gen_disulf_homodimer.cc File Reference

#include <basic/database/open.hh>
#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/conformation/Residue.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.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/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/constraints/AmbiguousConstraint.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/constraints/MultiConstraint.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 <protocols/moves/Mover.hh>
#include <protocols/minimization_packing/symmetry/SymMinMover.hh>
#include <protocols/minimization_packing/symmetry/SymPackRotamersMover.hh>
#include <protocols/scoring/ImplicitFastClashCheck.hh>
#include <protocols/symmetry/SymDockingInitialPerturbation.hh>
#include <sstream>
#include <utility/io/izstream.hh>
#include <protocols/moves/MoverStatistics.hh>
#include <utility/vector0.hh>
#include <utility/vector1.hh>
#include <core/pose/init_id_map.hh>
#include <apps/pilot/will/mynamespaces.ihh>
#include <apps/pilot/will/will_util.ihh>
#include <numeric/NumericTraits.hh>

Classes
struct	Hit
struct	HitCmp

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)
core::pack::rotamer_set::RotamerSetOP	get_rotset (Pose &pose, Size icys)
void	run (std::string fname)
int	main (int argc, char *argv[])

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

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().

main()

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

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

run()

void run

(

std::string

fname

)

References clash(), pyrosetta::create_score_function, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, basic::options::OptionKeys::in::file::dssp, willmatch::exclude_res1(), detail::find(), PREcst::fname, get_rotset(), h, create_a3b_hbs::i, evaluate_beta_mutants::ile, natoms(), numeric::xyzVector< T >::normalized(), create_a3b_hbs::nres, basic::options::option, option, PHI, PI, numeric::NumericTraits< T >::pi(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, projperp(), read_res_list(), numeric::rotation_matrix_degrees(), basic::options::OptionKeys::frags::scoring::scoring, THETA, TR, and basic::options::OptionKeys::in::file::xyz.

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().

Variable Documentation

TR

basic::Tracer TR("genmatch") ( "genmatch"  )

static

Referenced by design(), and run().