stepwise_helix_test.cc File Reference

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <protocols/viewer/viewers.hh>
#include <core/id/AtomID.hh>
#include <core/id/NamedAtomID.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/options/option.hh>
#include <core/options/after_opts.hh>
#include <core/options/util.hh>
#include <core/options/option_macros.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/util/basic.hh>
#include <core/io/database/open.hh>
#include <devel/init.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <utility/vector1.hh>
#include <numeric/xyzVector.hh>
#include <numeric/conversions.hh>
#include <numeric/xyz.functions.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <protocols/stepwise/modeler/util.hh>
#include <time.h>
#include <core/util/Tracer.hh>
#include <core/options/keys/out.OptionKeys.gen.hh>
#include <core/options/keys/in.OptionKeys.gen.hh>
#include <core/options/keys/swa.OptionKeys.gen.hh>
#include <core/options/keys/score.OptionKeys.gen.hh>

Typedefs
typedef numeric::xyzMatrix< Real >	Matrix

Functions
void	get_moment_of_inertia (pose::Pose const &pose, Vector &center_of_mass, Matrix &moment_of_inertia, utility::vector1< Size > const &moving_res)
void	get_euler_axes (Matrix const moment_of_inertia, Vector &axis1, Vector &axis2, Vector &axis3, Real &m1, Real &m2, Real &m3, Matrix &M)
void	get_euler_axes (Matrix const moment_of_inertia, Vector &axis1, Vector &axis2, Vector &axis3, Real &m1, Real &m2, Real &m3)
bool	check_hydrophobic (chemical::AA aa)
void	setup_hydrophobic_cbetas (pose::Pose const &pose, utility::vector1< Vector > &pose_hydrophobic_cbetas, utility::vector1< Size > const &subset_res)
void	setup_backbone_atoms (pose::Pose const &pose, utility::vector1< Vector > &backbone_atoms, utility::vector1< Size > const &subset_res)
bool	check_hydrophobic_contact (Vector const &translation, utility::vector1< Vector > const &moving_pose_cbetas, utility::vector1< Vector > const &partner_pose_cbetas)
bool	check_steric_overlap (Vector const &translation, utility::vector1< Vector > const &moving_pose_backbone_atoms, utility::vector1< Vector > const &partner_pose_backbone_atoms)
Real	check_rmsd (Vector const &translation, utility::vector1< Vector > const &moving_pose_backbone_atoms, utility::vector1< Vector > const &native_pose_backbone_atoms)
bool	check_filter_rmsd (Vector const &translation, utility::vector1< Vector > const &moving_pose_backbone_atoms, utility::vector1< Vector > const &native_pose_backbone_atoms, Real const &filter_rmsd)
bool	search_translations (pose::Pose &pose, pose::Pose const &pose_to_translate, utility::vector1< Size > const &moving_res, utility::vector1< Size > const &partner_res, id::AtomID const &tether_atom_id, Vector const &tether_xyz, Real const &tether_radius, Real const filter_rmsd, Size &count, bool const do_steric_check, std::string const &silent_file, pose::PoseCOP native_pose, Real &rmsd_min, pose::Pose &best_pose)
void	pack_it (pose::Pose &pose)
void	figure_out_best_alpha_beta_gamma (pose::Pose const &pose1, pose::Pose const &pose2, utility::vector1< Size > const &moving_res)
void	spinner_test ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Typedef Documentation

Matrix

typedef numeric::xyzMatrix< Real > Matrix

Function Documentation

check_filter_rmsd()

bool check_filter_rmsd	(	Vector const &	translation,
		utility::vector1< Vector > const &	moving_pose_backbone_atoms,
		utility::vector1< Vector > const &	native_pose_backbone_atoms,
		Real const &	filter_rmsd
	)

References create_a3b_hbs::i, natoms(), and basic::options::OptionKeys::rigid::translation.

Referenced by search_translations().

check_hydrophobic()

bool check_hydrophobic

(

chemical::AA

aa

)

References aa.

Referenced by setup_hydrophobic_cbetas().

check_hydrophobic_contact()

bool check_hydrophobic_contact	(	Vector const &	translation,
		utility::vector1< Vector > const &	moving_pose_cbetas,
		utility::vector1< Vector > const &	partner_pose_cbetas
	)

References DIST_CUTOFF, create_a3b_hbs::i, create_a3b_hbs::j, option, and basic::options::OptionKeys::rigid::translation.

Referenced by search_translations().

check_rmsd()

Real check_rmsd	(	Vector const &	translation,
		utility::vector1< Vector > const &	moving_pose_backbone_atoms,
		utility::vector1< Vector > const &	native_pose_backbone_atoms
	)

References create_a3b_hbs::i, natoms(), and basic::options::OptionKeys::rigid::translation.

Referenced by search_translations().

check_steric_overlap()

bool check_steric_overlap	(	Vector const &	translation,
		utility::vector1< Vector > const &	moving_pose_backbone_atoms,
		utility::vector1< Vector > const &	partner_pose_backbone_atoms
	)

References DIST_CUTOFF, create_a3b_hbs::i, create_a3b_hbs::j, option, and basic::options::OptionKeys::rigid::translation.

Referenced by search_translations().

figure_out_best_alpha_beta_gamma()

void figure_out_best_alpha_beta_gamma	(	pose::Pose const &	pose1,
		pose::Pose const &	pose2,
		utility::vector1< Size > const &	moving_res
	)

References compute_difference::alpha, basic::options::OptionKeys::corrections::beta, utility::io::oc::cout, loops::gamma, get_euler_axes(), get_moment_of_inertia(), test.T008_Serialization::pose1, test.T008_Serialization::pose2, and numeric::conversions::radians().

Referenced by spinner_test().

get_euler_axes() [1/2]

void get_euler_axes	(	Matrix const	moment_of_inertia,
		Vector &	axis1,
		Vector &	axis2,
		Vector &	axis3,
		Real &	m1,
		Real &	m2,
		Real &	m3
	)

References get_euler_axes().

get_euler_axes() [2/2]

void get_euler_axes	(	Matrix const	moment_of_inertia,
		Vector &	axis1,
		Vector &	axis2,
		Vector &	axis3,
		Real &	m1,
		Real &	m2,
		Real &	m3,
		Matrix &	M
	)

References subloop_histogram::axes, utility::io::oc::cout, numeric::eigenvector_jacobi(), create_a3b_hbs::k, and loops_kic::tol.

Referenced by figure_out_best_alpha_beta_gamma(), get_euler_axes(), and spinner_test().

get_moment_of_inertia()

void get_moment_of_inertia	(	pose::Pose const &	pose,
		Vector &	center_of_mass,
		Matrix &	moment_of_inertia,
		utility::vector1< Size > const &	moving_res
	)

References center_of_mass(), create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, natoms(), and beta_nonlocal::pose.

Referenced by figure_out_best_alpha_beta_gamma(), and spinner_test().

main()

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

References argv, test.T005_Bindings::base, test.T009_Exceptions::e, utility::options::OptionKeys::options::exit, basic::init(), my_main(), basic::options::OptionKeys::stepwise::protein::n_sample, NEW_OPT, basic::options::OptionKeys::full_model::sample_res, and viewer_main().

my_main()

void* my_main

(

void *

)

References utility::options::OptionKeys::options::exit, option, and spinner_test().

Referenced by main().

pack_it()

void pack_it

(

pose::Pose &

pose

)

References create_a3b_hbs::i, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, and vancomycin::task.

Referenced by spinner_test().

search_translations()

bool search_translations	(	pose::Pose &	pose,
		pose::Pose const &	pose_to_translate,
		utility::vector1< Size > const &	moving_res,
		utility::vector1< Size > const &	partner_res,
		id::AtomID const &	tether_atom_id,
		Vector const &	tether_xyz,
		Real const &	tether_radius,
		Real const	filter_rmsd,
		Size &	count,
		bool const	do_steric_check,
		std::string const &	silent_file,
		pose::PoseCOP	native_pose,
		Real &	rmsd_min,
		pose::Pose &	best_pose
	)

References create_a3b_hbs::best_pose, check_filter_rmsd(), check_hydrophobic_contact(), check_rmsd(), check_steric_overlap(), count, create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, ObjexxFCL::lead_zero_string_of(), numeric::xyzVector< T >::length_squared(), docking::native_pose, option, beta_nonlocal::pose, average_rmsds::rmsd, docking::s, setup_backbone_atoms(), setup_hydrophobic_cbetas(), sfd, basic::options::OptionKeys::in::file::silent, tag, beta_nonlocal::translate, and basic::options::OptionKeys::rigid::translation.

Referenced by spinner_test().

setup_backbone_atoms()

void setup_backbone_atoms	(	pose::Pose const &	pose,
		utility::vector1< Vector > &	backbone_atoms,
		utility::vector1< Size > const &	subset_res
	)

References create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, and beta_nonlocal::pose.

Referenced by search_translations().

setup_hydrophobic_cbetas()

void setup_hydrophobic_cbetas	(	pose::Pose const &	pose,
		utility::vector1< Vector > &	pose_hydrophobic_cbetas,
		utility::vector1< Size > const &	subset_res
	)

References check_hydrophobic(), create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, and beta_nonlocal::pose.

Referenced by search_translations().

spinner_test()

void spinner_test

(

)

References compute_difference::alpha, basic::options::OptionKeys::sample_around::alpha_increment, create_a3b_hbs::best_pose, basic::options::OptionKeys::corrections::beta, center_of_mass(), basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::constraints, count, utility::io::oc::cout, numeric::conversions::degrees(), create_a3b_hbs::f, figure_out_best_alpha_beta_gamma(), loops::gamma, basic::options::OptionKeys::sample_around::gamma_increment, get_euler_axes(), get_moment_of_inertia(), create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::stepwise::protein::n_sample, in::file::native(), docking::native_pose, basic::options::OptionKeys::dna::specificity::nloop, option, pack_it(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, numeric::conversions::radians(), pyrosetta.bindings.pose::rotate(), in::file::s(), basic::options::OptionKeys::full_model::sample_res, basic::options::OptionKeys::frags::scoring::scoring, search_translations(), out::file::silent(), beta_nonlocal::translate, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by my_main().