polar_pdbstats.cc File Reference

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/conformation/Residue.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/rna/RNA_AtomVDW.hh>
#include <core/chemical/rna/util.hh>
#include <core/scoring/hbonds/hbonds_geom.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/import_pose/import_pose.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Stub.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID.hh>
#include <core/id/DOF_ID.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/Jump.hh>
#include <basic/options/option.hh>
#include <basic/options/after_opts.hh>
#include <basic/options/option_macros.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.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/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 <numeric/xyz.functions.hh>

Typedefs
typedef numeric::xyzMatrix< Real >	Matrix

Functions
core::kinematics::Stub	get_phosphate_stub (core::conformation::Residue const &rsd)
void	search_other_atoms (pose::Pose const &pose, Vector const &xyz_polarH, Vector const &xyz_base, Size const count, conformation::Residue const &rsd_i, Size const ii, utility::io::ozstream &out)
void	polar_pdbstats_from_pose (utility::io::ozstream &out1, utility::io::ozstream &out2, pose::Pose &pose, Size const count, Size &total_residues, std::string const pdb_file)
void	polar_pdbstats_test ()
int	main (int argc, char *argv[])

Typedef Documentation

Matrix

typedef numeric::xyzMatrix< Real > Matrix

Function Documentation

get_phosphate_stub()

core::kinematics::Stub get_phosphate_stub

(

core::conformation::Residue const &

rsd

)

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

main()

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

References argv, basic::options::OptionKeys::magnesium::montecarlo::dump, utility::options::OptionKeys::options::exit, basic::init(), NEW_OPT, and polar_pdbstats_test().

polar_pdbstats_from_pose()

void polar_pdbstats_from_pose	(	utility::io::ozstream &	out1,
		utility::io::ozstream &	out2,
		pose::Pose &	pose,
		Size const	count,
		Size &	total_residues,
		std::string const	pdb_file
	)

References basic::options::OptionKeys::in::file::centroid, basic::options::OptionKeys::chemical::chemical, count, utility::io::oc::cout, create_a3b_hbs::i, create_a3b_hbs::ii, create_a3b_hbs::j, create_a3b_hbs::nres, beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, and search_other_atoms().

Referenced by polar_pdbstats_test().

polar_pdbstats_test()

void polar_pdbstats_test

(

)

References utility::io::oc::cerr, basic::options::OptionKeys::chemical::chemical, count, utility::io::oc::cout, basic::options::OptionKeys::magnesium::montecarlo::dump, utility::exit(), erraser::file_path, getline(), test.T110_numeric::I, in::file::l(), line, out::file::o(), option, lactamize::outfile, in::path::pdb(), bur_nodon_tyr::pdb_list, polar_pdbstats_from_pose(), beta_nonlocal::pose, and pyrosetta.distributed.io::pose_from_file.

Referenced by main().

search_other_atoms()

void search_other_atoms	(	pose::Pose const &	pose,
		Vector const &	xyz_polarH,
		Vector const &	xyz_base,
		Size const	count,
		conformation::Residue const &	rsd_i,
		Size const	ii,
		utility::io::ozstream &	out
	)

References numeric::angle_of(), count, numeric::conversions::degrees(), DIST_CUTOFF, build_jacobian::distance, ObjexxFCL::format::F(), create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::ii, create_a3b_hbs::j, beta_nonlocal::jj, oop_conformations::length, create_a3b_hbs::nres, and beta_nonlocal::pose.

Referenced by polar_pdbstats_from_pose().