gen_d2.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/willmatch.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/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/symmetry/SymDof.hh>
#include <core/conformation/symmetry/SymmData.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/Stub.hh>
#include <utility/graph/Graph.hh>
#include <core/pack/packer_neighbors.hh>
#include <core/pack/rotamer_set/RotamerSetFactory.hh>
#include <core/pack/rotamer_set/RotamerSet.hh>
#include <core/pack/optimizeH.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.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/func/HarmonicFunc.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/sasa.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.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 <numeric/kinematic_closure/bridgeObjects.hh>
#include <protocols/moves/Mover.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/vector0.hh>
#include <utility/vector1.hh>
#include <platform/types.hh>
#include <core/pose/init_id_map.hh>
#include <protocols/moves/MoverStatistics.hh>
#include <apps/pilot/will/mynamespaces.ihh>
#include <apps/pilot/will/will_util.ihh>

Classes
struct	Hit

Typedefs
typedef utility::vector1< core::Real >	Reals
typedef utility::vector1< core::Size >	Sizes
typedef numeric::xyzVector< Real >	Vec
typedef numeric::xyzMatrix< Real >	Mat
typedef utility::vector1< Vec >	Vecs
typedef utility::pointer::shared_ptr< Hit >	HitOP

Functions
Real	sqr (Real const r)
Real	sigmoidish_neighbor (Real const &sqdist)
vector1< Size >	read_res_list (string fn)
void	repack (Pose &pose, Size nres, ScoreFunctionOP sf)
void	design (Pose &pose, Size nres, ScoreFunctionOP sf)
void	minimize (Pose &pose, Size nres, Size, ScoreFunctionOP sf, int bb=0)
vector1< Reals >	vecs2vv (Vecs const &v)
vector1< Vec >	vv2vecs (vector1< Reals > const &vv)
core::pack::rotamer_set::RotamerSetOP	get_rotset (Pose &pose, Size icys)
double	isctfast (vector1< Vec > pa, vector1< Vec > pb, Vec ori, bool debug=false)
double	isctfast (Pose const &a, Pose const &b, Vec ori_in)
core::kinematics::Stub	res2stub (core::pose::Pose const &pose, Size rsd, core::kinematics::Stub ref=core::kinematics::Stub())
void	ik_his4 (Pose &, Pose &his4, Size, Size, Size, Size, Vec symcen1, Vec symaxs1, Vec ZN)
Real	ik_his_clamp (Pose &pose, Size rsd1, Size rsd2, ImplicitFastClashCheck &ifc, vector1< HitOP > &, vector1< core::pack::rotamer_set::RotamerSetOP > const &rotsets)
void	run (std::string fname)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("gen_d2")

Typedef Documentation

HitOP

typedef utility::pointer::shared_ptr<Hit> HitOP

Mat

typedef numeric::xyzMatrix<Real> Mat

Reals

typedef utility::vector1<core::Real> Reals

Sizes

typedef utility::vector1<core::Size> Sizes

Vec

typedef numeric::xyzVector<Real> Vec

Vecs

typedef utility::vector1<Vec> Vecs

Function Documentation

design()

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

References basic::options::OptionKeys::smhybrid::design_hydrophobic, basic::options::OptionKeys::willmatch::design_interface, basic::options::OptionKeys::willmatch::exclude_ala, detail::find(), basic::options::OptionKeys::willmatch::fixed_res, create_a3b_hbs::i, basic::options::OptionKeys::in::in, interface, create_a3b_hbs::j, create_a3b_hbs::nres, option, beta_nonlocal::pose, repack(), basic::options::OptionKeys::AnchoredDesign::filters::sasa, basic::options::OptionKeys::out::sf, vancomycin::task, TR, basic::options::OptionKeys::inout::dbms::user, and basic::options::OptionKeys::in::file::xyz.

get_rotset()

core::pack::rotamer_set::RotamerSetOP get_rotset	(	Pose &	pose,
		Size	icys
	)

References beta_nonlocal::pose.

Referenced by run().

ik_his4()

void ik_his4	(	Pose &	,
		Pose &	his4,
		Size	,
		Size	,
		Size	,
		Size	,
		Vec	symcen1,
		Vec	symaxs1,
		Vec	ZN
	)

References atoms, numeric::kinematic_closure::bridgeObjects(), numeric::kinematic_closure::chainTORS(), numeric::kinematic_closure::chainXYZ(), ObjexxFCL::format::F(), test.T110_numeric::I, erraser_single_res_analysis::out, run_backbone::pivots, numeric::projection_matrix(), TR, utility_exit_with_message, vecs2vv(), vv2vecs(), x, predPRE::y, and predPRE::z.

ik_his_clamp()

Real ik_his_clamp	(	Pose &	pose,
		Size	rsd1,
		Size	rsd2,
		ImplicitFastClashCheck &	ifc,
		vector1< HitOP > &	,
		vector1< core::pack::rotamer_set::RotamerSetOP > const &	rotsets
	)

References ObjexxFCL::abs(), angle_degrees(), atoms, numeric::kinematic_closure::bridgeObjects(), CB, numeric::kinematic_closure::chainTORS(), numeric::kinematic_closure::chainXYZ(), clash(), measure_params::cross(), numeric::xyzVector< T >::cross(), spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, numeric::dihedral_degrees(), numeric::distance_squared(), numeric::xyzVector< T >::dot(), create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, extract_by_sidechain_sasa_score::l, numeric::xyzVector< T >::length(), numeric::xyzVector< T >::normalized(), adapt_rotamers::ori, run_backbone::pivots, beta_nonlocal::pose, numeric::projection_matrix(), projperp(), rot_pose(), numeric::rotation_matrix_degrees(), test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, basic::options::TR, trans_pose(), utility_exit_with_message, vecs2vv(), and vv2vecs().

Referenced by run().

isctfast() [1/2]

double isctfast	(	Pose const &	a,
		Pose const &	b,
		Vec	ori_in
	)

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

isctfast() [2/2]

double isctfast	(	vector1< Vec >	pa,
		vector1< Vec >	pb,
		Vec	ori,
		bool	debug = false
	)

References BIN, 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, 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 isctfast().

main()

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

References argv, test.T009_Exceptions::e, basic::init(), basic::options::option, run(), and basic::options::OptionKeys::in::file::s.

minimize()

void minimize	(	Pose &	pose,
		Size	nres,
		Size	,
		ScoreFunctionOP	sf,
		int	bb = 0
	)

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

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.

Referenced by run().

repack()

void repack	(	Pose &	pose,
		Size	nres,
		ScoreFunctionOP	sf
	)

References create_a3b_hbs::i, create_a3b_hbs::nres, beta_nonlocal::pose, basic::options::OptionKeys::out::sf, and vancomycin::task.

Referenced by design().

res2stub()

core::kinematics::Stub res2stub	(	core::pose::Pose const &	pose,
		Size	rsd,
		core::kinematics::Stub	ref = core::kinematics::Stub()
	)

References p2, and beta_nonlocal::pose.

run()

void run

(

std::string

fname

)

References pyrosetta::create_score_function, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, basic::options::OptionKeys::in::file::dssp, basic::options::OptionKeys::willmatch::exclude_res1, detail::find(), PREcst::fname, get_rotset(), create_a3b_hbs::i, ik_his_clamp(), evaluate_beta_mutants::ile, enumerate_junctions::int, create_a3b_hbs::nres, basic::options::option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, read_res_list(), basic::options::OptionKeys::in::file::residue_type_set, basic::options::OptionKeys::frags::scoring::scoring, and basic::options::TR.

Referenced by main().

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().

vecs2vv()

vector1<Reals> vecs2vv

(

Vecs const &

v

)

References create_a3b_hbs::i, create_a3b_hbs::r, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

Referenced by ik_his4(), and ik_his_clamp().

vv2vecs()

vector1<Vec> vv2vecs

(

vector1< Reals > const &

vv

)

References create_a3b_hbs::i, and create_a3b_hbs::r.

Referenced by ik_his4(), and ik_his_clamp().

Variable Documentation

TR

basic::Tracer TR("gen_d2") ( "gen_d2"  )

static

Referenced by design(), and ik_his4().