genI213.cc File Reference

#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/option.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 <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/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/Stub.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/pack/dunbrack/RotamerLibraryScratchSpace.hh>
#include <core/pack/dunbrack/SingleResidueDunbrackLibrary.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/Pose.hh>
#include <core/pose/symmetry/util.hh>
#include <core/pose/util.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <numeric/conversions.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/minimization_packing/symmetry/SymMinMover.hh>
#include <protocols/minimization_packing/symmetry/SymPackRotamersMover.hh>
#include <protocols/scoring/ImplicitFastClashCheck.hh>
#include <sstream>
#include <utility/io/ozstream.hh>
#include <utility/string_constants.hh>
#include <utility/vector0.hh>
#include <utility/vector1.hh>
#include <platform/types.hh>
#include <core/pose/init_id_map.hh>
#include <apps/pilot/will/mynamespaces.ihh>
#include <apps/pilot/will/will_util.ihh>

Classes
struct	Hit

Functions
Real	sqr (Real const r)
Real	sigmoidish_neighbor (Real const &sqdist)
vector1< Size >	get_scanres (Pose const &pose)
void	dumpsym (Pose const &pose, Mat R2, Mat R3a, Mat R3b, Vec cen2, string fname)
void	dumpsym6 (Pose const &pose, Mat R2, Mat R3a, Mat R3b, Vec HG, string fname, Size irsd, Size ch1, Size ch2, Real ANG)
void	dumpsym2 (Pose const &pose, Mat R2, Mat R3a, Mat R3b, Vec HG, string fname, Size irsd, Size ch1, Size ch2, Real ANG)
std::pair< vector1< Hit >, vector1< Hit > >	dock (Pose &init, string)
void	design (Pose &pose, ScoreFunctionOP sf, Size Ntri)
void	repack_iface (Pose &pose, ScoreFunctionOP sf, Size Ntri)
void	repack_all (Pose &pose, ScoreFunctionOP sf, Size Ntri)
void	design_hits (Pose &p, string fn, vector1< Hit > h, vector1< Hit > allh)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("genI213")
static core::io::silent::SilentFileData	sfd

Function Documentation

design()

void design	(	Pose &	pose,
		ScoreFunctionOP	sf,
		Size	Ntri
	)

References CA, CB, test.T009_Exceptions::e, create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, min(), basic::options::OptionKeys::in::file::movemap, beta_nonlocal::pose, basic::options::OptionKeys::casp::repack, basic::options::OptionKeys::AnchoredDesign::filters::sasa, basic::options::OptionKeys::out::sf, and vancomycin::task.

Referenced by design_hits().

design_hits()

void design_hits	(	Pose &	p,
		string	fn,
		vector1< Hit >	h,
		vector1< Hit >	allh
	)

References orn_macrocycle::ala, alignaxis(), Hit::axs, Hit::cen, Hit::chi1, Hit::chi2, design(), dumpsym(), utility::file_basename(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, h, numeric::xyzMatrix< Real >::identity(), create_a3b_hbs::j, basic::options::OptionKeys::out::file::o, basic::options::option, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, predPRE::R2, repack_all(), rot_pose(), numeric::rotation_matrix_degrees(), Hit::rsd, basic::options::OptionKeys::out::sf, sfd, Hit::sym, tag, basic::options::TR, trans_pose(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

dock()

std::pair<vector1<Hit>,vector1<Hit> > dock	(	Pose &	init,
		string
	)

References docking::a1, docking::a2, angle_degrees(), CA, CB, evaluate_beta_mutants::ch2, measure_params::cross(), numeric::distance_squared(), numeric::xyzVector< T >::distance_squared(), basic::options::OptionKeys::in::file::dssp, get_scanres(), h, create_a3b_hbs::i, numeric::xyzMatrix< Real >::identity(), basic::init(), enumerate_junctions::int, test.T008_Serialization::iss, numeric::xyzVector< T >::normalized(), beta_nonlocal::pose, projperp(), predPRE::R2, numeric::rotation_matrix_degrees(), basic::options::OptionKeys::out::path::scratch, basic::options::OptionKeys::out::sf, basic::options::TR, utility_exit_with_message, and numeric::xyzVector< T >::z().

Referenced by main().

dumpsym()

void dumpsym	(	Pose const &	pose,
		Mat	R2,
		Mat	R3a,
		Mat	R3b,
		Vec	cen2,
		string	fname
	)

References predPRE::chain, ObjexxFCL::format::F(), PREcst::fname, create_a3b_hbs::i, test.T110_numeric::I, numeric::xyzMatrix< Real >::identity(), erraser_single_res_analysis::out, beta_nonlocal::pose, predPRE::R2, TR, utility::UPPERCASE_LETTERS(), numeric::xyzVector< T >::x(), numeric::xyzVector< T >::y(), and numeric::xyzVector< T >::z().

Referenced by design_hits().

dumpsym2()

void dumpsym2	(	Pose const &	pose,
		Mat	R2,
		Mat	R3a,
		Mat	R3b,
		Vec	HG,
		string	fname,
		Size	irsd,
		Size	ch1,
		Size	ch2,
		Real	ANG
	)

References evaluate_beta_mutants::ch2, ObjexxFCL::format::F(), utility::file_basename(), PREcst::fname, create_a3b_hbs::i, numeric::xyzMatrix< Real >::identity(), beta_nonlocal::pose, predPRE::R2, rot_pose(), and TR.

dumpsym6()

void dumpsym6	(	Pose const &	pose,
		Mat	R2,
		Mat	R3a,
		Mat	R3b,
		Vec	HG,
		string	fname,
		Size	irsd,
		Size	ch1,
		Size	ch2,
		Real	ANG
	)

References evaluate_beta_mutants::ch2, ObjexxFCL::format::F(), utility::file_basename(), PREcst::fname, create_a3b_hbs::i, numeric::xyzMatrix< Real >::identity(), beta_nonlocal::pose, predPRE::R2, rot_pose(), and TR.

get_scanres()

vector1<Size> get_scanres

(

Pose const &

pose

)

References create_a3b_hbs::i, and beta_nonlocal::pose.

Referenced by dock().

main()

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

References argv, design_hits(), dock(), test.T009_Exceptions::e, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, basic::init(), basic::options::option, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::in::file::s, subloop_histogram::size, and basic::options::TR.

repack_all()

void repack_all	(	Pose &	pose,
		ScoreFunctionOP	sf,
		Size	Ntri
	)

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, basic::options::OptionKeys::casp::repack, basic::options::OptionKeys::out::sf, and vancomycin::task.

Referenced by TestQuickRelaxMover::apply(), and design_hits().

repack_iface()

void repack_iface	(	Pose &	pose,
		ScoreFunctionOP	sf,
		Size	Ntri
	)

References create_a3b_hbs::i, min(), beta_nonlocal::pose, basic::options::OptionKeys::casp::repack, basic::options::OptionKeys::out::sf, and vancomycin::task.

sigmoidish_neighbor()

Real sigmoidish_neighbor ( Real const &  sqdist )

inline

References dist(), and sqr().

sqr()

Real sqr ( Real const  r )

inline

References create_a3b_hbs::r.

Referenced by sigmoidish_neighbor().

Variable Documentation

sfd

core::io::silent::SilentFileData sfd

static

Referenced by design_hits().

TR

basic::Tracer TR("genI213") ( "genI213"  )

static

Referenced by dumpsym(), dumpsym2(), and dumpsym6().