surfacescore.cc File Reference

#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <basic/options/util.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/Pose.hh>
#include <core/conformation/Residue.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/metrics/CalculatorFactory.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreFunctionInfo.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/TenANeighborGraph.hh>
#include <protocols/jobdist/standard_mains.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/pose_metric_calculators/SurfaceCalculator.hh>
#include <protocols/pose_metric_calculators/NeighborsByDistanceCalculator.hh>
#include <protocols/task_operations/RestrictToNeighborhoodOperation.hh>
#include <basic/Tracer.hh>
#include <basic/MetricValue.hh>
#include <basic/prof.hh>
#include <utility/file/file_sys_util.hh>
#include <ObjexxFCL/format.hh>
#include <sstream>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>

Namespaces
	surface_app

Functions
void	init_usage_prompt (std::string exe)
void	print_energies (pose::Pose &pose, scoring::ScoreFunctionOP scorefxn)
	Helper method for the main function. Takes in a pose, the scorefunction, surface energies and weights and prints everything out in a pretty format. More...
void	fill_num_neighbors (pose::Pose &pose, utility::vector1< int > &num_nbs)
	helper method which uses the tenA nb graph in the pose object to fill a vector with nb counts More...
void	print_surface_score_by_res (pose::Pose &pose, utility::vector1< int > &num_nbs, basic::MetricValue< utility::vector1< core::Real > > &pose_residue_surface, Real surface_score_weight)
	helper method which pretty prints the surface scores More...
void	repack_pose (pose::Pose &pose, scoring::ScoreFunctionOP scorefxn)
	Takes the input Pose and runs a fast repack protocol on it. More...
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("surface_app")
BooleanOptionKey const	surface_app::surfacescore ("surface_app::surfacescore")
BooleanOptionKey const	surface_app::surfacedesign ("surface_app::surfacedesign")
BooleanOptionKey const	surface_app::surfacescan ("surface_app::surfacescan")
BooleanOptionKey const	surface_app::no_repack_before_scoring ("surface_app::no_repack_before_scoring")
BooleanOptionKey const	surface_app::no_repack_before_design ("surface_app::no_repack_before_design")
BooleanOptionKey const	surface_app::output_by_res_surface_score ("surface_app::output_by_res_surface_score")
BooleanOptionKey const	surface_app::repack_mutant_position_only ("surface_app::repack_mutant_position_only")
BooleanOptionKey const	surface_app::use_reweighted_score12_with_surfaceE_scorefunction ("surface_app::use_reweighted_score12_with_surfaceE_scorefunction")
BooleanOptionKey const	surface_app::use_reweighted_score12_score_function ("surface_app::use_reweighted_score12_score_function")
StringOptionKey const	surface_app::native ("surface_app::native")
std::string	usage_string

Function Documentation

fill_num_neighbors()

void fill_num_neighbors	(	pose::Pose &	pose,
		utility::vector1< int > &	num_nbs
	)

helper method which uses the tenA nb graph in the pose object to fill a vector with nb counts

References create_a3b_hbs::ii, and beta_nonlocal::pose.

Referenced by main().

init_usage_prompt()

void init_usage_prompt

(

std::string

exe

)

References usage_string.

Referenced by main().

main()

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

References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::A, argv, utility::io::oc::cerr, utility::io::oc::cout, data, basic::options::OptionKeys::antibody::design::design_protocol, test.T009_Exceptions::e, ObjexxFCL::format::F(), utility::file::file_basename(), utility::file::file_exists(), file_exists(), lactamize::filename, fill_num_neighbors(), pyrosetta.distributed.io::get_score_function(), getline(), create_a3b_hbs::i, create_a3b_hbs::ii, basic::init(), init_usage_prompt(), subloop_histogram::iterator, in::file::l(), line, surface_app::native, docking::native_pose, packing::ndruns(), surface_app::no_repack_before_design, surface_app::no_repack_before_scoring, basic::options::OptionKeys::AnchoredDesign::filters::omega, basic::options::option, option, erraser_single_res_analysis::out, surface_app::output_by_res_surface_score, basic::options::OptionKeys::corrections::score::p_aa_pp, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file(), print_energies(), print_surface_score_by_res(), basic::prof_reset(), basic::options::OptionKeys::remodel::rama, surface_app::repack_mutant_position_only, repack_pose(), in::file::s(), oop_conformations::scorefxn, surface, surface_app::surfacedesign, surface_app::surfacescan, surface_app::surfacescore, test.G200_Module_Region::tf, TR, usage_string, surface_app::use_reweighted_score12_score_function, surface_app::use_reweighted_score12_with_surfaceE_scorefunction, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, utility_exit_with_message_status, and value.

print_energies()

void print_energies	(	pose::Pose &	pose,
		scoring::ScoreFunctionOP	scorefxn
	)

Helper method for the main function. Takes in a pose, the scorefunction, surface energies and weights and prints everything out in a pretty format.

References utility::io::oc::cout, enumerate_junctions::default, ObjexxFCL::format::F(), test.T110_numeric::I, create_a3b_hbs::ii, beta_nonlocal::jj, basic::options::OptionKeys::AnchoredDesign::filters::omega, basic::options::OptionKeys::corrections::score::p_aa_pp, beta_nonlocal::pose, basic::options::OptionKeys::remodel::rama, oop_conformations::scorefxn, surface, and basic::options::OptionKeys::sc::weight.

Referenced by main().

print_surface_score_by_res()

void print_surface_score_by_res	(	pose::Pose &	pose,
		utility::vector1< int > &	num_nbs,
		basic::MetricValue< utility::vector1< core::Real > > &	pose_residue_surface,
		Real	surface_score_weight
	)

helper method which pretty prints the surface scores

References utility::io::oc::cout, ObjexxFCL::format::F(), test.T110_numeric::I, beta_nonlocal::jj, and beta_nonlocal::pose.

Referenced by main().

repack_pose()

void repack_pose	(	pose::Pose &	pose,
		scoring::ScoreFunctionOP	scorefxn
	)

Takes the input Pose and runs a fast repack protocol on it.

References beta_nonlocal::pose, and oop_conformations::scorefxn.

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("surface_app") ( "surface_app"  )

static

Referenced by main().

usage_string

std::string usage_string

Referenced by init_usage_prompt(), and main().