general_pair_counting.cc File Reference

generate octave "load_table" scripts for calculating env and pair term More...

#include <core/chemical/AA.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/conformation/Residue.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/Stub.hh>
#include <core/types.hh>
#include <core/id/AtomID.hh>
#include <core/id/DOF_ID.hh>
#include <core/pose/Pose.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/import_pose/import_pose.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/dunbrack/cenrot/SingleResidueCenrotLibrary.hh>
#include <devel/init.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/option_macros.hh>
#include <basic/Tracer.hh>
#include <numeric/random/random.hh>
#include <numeric/constants.hh>
#include <numeric/xyz.functions.hh>
#include <utility/vector1.hh>
#include <utility/fixedsizearray1.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <sstream>
#include <iostream>
#include <fstream>
#include <string>

Functions
void	my_main ()
int	main (int argc, char *argv[])
Size	get_env_bin_number (Size nbr_num)
Size	get_best_rotamer_index (Pose &p, Size ndx)
Size	get_rotamer_type_index (std::string const &aa, Size nrot, Size nenv=0)
void	fill_1D_vector (utility::vector1< Size > &t1, Size nx)
void	fill_2D_vector (utility::vector1< utility::vector1< Size > > &t2, Size nx, Size ny)
void	fill_3D_vector (utility::vector1< utility::vector1< utility::vector1< Size > > > &t3, Size nx, Size ny, Size nz)
void	fill_4D_vector (utility::vector1< utility::vector1< utility::vector1< utility::vector1< Size > > > > &t4, Size nx, Size ny, Size nz, Size no)

Variables
static basic::Tracer	TR ("pilot.wendao.cenrot")
utility::vector1< std::string >	rot_type_list
utility::vector1< Size >	rot_list_num

Detailed Description

generate octave "load_table" scripts for calculating env and pair term

Author

Yuan Liu (wenda.nosp@m.o@uw.nosp@m..edu)

Function Documentation

fill_1D_vector()

void fill_1D_vector	(	utility::vector1< Size > &	t1,
		Size	nx
	)

References create_a3b_hbs::i.

Referenced by fill_2D_vector().

fill_2D_vector()

void fill_2D_vector	(	utility::vector1< utility::vector1< Size > > &	t2,
		Size	nx,
		Size	ny
	)

References fill_1D_vector(), and create_a3b_hbs::i.

Referenced by fill_3D_vector(), and my_main().

fill_3D_vector()

void fill_3D_vector	(	utility::vector1< utility::vector1< utility::vector1< Size > > > &	t3,
		Size	nx,
		Size	ny,
		Size	nz
	)

References fill_2D_vector(), and create_a3b_hbs::i.

Referenced by fill_4D_vector(), and my_main().

fill_4D_vector()

void fill_4D_vector	(	utility::vector1< utility::vector1< utility::vector1< utility::vector1< Size > > > > &	t4,
		Size	nx,
		Size	ny,
		Size	nz,
		Size	no
	)

References fill_3D_vector(), and create_a3b_hbs::i.

Referenced by my_main().

get_best_rotamer_index()

Size get_best_rotamer_index	(	Pose &	p,
		Size	ndx
	)

References ndx, option, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::p.

Referenced by my_main().

get_env_bin_number()

Size get_env_bin_number

(

Size

nbr_num

)

References create_a3b_hbs::i, option, and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

get_rotamer_type_index()

Size get_rotamer_type_index	(	std::string const &	aa,
		Size	nrot,
		Size	nenv = 0
	)

References aa, create_a3b_hbs::i, kmeans_bb_dependent_rotlib::nrot, option, rot_list_num, rot_type_list, and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

main()

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

References argv, basic::init(), my_main(), and NEW_OPT.

my_main()

void my_main

(

)

References a, numeric::angle_radians(), utility::io::oc::cerr, utility::graph::Node::const_edge_list_end(), utility::graph::Node::const_upper_edge_list_end(), utility::io::oc::cout, kmeans_adaptive_kernel_density_bb_dependent_rotlib::dih, dih_table, numeric::dihedral_degrees(), basic::Tracer::Error, fill_2D_vector(), fill_3D_vector(), fill_4D_vector(), get_best_rotamer_index(), get_env_bin_number(), utility::graph::Edge::get_node(), get_rotamer_type_index(), create_a3b_hbs::i, enumerate_junctions::int, create_a3b_hbs::j, create_a3b_hbs::k, in::file::l(), option, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, numeric::constants::r::radians_to_degrees, res_index, rot_list_num, rot_type_list, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, beta_nonlocal::score_fxn, subloop_histogram::size, th1_table, th2_table, TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

Variable Documentation

rot_list_num

utility::vector1<Size> rot_list_num

Referenced by get_rotamer_type_index(), and my_main().

rot_type_list

utility::vector1<std::string> rot_type_list

Referenced by get_rotamer_type_index(), and my_main().

TR

basic::Tracer TR("pilot.wendao.cenrot") ( "pilot.wendao.cenrot"  )

static

Referenced by my_main().