pdbstats_test.cc File Reference

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/conformation/Residue.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/chemical/rna/util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <protocols/rna/denovo/util.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID.hh>
#include <core/id/DOF_ID.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/Stub.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <devel/init.hh>
#include <core/import_pose/import_pose.hh>
#include <utility/vector1.hh>
#include <utility/tools/make_vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/conversions.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/string.functions.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <core/conformation/Conformation.hh>
#include <core/scoring/constraints/Constraint.hh>
#include <numeric/xyz.functions.hh>

Namespaces
	centroid_stats

Typedefs
typedef numeric::xyzMatrix< Real >	Matrix

Functions
bool	path_distance_OK (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Size const ii, Size const jj)
void	ch_o_pdbstats_from_pose (utility::io::ozstream &out, pose::Pose &pose, Size const count, char const chain, Size &total_residues)
Vector	get_centroid (conformation::Residue const &rsd)
Real const	centroid_stats::bin_width (0.25)
Size const	centroid_stats::max_bins (120)
void	fa_cenpack_pdbstats_from_pose (utility::io::ozstream &out, pose::Pose &pose, Size const count, char const chain, Size &total_residues)
kinematics::Stub	get_base_coordinate_system (conformation::Residue const &rsd, Vector const &centroid)
void	aro_pack_output (utility::io::ozstream &out, Size const &count, Size const &i, Size const &j, kinematics::Stub const &stub1, conformation::Residue const &rsd1, conformation::Residue const &rsd2, Vector const &centroid2, kinematics::Stub const &stub2)
void	aro_pack_pdbstats_from_pose (utility::io::ozstream &out, pose::Pose &pose, Size const count, char const chain, Size &total_residues)
void	proline_rama_pdbstats_from_pose (utility::io::ozstream &out, pose::Pose &pose, Size const count, char const chain, Size &total_residues)
utility::vector1< utility::vector1< std::string > >	get_ring_atoms (core::conformation::Residue const &rsd)
std::string	get_WC_atom (core::chemical::AA const &res_type)
std::string	get_H_atom (core::chemical::AA const &res_type)
void	get_ring_centroids_and_stubs (core::conformation::Residue const &rsd, utility::vector1< Vector > &ring_centroids, utility::vector1< core::kinematics::Stub > &ring_stubs)
Size	base_type_num (core::chemical::AA res_type)
void	rna_stack_pdbstats_from_pose (utility::io::ozstream &out, pose::Pose &pose, Size const count, char const chain, Size &total_residues)
void	output_centroid_stats (utility::io::ozstream &out)
void	lowercase (char string[])
void	rhiju_pdbstats ()
int	main (int argc, char *argv[])

Variables
ObjexxFCL::FArray2D< Size >	centroid_stats::centroid_counts (20, max_bins)

Typedef Documentation

Matrix

typedef numeric::xyzMatrix< Real > Matrix

Function Documentation

aro_pack_output()

void aro_pack_output	(	utility::io::ozstream &	out,
		Size const &	count,
		Size const &	i,
		Size const &	j,
		kinematics::Stub const &	stub1,
		conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		Vector const &	centroid2,
		kinematics::Stub const &	stub2
	)

References basic::options::OptionKeys::in::file::centroid, count, ObjexxFCL::format::F(), create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, test.T200_Scoring::rsd1, and test.T200_Scoring::rsd2.

Referenced by aro_pack_pdbstats_from_pose().

aro_pack_pdbstats_from_pose()

void aro_pack_pdbstats_from_pose	(	utility::io::ozstream &	out,
		pose::Pose &	pose,
		Size const	count,
		char const	chain,
		Size &	total_residues
	)

References aro_pack_output(), predPRE::chain, basic::options::OptionKeys::chemical::chemical, count, utility::io::oc::cout, DIST_CUTOFF, get_base_coordinate_system(), get_centroid(), create_a3b_hbs::i, basic::init(), create_a3b_hbs::j, oop_conformations::length, create_a3b_hbs::nres, beta_nonlocal::pose, test.T200_Scoring::rsd1, and test.T200_Scoring::rsd2.

Referenced by rhiju_pdbstats().

base_type_num()

Size base_type_num

(

core::chemical::AA

res_type

)

References basic::options::OptionKeys::chemical::chemical.

Referenced by rna_stack_pdbstats_from_pose().

ch_o_pdbstats_from_pose()

void ch_o_pdbstats_from_pose	(	utility::io::ozstream &	out,
		pose::Pose &	pose,
		Size const	count,
		char const	chain,
		Size &	total_residues
	)

References numeric::angle_radians(), predPRE::chain, count, utility::io::oc::cout, measure_params::cross(), numeric::conversions::degrees(), numeric::dihedral_degrees(), measure_params::dot(), ObjexxFCL::format::F(), create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, numeric::xyzVector< T >::length(), create_a3b_hbs::nres, path_distance_OK(), beta_nonlocal::pose, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, x, predPRE::y, and predPRE::z.

Referenced by rhiju_pdbstats().

fa_cenpack_pdbstats_from_pose()

void fa_cenpack_pdbstats_from_pose	(	utility::io::ozstream &	out,
		pose::Pose &	pose,
		Size const	count,
		char const	chain,
		Size &	total_residues
	)

References centroid_stats::bin_width(), centroid_stats::centroid_counts, kmeans_adaptive_kernel_density_bb_dependent_rotlib::centroids, predPRE::chain, count, utility::io::oc::cout, DIST_CUTOFF, ObjexxFCL::format::F(), get_centroid(), create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, oop_conformations::length, centroid_stats::max_bins(), create_a3b_hbs::nres, beta_nonlocal::pose, test.T200_Scoring::rsd1, and test.T200_Scoring::rsd2.

Referenced by rhiju_pdbstats().

get_base_coordinate_system()

kinematics::Stub get_base_coordinate_system	(	conformation::Residue const &	rsd,
		Vector const &	centroid
	)

References basic::options::OptionKeys::in::file::centroid, cols(), measure_params::cross(), x, predPRE::y, and predPRE::z.

Referenced by aro_pack_pdbstats_from_pose().

get_centroid()

Vector get_centroid

(

conformation::Residue const &

rsd

)

References basic::options::OptionKeys::in::file::centroid, and create_a3b_hbs::i.

Referenced by aro_pack_pdbstats_from_pose(), and fa_cenpack_pdbstats_from_pose().

get_H_atom()

std::string get_H_atom

(

core::chemical::AA const &

res_type

)

References basic::options::OptionKeys::chemical::chemical.

get_ring_atoms()

utility::vector1< utility::vector1< std::string > > get_ring_atoms

(

core::conformation::Residue const &

rsd

)

References basic::options::OptionKeys::chemical::chemical.

Referenced by get_ring_centroids_and_stubs().

get_ring_centroids_and_stubs()

void get_ring_centroids_and_stubs	(	core::conformation::Residue const &	rsd,
		utility::vector1< Vector > &	ring_centroids,
		utility::vector1< core::kinematics::Stub > &	ring_stubs
	)

References basic::options::OptionKeys::in::file::centroid, basic::options::OptionKeys::chemical::chemical, get_ring_atoms(), create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, and basic::options::OptionKeys::full_model::rna::rna.

Referenced by rna_stack_pdbstats_from_pose().

get_WC_atom()

std::string get_WC_atom

(

core::chemical::AA const &

res_type

)

References basic::options::OptionKeys::chemical::chemical.

lowercase()

void lowercase

(

char

string[]

)

References create_a3b_hbs::i.

main()

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

References argv, test.T009_Exceptions::e, utility::options::OptionKeys::options::exit, basic::init(), NEW_OPT, and rhiju_pdbstats().

output_centroid_stats()

void output_centroid_stats

(

utility::io::ozstream &

out

)

References centroid_stats::centroid_counts, create_a3b_hbs::i, test.T110_numeric::I, and create_a3b_hbs::j.

Referenced by rhiju_pdbstats().

path_distance_OK()

bool path_distance_OK	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		Size const	ii,
		Size const	jj
	)

References create_a3b_hbs::i, create_a3b_hbs::ii, create_a3b_hbs::j, beta_nonlocal::jj, SewAssembler::path_size, test.T200_Scoring::rsd1, and test.T200_Scoring::rsd2.

Referenced by ch_o_pdbstats_from_pose().

proline_rama_pdbstats_from_pose()

void proline_rama_pdbstats_from_pose	(	utility::io::ozstream &	out,
		pose::Pose &	pose,
		Size const	count,
		char const	chain,
		Size &	total_residues
	)

References predPRE::chain, basic::options::OptionKeys::chemical::chemical, count, utility::io::oc::cout, DIST_CUTOFF, ObjexxFCL::format::F(), create_a3b_hbs::i, test.T110_numeric::I, basic::init(), create_a3b_hbs::nres, and beta_nonlocal::pose.

Referenced by rhiju_pdbstats().

rhiju_pdbstats()

void rhiju_pdbstats

(

)

References aro_pack_pdbstats_from_pose(), utility::io::oc::cerr, ch_o_pdbstats_from_pose(), predPRE::chain, basic::options::OptionKeys::chemical::chemical, count, utility::io::oc::cout, utility::exit(), fa_cenpack_pdbstats_from_pose(), erraser::file_path, getline(), test.T110_numeric::I, in::file::l(), line, out::file::o(), option, erraser_single_res_analysis::out, lactamize::outfile, output_centroid_stats(), in::path::pdb(), bur_nodon_tyr::pdb_list, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, proline_rama_pdbstats_from_pose(), and rna_stack_pdbstats_from_pose().

Referenced by main().

rna_stack_pdbstats_from_pose()

void rna_stack_pdbstats_from_pose	(	utility::io::ozstream &	out,
		pose::Pose &	pose,
		Size const	count,
		char const	chain,
		Size &	total_residues
	)

References ObjexxFCL::abs(), base_type_num(), predPRE::chain, basic::options::OptionKeys::chemical::chemical, count, utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::denovo, DIST_CUTOFF, measure_params::dot(), ObjexxFCL::format::F(), get_ring_centroids_and_stubs(), create_a3b_hbs::i, test.T110_numeric::I, basic::init(), create_a3b_hbs::j, oop_conformations::length, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, create_a3b_hbs::nres, beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, secstruct(), x, predPRE::y, and predPRE::z.

Referenced by rhiju_pdbstats().