gentetra.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/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/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/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 <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 <apps/pilot/will/will_util.ihh>
#include <apps/pilot/will/mynamespaces.ihh>

Functions
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)
void	repack (Pose &pose, Size nres, ScoreFunctionOP sf)
void	design (Pose &pose, Size nres, ScoreFunctionOP sf)
vector1< Vec >	line_cone_intersection (Vec p, Vec d, Vec v, Vec a, Real t)
Vec	projperp (Vec u, Vec v)
vector1< std::pair< Vec, Vec > >	intersecting_disulfide_axes (Vec CB, Vec SG, Vec symmaxis, Vec symmcen=Vec(0, 0, 0))
void	minimize (Pose &pose, Size nres, Size, ScoreFunctionOP sf, int bb=0)
std::pair< Size, Size >	makesplitwork_3bpy (Size total)
void	run ()
int	main (int argc, char *argv[])

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

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.

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_disulfide_axes()

vector1<std::pair<Vec,Vec> > intersecting_disulfide_axes	(	Vec	CB,
		Vec	SG,
		Vec	symmaxis,
		Vec	symmcen = Vec(0,0,0)
	)

References a, kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, CB, numeric::conversions::degrees(), create_a3b_hbs::i, 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, projperp(), numeric::rotation_matrix_degrees(), predPRE::t, kmeans_adaptive_kernel_density_bb_dependent_rotlib::v, and x.

Referenced by run().

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_disulfide_axes().

main()

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

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

makesplitwork_3bpy()

std::pair<Size,Size> makesplitwork_3bpy

(

Size

total

)

References basic::options::option, basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::willmatch::splitwork, basic::options::TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by run().

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.

projperp()

Vec projperp	(	Vec	u,
		Vec	v
	)

References numeric::projection_matrix(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::u, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

Referenced by dock(), get_zn_axes(), ik_his_clamp(), intersecting_bpy_axes(), intersecting_disulfide_axes(), main(), TCDock::min_termini_proj(), run(), run_m8(), test_chi_xform(), and test_MAT_VEC().

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.

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().

run()

void run

(

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, angle_degrees(), subloop_histogram::axes, CA, CB, basic::options::OptionKeys::willmatch::chi1_increment, basic::options::OptionKeys::willmatch::chi2_increment, measure_params::cross(), numeric::dihedral_degrees(), numeric::distance_squared(), numeric::xyzVector< T >::distance_squared(), utility::file_basename(), PREcst::fname, test.T020_Pose_Bindings::ft, create_a3b_hbs::i, basic::init(), intersecting_disulfide_axes(), ObjexxFCL::lead_zero_string_of(), makesplitwork_3bpy(), max(), min(), create_a3b_hbs::nres, basic::options::option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, predPRE::R2, basic::options::OptionKeys::remodel::rg, rot_pose(), numeric::rotation_matrix_degrees(), basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::out::sf, sfd, basic::options::OptionKeys::out::file::silent, subloop_histogram::size, binder::split(), superimpose_pose(), symm, basic::options::TR, trans_pose(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::u, and predPRE::z.

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().

Variable Documentation

sfd

core::io::silent::SilentFileData sfd

static

Referenced by run().

TR

basic::Tracer TR("gentetra") ( "gentetra"  )

static

Referenced by design().