gen_trimer_disulf.cc File Reference

#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/option_macros.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/kinematics/RT.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 <utility/graph/Graph.hh>
#include <core/pack/packer_neighbors.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/rotamer_set/RotamerSetFactory.hh>
#include <core/pack/rotamer_set/RotamerSet.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/rms_util.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 <protocols/sic_dock/xyzStripeHashPoseWithMeta.hh>
#include <sstream>
#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 <apps/pilot/will/mynamespaces.ihh>
#include <apps/pilot/will/will_util.ihh>

Classes
struct	HIT

Functions
void	register_options ()
Real	norm_degrees (Real x)
core::pack::rotamer_set::RotamerSetOP	get_rotamers (core::pose::Pose &pose, core::Size irsd, bool ex1, bool ex2)
vector1< vector1< Real > >	get_chis_complicated (core::pose::Pose &pose, core::Size irsd)
vector1< vector1< Real > >	get_chis (core::pose::Pose &pose, core::Size irsd)
int	get_N (core::pose::Pose const &inp)
core::pose::Pose	make_two_trimers (core::pose::Pose const &inp, Size icys, Size N)
void	set_disulf (core::pose::Pose &pose, Size icys, Size N, Size Nsub, Real chi1, Real chi2, Real chiss, Real chi2b, Real chi1b)
bool	clash_check_bb (core::pose::Pose &pose, Size icys, Size N, Size Nsub)
Real	repackmin (core::pose::Pose &pose, core::scoring::ScoreFunction const &sfxn, Size icys, Size N)
void	generate_disulfide_conformations (core::pose::Pose const &in_pose, Size icys, Size N)
int	main (int argc, char *argv[])

Function Documentation

clash_check_bb()

bool clash_check_bb	(	core::pose::Pose &	pose,
		Size	icys,
		Size	N,
		Size	Nsub
	)

References numeric::distance_squared(), N, and beta_nonlocal::pose.

Referenced by generate_disulfide_conformations().

generate_disulfide_conformations()

void generate_disulfide_conformations	(	core::pose::Pose const &	in_pose,
		Size	icys,
		Size	N
	)

References clash_check_bb(), utility::io::oc::cout, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, numeric::dihedral_degrees(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, get_chis(), enumerate_junctions::int, max(), min(), N, basic::options::OptionKeys::out::file::o, basic::options::option, beta_nonlocal::pose, repackmin(), score_ref, oop_conformations::scorefxn, set_disulf(), basic::options::OptionKeys::out::sf, ObjexxFCL::string_of(), THETA, and utility_exit_with_message.

Referenced by main().

get_chis()

vector1<vector1<Real> > get_chis	(	core::pose::Pose &	pose,
		core::Size	irsd
	)

References get_rotamers(), and beta_nonlocal::pose.

Referenced by generate_disulfide_conformations().

get_chis_complicated()

vector1<vector1<Real> > get_chis_complicated	(	core::pose::Pose &	pose,
		core::Size	irsd
	)

References get_rotamers(), create_a3b_hbs::i, norm_degrees(), and beta_nonlocal::pose.

get_N()

int get_N

(

core::pose::Pose const &

inp

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, create_a3b_hbs::i, build_restypes::inp, N, norm_degrees(), ObjexxFCL::string_of(), and utility_exit_with_message.

Referenced by main().

get_rotamers()

core::pack::rotamer_set::RotamerSetOP get_rotamers	(	core::pose::Pose &	pose,
		core::Size	irsd,
		bool	ex1,
		bool	ex2
	)

References basic::options::OptionKeys::packing::ex1::ex1, basic::options::OptionKeys::packing::ex2::ex2, and beta_nonlocal::pose.

Referenced by get_chis(), and get_chis_complicated().

main()

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

References argv, test.T009_Exceptions::e, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, generate_disulfide_conformations(), get_N(), basic::init(), make_two_trimers(), N, basic::options::option, pyrosetta.distributed.io::pose_from_file, register_options(), basic::options::OptionKeys::in::file::s, and subloop_histogram::size.

make_two_trimers()

core::pose::Pose make_two_trimers	(	core::pose::Pose const &	inp,
		Size	icys,
		Size	N
	)

References a, utility::io::oc::cout, test.T020_Pose_Bindings::ft, create_a3b_hbs::i, build_restypes::inp, docking::jumps, N, beta_nonlocal::pose, rot, rot_pose(), and numeric::rotation_matrix_degrees().

Referenced by main().

norm_degrees()

Real norm_degrees

(

Real

x

)

References x.

Referenced by get_chis_complicated(), and get_N().

register_options()

void register_options

(

)

References NEW_OPT.

Referenced by main().

repackmin()

Real repackmin	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction const &	sfxn,
		Size	icys,
		Size	N
	)

References test.T009_Exceptions::e, min(), basic::options::OptionKeys::in::file::movemap, N, beta_nonlocal::pose, docking::s, test.T120_core::sfxn, and vancomycin::task.

Referenced by generate_disulfide_conformations().

set_disulf()

void set_disulf	(	core::pose::Pose &	pose,
		Size	icys,
		Size	N,
		Size	Nsub,
		Real	chi1,
		Real	chi2,
		Real	chiss,
		Real	chi2b,
		Real	chi1b
	)

References CA, CB, numeric::dihedral_degrees(), N, beta_nonlocal::pose, rot_pose(), and numeric::rotation_matrix_degrees().

Referenced by generate_disulfide_conformations().