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/options/keys/parser.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <basic/Tracer.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/util.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/symmetry/SymDof.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/id/AtomID_Map.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/io/silent/ScoreFileSilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pack/make_symmetric_task.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/operation/NoRepackDisulfides.hh>
#include <protocols/simple_task_operations/RestrictToInterface.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/init_id_map.hh>
#include <core/pose/symmetry/util.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/packing/compute_holes_score.hh>
#include <core/scoring/packing/HolesParams.hh>
#include <core/scoring/packstat/compute_sasa.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/sasa.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/types.hh>
#include <fstream>
#include <iostream>
#include <math.h>
#include <numeric/random/random.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/format.hh>
#include <protocols/docking/util.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/minimization_packing/symmetry/SymPackRotamersMover.hh>
#include <protocols/minimization_packing/symmetry/SymMinMover.hh>
#include <sstream>
#include <string>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/mpistream.hh>
#include <utility/string_util.hh>
#include <core/scoring/sc/ShapeComplementarityCalculator.hh>
#include <core/scoring/constraints/ResidueTypeConstraint.hh>
#include <protocols/simple_ddg/ddG.hh>
#include <protocols/task_operations/LimitAromaChi2Operation.hh>
#include <core/pack/task/ResfileReader.hh>
#include <protocols/simple_pose_metric_calculators/BuriedUnsatisfiedPolarsCalculator.hh>
#include <core/pose/metrics/CalculatorFactory.hh>
#include <core/pose/metrics/PoseMetricCalculatorBase.hh>
#include <protocols/simple_pose_metric_calculators/NumberHBondsCalculator.hh>
#include <basic/MetricValue.hh>

Typedefs
typedef numeric::xyzVector< Real >	Vec
typedef numeric::xyzMatrix< Real >	Mat
typedef vector1< Size >	Sizes

Functions
void	register_options ()
core::kinematics::Stub	getxform (core::conformation::Residue const &move_resi, core::conformation::Residue const &fixd_resi)
void	trans_pose (Pose &pose, Vec const &trans, Size start=1, Size end=0)
void	rot_pose (Pose &pose, Mat const &rot, Size start=1, Size end=0)
void	rot_pose (Pose &pose, Mat const &rot, Vec const &cen, Size start=1, Size end=0)
void	rot_pose (Pose &pose, Vec const &axis, double const &ang, Size start=1, Size end=0)
void	rot_pose (Pose &pose, Vec const &axis, double const &ang, Vec const &cen, Size start=1, Size end=0)
void	alignaxis (core::pose::Pose &pose, Vec newaxis, Vec oldaxis, Vec cen=Vec(0, 0, 0))
Real	sqr (Real x)
void	print_movemap (core::kinematics::MoveMap const &movemap)
void	design (Pose &pose, ScoreFunctionOP sf, utility::vector1< Size > design_pos, bool hphobic_only)
void	design_using_resfile (Pose &pose, ScoreFunctionOP sf, std::string resfile, utility::vector1< Size > &design_pos)
void	repack (Pose &pose, ScoreFunctionOP sf, utility::vector1< Size > design_pos)
void	minimize (Pose &pose, ScoreFunctionOP sf, utility::vector1< Size > design_pos, bool move_bb, bool move_sc, bool move_rb)
int	which_subsub (int i, Pose const &p1, Pose const &p2)
utility::vector1< Real >	sidechain_sasa (Pose const &pose, Real probe_radius)
void	new_sc (Pose &pose, Sizes isubs1, Sizes isubs2, Pose const &p1, Pose const &p2, Real &int_area, Real &sc)
Pose	get_neighbor_subs (Pose const &pose, Sizes intra_subs1, Sizes intra_subs2, Pose const &p1, Pose const &p2)
Real	get_unsat_polars (Pose const &bound, Pose const &unbound, Size nres_monomer, string fn)
Real	get_atom_packing_score (Pose const &pose, Sizes intra_subs1, Sizes intra_subs2, Pose const &p1, Pose const &p2, Real cutoff=9.0)
Real	average_degree (Pose const &pose, vector1< Size > mutalyze_pos, Sizes intra_subs1, Sizes intra_subs2, Pose const &p1, Pose const &p2, Real distance_threshold=10.0)
void *	dostuff (void *)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("2comp_design")

Typedef Documentation

Mat

typedef numeric::xyzMatrix<Real> Mat

Sizes

typedef vector1<Size> Sizes

Vec

typedef numeric::xyzVector<Real> Vec

Function Documentation

alignaxis()

void alignaxis	(	core::pose::Pose &	pose,
		Vec	newaxis,
		Vec	oldaxis,
		Vec	cen = Vec(0,0,0)
	)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, numeric::xyzVector< T >::cross(), numeric::xyzVector< T >::dot(), numeric::max(), numeric::min(), numeric::xyzVector< T >::normalize(), numeric::xyzVector< T >::normalized(), numeric::constants::d::pi, beta_nonlocal::pose, and rot_pose().

Referenced by alncys(), design_hits(), dock(), dostuff(), TCDock::dump_pdb(), get_cys_rts(), TCDock::init(), run(), and run_sf4h().

average_degree()

Real average_degree	(	Pose const &	pose,
		vector1< Size >	mutalyze_pos,
		Sizes	intra_subs1,
		Sizes	intra_subs2,
		Pose const &	p1,
		Pose const &	p2,
		Real	distance_threshold = 10.0
	)

References count_neighbors(), build_jacobian::distance, detail::find(), create_a3b_hbs::i, p2, beta_nonlocal::pose, pna::resi, basic::options::OptionKeys::cmiles::jumping::resj, TR, and which_subsub().

Referenced by dostuff().

design()

void design	(	Pose &	pose,
		ScoreFunctionOP	sf,
		utility::vector1< Size >	design_pos,
		bool	hphobic_only
	)

References detail::find(), create_a3b_hbs::i, vancomycin::pack, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::sf, basic::options::OptionKeys::symmetry::symmetry, vancomycin::task, and erraser_analysis::temp.

design_using_resfile()

void design_using_resfile	(	Pose &	pose,
		ScoreFunctionOP	sf,
		std::string	resfile,
		utility::vector1< Size > &	design_pos
	)

References detail::find(), create_a3b_hbs::i, vancomycin::pack, parse_resfile(), beta_nonlocal::pose, basic::options::OptionKeys::packing::resfile, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::sf, basic::options::OptionKeys::symmetry::symmetry, and vancomycin::task.

Referenced by dostuff().

dostuff()

void* dostuff

(

void *

)

References alignaxis(), average_degree(), basic::options::OptionKeys::matdes::design::contact_dist, matdes::design::contact_dist(), utility::io::oc::cout, design_using_resfile(), extract_scores(), fav_nat_bonus, matdes::design::fav_nat_bonus(), detail::find(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, get_atom_packing_score(), get_unsat_polars(), basic::options::OptionKeys::matdes::design::grid_nsamp_angle, matdes::design::grid_nsamp_angle(), basic::options::OptionKeys::matdes::design::grid_nsamp_radius, matdes::design::grid_nsamp_radius(), basic::options::OptionKeys::matdes::design::grid_size_angle, matdes::design::grid_size_angle(), basic::options::OptionKeys::matdes::design::grid_size_radius, matdes::design::grid_size_radius(), create_a3b_hbs::i, basic::options::OptionKeys::matdes::mutalyze::min_rb, matdes::mutalyze::min_rb(), minimize(), new_sc(), numeric::xyzVector< T >::normalized(), out::file::o(), basic::options::option, option, erraser_single_res_analysis::out, p2, matdes::pdbID(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, matdes::prefix(), repack(), basic::options::OptionKeys::packing::resfile, rot_pose(), numeric::rotation_matrix_degrees(), basic::options::OptionKeys::canonical_sampling::probabilities::sc, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::sf, sfd, sidechain_sasa(), out::file::silent(), ObjexxFCL::string_of(), basic::options::OptionKeys::symmetry::symmetry, basic::options::OptionKeys::symmetry::symmetry_definition, tag, TR, vancomycin::trans2, trans_pose(), numeric::random::uniform(), basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and which_subsub().

Referenced by main().

get_atom_packing_score()

Real get_atom_packing_score	(	Pose const &	pose,
		Sizes	intra_subs1,
		Sizes	intra_subs2,
		Pose const &	p1,
		Pose const &	p2,
		Real	cutoff = 9.0
	)

References count, extract_by_sidechain_sasa_score::cutoff, basic::database::full_name(), get_neighbor_subs(), p2, and beta_nonlocal::pose.

Referenced by dostuff().

get_neighbor_subs()

Pose get_neighbor_subs	(	Pose const &	pose,
		Sizes	intra_subs1,
		Sizes	intra_subs2,
		Pose const &	p1,
		Pose const &	p2
	)

References detail::find(), create_a3b_hbs::i, p2, beta_nonlocal::pose, basic::options::OptionKeys::cutoutdomain::start, and which_subsub().

Referenced by get_atom_packing_score().

get_unsat_polars()

Real get_unsat_polars	(	Pose const &	bound,
		Pose const &	unbound,
		Size	nres_monomer,
		string	fn
	)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::flag, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, ObjexxFCL::string_of(), TR, and basic::MetricValue< T >::value().

Referenced by dostuff().

getxform()

core::kinematics::Stub getxform	(	core::conformation::Residue const &	move_resi,
		core::conformation::Residue const &	fixd_resi
	)

References numeric::alignVectorSets(), and docking::s.

Referenced by bound_petf_clash(), build_algned_linker(), doit(), and main().

main()

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

References argv, dostuff(), test.T009_Exceptions::e, func, basic::init(), and register_options().

minimize()

void minimize	(	Pose &	pose,
		ScoreFunctionOP	sf,
		utility::vector1< Size >	design_pos,
		bool	move_bb,
		bool	move_sc,
		bool	move_rb
	)

References test.T009_Exceptions::e, create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, basic::options::OptionKeys::in::file::movemap, beta_nonlocal::pose, and basic::options::OptionKeys::out::sf.

Referenced by dostuff().

new_sc()

void new_sc	(	Pose &	pose,
		Sizes	isubs1,
		Sizes	isubs2,
		Pose const &	p1,
		Pose const &	p2,
		Real &	int_area,
		Real &	sc
	)

References utility::io::oc::cout, detail::find(), create_a3b_hbs::i, p2, beta_nonlocal::pose, basic::options::OptionKeys::canonical_sampling::probabilities::sc, TR, and which_subsub().

Referenced by dostuff().

print_movemap()

void print_movemap

(

core::kinematics::MoveMap const &

movemap

)

References create_a3b_hbs::i, basic::options::OptionKeys::in::file::movemap, and TR.

register_options()

void register_options

(

)

References NEW_OPT.

Referenced by main().

repack()

void repack	(	Pose &	pose,
		ScoreFunctionOP	sf,
		utility::vector1< Size >	design_pos
	)

References detail::find(), create_a3b_hbs::i, vancomycin::pack, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::sf, basic::options::OptionKeys::symmetry::symmetry, and vancomycin::task.

Referenced by dostuff().

rot_pose() [1/4]

void rot_pose	(	Pose &	pose,
		Mat const &	rot,
		Size	start = 1,
		Size	end = 0
	)

References end, natoms(), beta_nonlocal::pose, rot, and basic::options::OptionKeys::cutoutdomain::start.

Referenced by align_native_state(), alignaxis(), alncys(), calc_c3_rmsd(), MatchSet::cross(), MatchSet::cross_homodimer(), cxdock_design(), design_hits(), dock(), dostuff(), TCDock::dump_pdb(), dumpsym2(), dumpsym6(), get_cys_rts(), get_rmsd_debug(), ik_arg_asp_frnt(), ik_arg_asp_side(), ik_arg_glu_frnt(), ik_arg_glu_side(), ik_his_clamp(), TCDock::init(), main(), make_native_olig(), make_two_trimers(), rot_pose(), run(), run_m8(), run_sf4h(), set_disulf(), and test_chi_xform().

rot_pose() [2/4]

void rot_pose	(	Pose &	pose,
		Mat const &	rot,
		Vec const &	cen,
		Size	start = 1,
		Size	end = 0
	)

References end, beta_nonlocal::pose, rot, rot_pose(), basic::options::OptionKeys::cutoutdomain::start, and trans_pose().

rot_pose() [3/4]

void rot_pose	(	Pose &	pose,
		Vec const &	axis,
		double const &	ang,
		Size	start = 1,
		Size	end = 0
	)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, end, beta_nonlocal::pose, rot_pose(), numeric::rotation_matrix_degrees(), and basic::options::OptionKeys::cutoutdomain::start.

rot_pose() [4/4]

void rot_pose	(	Pose &	pose,
		Vec const &	axis,
		double const &	ang,
		Vec const &	cen,
		Size	start = 1,
		Size	end = 0
	)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, end, beta_nonlocal::pose, rot_pose(), numeric::rotation_matrix_degrees(), and basic::options::OptionKeys::cutoutdomain::start.

sidechain_sasa()

utility::vector1<Real> sidechain_sasa	(	Pose const &	pose,
		Real	probe_radius
	)

References basic::options::OptionKeys::edensity::atom_mask, create_a3b_hbs::i, create_a3b_hbs::j, beta_nonlocal::pose, and bur_nodon_tyr::probe_radius.

Referenced by dostuff().

sqr()

Real sqr ( Real  x )

inline

References x.

trans_pose()

void trans_pose	(	Pose &	pose,
		Vec const &	trans,
		Size	start = 1,
		Size	end = 0
	)

References end, natoms(), beta_nonlocal::pose, basic::options::OptionKeys::cutoutdomain::start, and trans.

Referenced by alncys(), calc_c3_rmsd(), MatchSet::cross(), MatchSet::cross_homodimer(), cxdock_design(), design_hits(), dock(), dostuff(), TCDock::dump_pdb(), get_centered_pose(), get_cys_rts(), gpu_score_test(), ik_arg_asp_frnt(), ik_arg_asp_side(), ik_arg_glu_frnt(), ik_arg_glu_side(), ik_his_clamp(), main(), rot_pose(), run(), run_sf4h(), HubDenovo::stupid_ddg(), and test_chi_xform().

which_subsub()

int which_subsub	(	int	i,
		Pose const &	p1,
		Pose const &	p2
	)

References create_a3b_hbs::i, N, and p2.

Referenced by average_degree(), dostuff(), get_neighbor_subs(), and new_sc().

Variable Documentation

TR

basic::Tracer TR("2comp_design") ( "2comp_design"  )

static

Referenced by average_degree(), dostuff(), get_unsat_polars(), new_sc(), and print_movemap().