gensym_3bpy_from_dimer.cc File Reference

#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/symmetry.OptionKeys.gen.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/option.hh>
#include <basic/options/util.hh>
#include <basic/Tracer.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/util.hh>
#include <core/chemical/VariantType.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/symmetry/SymDof.hh>
#include <core/conformation/symmetry/SymmData.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/conformation/symmetry/util.hh>
#include <utility/graph/Graph.hh>
#include <core/import_pose/import_pose.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/io/silent/ScoreFileSilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/Stub.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/pack/dunbrack/RotamerLibraryScratchSpace.hh>
#include <core/pack/dunbrack/SingleResidueDunbrackLibrary.hh>
#include <core/pack/make_symmetric_task.hh>
#include <core/pack/optimizeH.hh>
#include <core/pack/packer_neighbors.hh>
#include <core/pack/rotamer_set/RotamerSet.hh>
#include <core/pack/rotamer_set/RotamerSetFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/Pose.hh>
#include <core/pose/symmetry/util.hh>
#include <core/pose/util.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/sc/ShapeComplementarityCalculator.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <devel/init.hh>
#include <numeric/conversions.hh>
#include <numeric/model_quality/rms.hh>
#include <numeric/random/random.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyz.io.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <protocols/filters/Filter.hh>
#include <protocols/filters/BasicFilters.hh>
#include <protocols/score_filters/ScoreTypeFilter.hh>
#include <protocols/scoring/ImplicitFastClashCheck.hh>
#include <protocols/design_opt/GreedyOptMutationMover.hh>
#include <protocols/symmetry/SetupForSymmetryMover.hh>
#include <protocols/minimization_packing/symmetry/SymMinMover.hh>
#include <protocols/minimization_packing/symmetry/SymPackRotamersMover.hh>
#include <protocols/task_operations/JointSequenceOperation.hh>
#include <sstream>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <apps/pilot/will/mynamespaces.ihh>
#include <apps/pilot/will/will_util.ihh>

Macros
#define	ATET   54.735610317245360079
#define	AOCT   35.264389682754668343
#define	AICS   20.89774264557

Functions
int	num_threads ()
int	thread_num ()
void	register_options ()
Real const	sqr (Real const r)
Real	sigmoidish_neighbor (Real const &sqdist)
Real	iface_check_c3 (Pose &pose, Size nres, vector1< Size > const &iface_candidates)
vector1< Size >	read_res_list (string fn)
vector1< Vec >	line_cone_intersection (Vec p, Vec d, Vec v, Vec a, Real t)
vector1< std::pair< Vec, Vec > >	intersecting_bpy_axes (Vec CB, Vec CG, Vec FE, Vec symmaxis, Vec symmcen=Vec(0, 0, 0))
bool	is_near_C2Z_iface (Pose const &p, Size rsd)
void	fixbb_design (Pose &pose, Size ibpy, Size dsub)
void	refine (Pose &pose, Size ibpy, Size dsub)
void	repack (Pose &pose, Size ibpy, Size dsub)
void	new_sc (Pose &pose, utility::vector1< Size > intra_subs, Real &int_area, Real &sc)
Size	num_trimer_contacts (Pose const &psym, Size nres)
Real	dimer_rms (Pose const &psym, Pose const &pdimer)
int	neighbor_count (Pose const &pose, int ires, double distance_threshold=10.0)
void	run ()
int	main (int argc, char **argv)

Variables
static basic::Tracer	TR ("gensym_3bpy_from_dimer")
static core::io::silent::SilentFileData	sfd

Macro Definition Documentation

AICS

#define AICS   20.89774264557

AOCT

#define AOCT   35.264389682754668343

ATET

#define ATET   54.735610317245360079

Function Documentation

dimer_rms()

Real dimer_rms	(	Pose const &	psym,
		Pose const &	pdimer
	)

References create_a3b_hbs::i.

Referenced by run().

fixbb_design()

void fixbb_design	(	Pose &	pose,
		Size	ibpy,
		Size	dsub
	)

References basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, detail::find(), create_a3b_hbs::i, create_a3b_hbs::j, beta_nonlocal::pose, basic::options::OptionKeys::out::sf, basic::options::OptionKeys::symmetry::symmetry, vancomycin::task, and erraser_analysis::temp.

Referenced by refine(), and run().

iface_check_c3()

Real iface_check_c3	(	Pose &	pose,
		Size	nres,
		vector1< Size > const &	iface_candidates
	)

References create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::nres, beta_nonlocal::pose, and sigmoidish_neighbor().

intersecting_bpy_axes()

vector1<std::pair<Vec,Vec> > intersecting_bpy_axes	(	Vec	CB,
		Vec	CG,
		Vec	FE,
		Vec	symmaxis,
		Vec	symmcen = Vec(0,0,0)
	)

References a, kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, CB, CG, numeric::conversions::degrees(), create_a3b_hbs::i, extract_by_sidechain_sasa_score::l, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::L, line_cone_intersection(), numeric::xyzVector< T >::normalized(), basic::options::OptionKeys::out::file::o, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, numeric::projection_matrix(), projperp(), numeric::rotation_matrix_degrees(), predPRE::t, kmeans_adaptive_kernel_density_bb_dependent_rotlib::v, and x.

Referenced by run().

is_near_C2Z_iface()

bool is_near_C2Z_iface	(	Pose const &	p,
		Size	rsd
	)

References CA, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, and numeric::rotation_matrix_degrees().

line_cone_intersection()

vector1<Vec> line_cone_intersection	(	Vec	p,
		Vec	d,
		Vec	v,
		Vec	a,
		Real	t
	)

References a, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, numeric::xyzVector< T >::dot(), numeric::xyzMatrix< Real >::identity(), numeric::outer_product(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, numeric::conversions::radians(), predPRE::t, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

Referenced by intersecting_bpy_axes().

main()

int main	(	int	argc,
		char **	argv
	)

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

neighbor_count()

int neighbor_count	(	Pose const &	pose,
		int	ires,
		double	distance_threshold = 10.0
	)

References build_jacobian::distance, beta_nonlocal::pose, pna::resi, and basic::options::OptionKeys::cmiles::jumping::resj.

Referenced by cone_cen_nc_calculator(), cone_FA_nc_anyatom_calculator(), cone_FA_nc_calculator(), cone_FA_nc_calculator_amide(), TCDock::init(), main(), nc_score(), run(), sphere_cen_nc_calculator(), sphere_FA_nc_anyatom_calculator(), and sphere_FA_nc_calculator().

new_sc()

void new_sc	(	Pose &	pose,
		utility::vector1< Size >	intra_subs,
		Real &	int_area,
		Real &	sc
	)

References detail::find(), create_a3b_hbs::i, beta_nonlocal::pose, basic::options::OptionKeys::canonical_sampling::probabilities::sc, and basic::options::OptionKeys::cutoutdomain::start.

Referenced by run().

num_threads()

int num_threads

(

)

num_trimer_contacts()

Size num_trimer_contacts	(	Pose const &	psym,
		Size	nres
	)

References count, and create_a3b_hbs::nres.

Referenced by run().

read_res_list()

vector1<Size> read_res_list

(

string

fn

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, basic::options::OptionKeys::in::in, extract_by_sidechain_sasa_score::l, create_a3b_hbs::r, and utility_exit_with_message.

refine()

void refine	(	Pose &	pose,
		Size	ibpy,
		Size	dsub
	)

References basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::constraints, test.T009_Exceptions::e, detail::find(), fixbb_design(), create_a3b_hbs::i, create_a3b_hbs::j, basic::options::OptionKeys::in::file::movemap, PI, numeric::NumericTraits< T >::pi(), beta_nonlocal::pose, basic::options::OptionKeys::out::sf, basic::options::OptionKeys::symmetry::symmetry, vancomycin::task, and erraser_analysis::temp.

register_options()

void register_options

(

)

References basic::options::OptionKeys::willmatch::chi1_increment, NEW_OPT, OPT, and basic::options::OptionKeys::in::file::s.

Referenced by main().

repack()

void repack	(	Pose &	pose,
		Size	ibpy,
		Size	dsub
	)

References basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::constraints, detail::find(), create_a3b_hbs::i, create_a3b_hbs::j, beta_nonlocal::pose, basic::options::OptionKeys::out::sf, basic::options::OptionKeys::symmetry::symmetry, and vancomycin::task.

run()

void run

(

)

References AICS, orn_macrocycle::ala, numeric::alignVectorSets(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, angle_degrees(), AOCT, ATET, test.T005_Bindings::base, CB, CG, basic::options::OptionKeys::willmatch::chi1_increment, clash(), erraser_analysis::clash2, basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, kmeans_adaptive_kernel_density_bb_dependent_rotlib::dang, numeric::dihedral_degrees(), dimer_rms(), numeric::xyzVector< T >::distance(), numeric::distance_squared(), numeric::xyzVector< T >::distance_squared(), basic::options::OptionKeys::in::file::dssp, test.T009_Exceptions::e, ObjexxFCL::format::F(), vancomycin::f2, utility::file_basename(), filter, fixbb_design(), PREcst::fname, create_a3b_hbs::i, test.T110_numeric::I, intersecting_bpy_axes(), ObjexxFCL::lead_zero_string_of(), min(), basic::options::OptionKeys::in::file::movemap, neighbor_count(), new_sc(), num_trimer_contacts(), basic::options::OptionKeys::out::file::o, basic::options::option, pyrosetta.distributed.io::pose_from_file, predPRE::R2, basic::options::OptionKeys::cp::relax_mover, rot_pose(), numeric::rotation_matrix_degrees(), basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::canonical_sampling::probabilities::sc, basic::options::OptionKeys::out::path::scratch, basic::options::OptionKeys::out::sf, basic::options::OptionKeys::symmetry::symmetry_definition, vancomycin::task, basic::options::TR, trans_pose(), and utility_exit_with_message.

Referenced by main().

sigmoidish_neighbor()

Real sigmoidish_neighbor ( Real const &  sqdist )

inline

References dist(), and sqr().

Referenced by iface_check_c3().

sqr()

Real const sqr ( Real const  r )

inline

References create_a3b_hbs::r.

Referenced by sigmoidish_neighbor().

thread_num()

int thread_num

(

)

Variable Documentation

sfd

core::io::silent::SilentFileData sfd

static

TR

basic::Tracer TR("gensym_3bpy_from_dimer") ( "gensym_3bpy_from_dimer"  )

static