per_residue_solvent_exposure.cc File Reference

Determines the per residue solvent exposure using one of the following methods: More...

#include <iostream>
#include <string>
#include <devel/init.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/file/FileName.hh>
#include <utility/vector1.hh>
#include <core/pose/Pose.hh>
#include <core/import_pose/import_pose.hh>
#include <core/conformation/Residue.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/solvent_exposure.OptionKeys.gen.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/corrections.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <numeric/NumericTraits.hh>

Functions
void	output_results (std::string const &outf)
core::Real	count_neighbors (std::string neighbor_oxygen, pose::Pose pose, core::Real distance_fn_midpoint, core::Real distance_fn_steepness, core::Real angle_fn_midpoint, core::Real angle_fn_steepness, core::Size res_count_target, std::string target_atom_vector_start, core::Real const distance_internal, numeric::xyzVector< core::Real > target_vector, core::Size res_count_neighbor)
void	sphere_FA_nc_calculator (pose::Pose pose, core::Real distance_fn_midpoint, core::Real distance_fn_steepness)
void	sphere_FA_nc_anyatom_calculator (pose::Pose pose, core::Real distance_fn_midpoint, core::Real distance_fn_steepness)
void	sphere_cen_nc_calculator (pose::Pose pose, core::Real distance_fn_midpoint, core::Real distance_fn_steepness)
void	cone_FA_nc_calculator (pose::Pose pose, core::Real distance_fn_midpoint, core::Real distance_fn_steepness, core::Real angle_fn_midpoint, core::Real angle_fn_steepness)
void	cone_FA_nc_calculator_amide (pose::Pose pose, core::Real distance_fn_midpoint, core::Real distance_fn_steepness, core::Real angle_fn_midpoint, core::Real angle_fn_steepness)
void	cone_FA_nc_anyatom_calculator (pose::Pose pose, core::Real distance_fn_midpoint, core::Real distance_fn_steepness, core::Real angle_fn_midpoint, core::Real angle_fn_steepness)
void	cone_cen_nc_calculator (pose::Pose pose, core::Real distance_fn_midpoint, core::Real distance_fn_steepness, core::Real angle_fn_midpoint, core::Real angle_fn_steepness)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.public.analysis.per_residue_solvent_exposure")

Detailed Description

Determines the per residue solvent exposure using one of the following methods:

Function Documentation

cone_cen_nc_calculator()

void cone_cen_nc_calculator	(	pose::Pose	pose,
		core::Real	distance_fn_midpoint,
		core::Real	distance_fn_steepness,
		core::Real	angle_fn_midpoint,
		core::Real	angle_fn_steepness
	)

References basic::options::OptionKeys::hotspot::angle, numeric::xyzVector< T >::dot(), neighbor_count(), bin_torsions::output, output_results(), beta_nonlocal::pose, and basic::options::OptionKeys::hotspot::target.

Referenced by main().

cone_FA_nc_anyatom_calculator()

void cone_FA_nc_anyatom_calculator	(	pose::Pose	pose,
		core::Real	distance_fn_midpoint,
		core::Real	distance_fn_steepness,
		core::Real	angle_fn_midpoint,
		core::Real	angle_fn_steepness
	)

References basic::options::OptionKeys::hotspot::angle, numeric::xyzVector< T >::dot(), natoms(), neighbor_count(), bin_torsions::output, output_results(), and beta_nonlocal::pose.

Referenced by main().

cone_FA_nc_calculator()

void cone_FA_nc_calculator	(	pose::Pose	pose,
		core::Real	distance_fn_midpoint,
		core::Real	distance_fn_steepness,
		core::Real	angle_fn_midpoint,
		core::Real	angle_fn_steepness
	)

References basic::options::OptionKeys::hotspot::angle, numeric::xyzVector< T >::dot(), neighbor_count(), bin_torsions::output, output_results(), and beta_nonlocal::pose.

Referenced by main().

cone_FA_nc_calculator_amide()

void cone_FA_nc_calculator_amide	(	pose::Pose	pose,
		core::Real	distance_fn_midpoint,
		core::Real	distance_fn_steepness,
		core::Real	angle_fn_midpoint,
		core::Real	angle_fn_steepness
	)

References count_neighbors(), neighbor_count(), bin_torsions::output, output_results(), and beta_nonlocal::pose.

Referenced by main().

count_neighbors()

core::Real count_neighbors	(	std::string	neighbor_oxygen,
		pose::Pose	pose,
		core::Real	distance_fn_midpoint,
		core::Real	distance_fn_steepness,
		core::Real	angle_fn_midpoint,
		core::Real	angle_fn_steepness,
		core::Size	res_count_target,
		std::string	target_atom_vector_start,
		core::Real const	distance_internal,
		numeric::xyzVector< core::Real >	target_vector,
		core::Size	res_count_neighbor
	)

References numeric::xyzVector< T >::dot(), and beta_nonlocal::pose.

Referenced by cone_FA_nc_calculator_amide().

main()

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

References argv, in::file::centroid(), cone_cen_nc_calculator(), cone_FA_nc_anyatom_calculator(), cone_FA_nc_calculator(), cone_FA_nc_calculator_amide(), test.T009_Exceptions::e, basic::init(), solvent_exposure::method(), NEW_OPT, OPT, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, sphere_cen_nc_calculator(), sphere_FA_nc_anyatom_calculator(), sphere_FA_nc_calculator(), basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

output_results()

void output_results

(

std::string const &

outf

)

References out::file::o(), option, lactamize::outfile, TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by cone_cen_nc_calculator(), cone_FA_nc_anyatom_calculator(), cone_FA_nc_calculator(), cone_FA_nc_calculator_amide(), sphere_cen_nc_calculator(), sphere_FA_nc_anyatom_calculator(), and sphere_FA_nc_calculator().

sphere_cen_nc_calculator()

void sphere_cen_nc_calculator	(	pose::Pose	pose,
		core::Real	distance_fn_midpoint,
		core::Real	distance_fn_steepness
	)

References build_jacobian::distance, neighbor_count(), bin_torsions::output, output_results(), beta_nonlocal::pose, and basic::options::OptionKeys::hotspot::target.

Referenced by main().

sphere_FA_nc_anyatom_calculator()

void sphere_FA_nc_anyatom_calculator	(	pose::Pose	pose,
		core::Real	distance_fn_midpoint,
		core::Real	distance_fn_steepness
	)

References build_jacobian::distance, natoms(), neighbor_count(), bin_torsions::output, output_results(), and beta_nonlocal::pose.

Referenced by main().

sphere_FA_nc_calculator()

void sphere_FA_nc_calculator	(	pose::Pose	pose,
		core::Real	distance_fn_midpoint,
		core::Real	distance_fn_steepness
	)

References build_jacobian::distance, neighbor_count(), bin_torsions::output, output_results(), and beta_nonlocal::pose.

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("apps.public.analysis.per_residue_solvent_exposure") ( "apps.public.analysis.per_residue_solvent_exposure"  )

static

Referenced by output_results().