genP23.cc File Reference

#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/smhybrid.OptionKeys.gen.hh>
#include <basic/options/keys/symmetry.OptionKeys.gen.hh>
#include <basic/options/keys/matdes.OptionKeys.gen.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 <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/optimizeH.hh>
#include <core/pack/make_symmetric_task.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/RotamerSampleOptions.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/constraints/Constraint.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/func/XYZ_Func.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <core/scoring/packing/compute_holes_score.hh>
#include <core/util/SwitchResidueTypeSet.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/symmetry/SetupForSymmetryMover.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/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/string_constants.hh>
#include <apps/pilot/will/will_util.ihh>
#include <apps/pilot/will/mynamespaces.ihh>
#include <sys/stat.h>

Classes
class	SameResidueTypeConstraint
struct	DsfHit
struct	Hit

Macros
#define	CONTACT_D2   36.0
#define	CONTACT_TH1   12
#define	CONTACT_TH2   15

Functions
Real const	sqr (Real const r)
Real	sigmoidish_neighbor (Real const &sqdist)
vector1< Size >	get_scanres (Pose const &pose)
bool	file_exists (string strFilename)
void	dumpsym (Pose const &pose, Mat R2, Mat R3a, Mat R3b, Vec cen2, string fname)
int	pose_cbcount (Pose const &a, Pose const &b)
double	sicfast (vector1< Vec > pa, vector1< Vec > pb, vector1< Vec > &cba, vector1< Vec > &cbb, Vec ori, int &cbcount, bool debug=false)
double	sicfast (Pose const &a, Pose const &b, Vec ori_in, int &cbcount)
vector1< DsfHit >	find_dsf (Pose &p3a, Pose &p3b, ImplicitFastClashCheck const &ifc, vector1< vector1< Real > > cyschi1, Mat const &R2, Vec const &C2, Real dunth, Real angth)
void	design_1comp (Pose &pose, ScoreFunctionOP sf, Size Ntri)
void	repack_iface (Pose &p, ScoreFunctionOP sf, Size Ntri, vector1< bool > &iface_io)
Real	ddg (Pose const &p_in, ScoreFunctionOP sf, Size Ntri, Real &rholes, Real &hsp, Real &ssp, Real &sht)
void	replace_nat_seq (Pose &p, Pose const &nat)
vector1< Hit >	dock (Pose &init, string fname)
int	main (int argc, char *argv[])

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

Macro Definition Documentation

CONTACT_D2

#define CONTACT_D2   36.0

CONTACT_TH1

#define CONTACT_TH1   12

CONTACT_TH2

#define CONTACT_TH2   15

Function Documentation

ddg()

Real ddg	(	Pose const &	p_in,
		ScoreFunctionOP	sf,
		Size	Ntri,
		Real &	rholes,
		Real &	hsp,
		Real &	ssp,
		Real &	sht
	)

References create_a3b_hbs::i, natoms(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, repack_iface(), basic::options::OptionKeys::stepwise::s1, basic::options::OptionKeys::out::sf, basic::options::OptionKeys::remodel::ss_pair, and TR.

Referenced by dock().

design_1comp()

void design_1comp	(	Pose &	pose,
		ScoreFunctionOP	sf,
		Size	Ntri
	)

References CA, CB, create_a3b_hbs::i, min(), create_a3b_hbs::nres, beta_nonlocal::pose, basic::options::OptionKeys::casp::repack, basic::options::OptionKeys::AnchoredDesign::filters::sasa, basic::options::OptionKeys::out::sf, and vancomycin::task.

Referenced by dock().

dock()

vector1<Hit> dock	(	Pose &	init,
		string	fname
	)

References orn_macrocycle::ala, alignaxis(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, CONTACT_D2, CONTACT_TH1, CONTACT_TH2, numeric::xyzVector< T >::cross(), spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, ddg(), design_1comp(), build_jacobian::distance, numeric::xyzVector< T >::dot(), basic::options::OptionKeys::in::file::dssp, ObjexxFCL::format::F(), utility::file_basename(), find_dsf(), PREcst::fname, basic::options::OptionKeys::matdes::design::grid_size_radius, create_a3b_hbs::i, numeric::xyzMatrix< Real >::identity(), basic::init(), enumerate_junctions::int, create_a3b_hbs::j, oop_conformations::length, max(), numeric::xyzVector< T >::normalized(), create_a3b_hbs::nres, basic::options::OptionKeys::out::file::o, basic::options::option, adapt_rotamers::ori, pi, predPRE::R2, repack_iface(), replace_nat_seq(), rot_pose(), numeric::rotation_matrix_degrees(), test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, basic::options::OptionKeys::out::sf, sfd, sicfast(), challenge::ss, basic::options::OptionKeys::symmetry::symmetry_definition, predPRE::t, tag, basic::options::TR, trans_pose(), x, and predPRE::y.

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().

file_exists()

bool file_exists

(

string

strFilename

)

find_dsf()

vector1<DsfHit> find_dsf	(	Pose &	p3a,
		Pose &	p3b,
		ImplicitFastClashCheck const &	ifc,
		vector1< vector1< Real > >	cyschi1,
		Mat const &	R2,
		Vec const &	C2,
		Real	dunth,
		Real	angth
	)

References angle_degrees(), begin, numeric::dihedral_degrees(), numeric::xyzVector< T >::distance(), numeric::xyzVector< T >::distance_squared(), h, create_a3b_hbs::i, create_a3b_hbs::j, predPRE::R2, numeric::rotation_matrix_degrees(), test.T200_Scoring::rsd1, and test.T200_Scoring::rsd2.

Referenced by dock().

get_scanres()

vector1<Size> get_scanres

(

Pose const &

pose

)

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

main()

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

References argv, utility::io::oc::cout, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, dock(), test.T009_Exceptions::e, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, basic::init(), basic::options::OptionKeys::out::file::o, basic::options::option, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::in::file::s, subloop_histogram::size, and basic::options::TR.

pose_cbcount()

int pose_cbcount	(	Pose const &	a,
		Pose const &	b
	)

References a, compute_difference::b, count, create_a3b_hbs::i, and create_a3b_hbs::j.

repack_iface()

void repack_iface	(	Pose &	p,
		ScoreFunctionOP	sf,
		Size	Ntri,
		vector1< bool > &	iface_io
	)

References numeric::distance_squared(), create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, basic::options::OptionKeys::casp::repack, basic::options::OptionKeys::out::sf, and vancomycin::task.

Referenced by ddg(), and dock().

replace_nat_seq()

void replace_nat_seq	(	Pose &	p,
		Pose const &	nat
	)

References create_a3b_hbs::i, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::p.

Referenced by dock().

sicfast() [1/2]

double sicfast	(	Pose const &	a,
		Pose const &	b,
		Vec	ori_in,
		int &	cbcount
	)

References a, compute_difference::b, measure_params::cross(), measure_params::dot(), create_a3b_hbs::i, numeric::xyzMatrix< Real >::identity(), enumerate_junctions::int, create_a3b_hbs::j, numeric::xyzVector< T >::normalized(), adapt_rotamers::ori, rot, numeric::rotation_matrix(), and sicfast().

sicfast() [2/2]

double sicfast	(	vector1< Vec >	pa,
		vector1< Vec >	pb,
		vector1< Vec > &	cba,
		vector1< Vec > &	cbb,
		Vec	ori,
		int &	cbcount,
		bool	debug = false
	)

References BIN, CONTACT_D2, measure_params::cross(), basic::options::OptionKeys::msd::debug, measure_params::dot(), 3d_histogram::dz, ObjexxFCL::format::F(), create_a3b_hbs::i, test.T110_numeric::I, numeric::xyzMatrix< Real >::identity(), enumerate_junctions::int, subloop_histogram::iterator, create_a3b_hbs::j, create_a3b_hbs::k, extract_by_sidechain_sasa_score::l, max(), min(), adapt_rotamers::ori, erraser_single_res_analysis::out, rot, numeric::rotation_matrix(), numeric::xyzVector< T >::x(), xmn, xmx, numeric::xyzVector< T >::y(), ymn, ymx, and numeric::xyzVector< T >::z().

Referenced by dock(), and sicfast().

sigmoidish_neighbor()

Real sigmoidish_neighbor ( Real const &  sqdist )

inline

References dist(), and sqr().

sqr()

Real const 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 dock().

TR

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

static

Referenced by ddg(), and dumpsym().