core::pack::guidance_scoreterms::sap Namespace Reference

Classes
class	PerResidueSapScoreMetric
	A per-residue metric that will calculate SASA for each residue given in a selector. More...
class	PerResidueSapScoreMetricCreator
class	SapConstraint
class	SapConstraintEnergy
class	SapConstraintEnergyCreator
struct	MyTemplatePointerHash1
struct	RotamerRotamerHasher
class	SapConstraintHelper
class	SapConstraintOptions
struct	BlockParam
class	SapDatabase
class	SapMathConstraint
class	SapParameterOptions
class	SapScoreMetric
	A metric to report the SapScore of a pose. More...
class	SapScoreMetricCreator

Typedefs
typedef utility::pointer::shared_ptr< PerResidueSapScoreMetric >	PerResidueSapScoreMetricOP
typedef utility::pointer::shared_ptr< PerResidueSapScoreMetric const >	PerResidueSapScoreMetricCOP
typedef utility::pointer::shared_ptr< SapConstraint >	SapConstraintOP
typedef utility::pointer::shared_ptr< SapConstraint const >	SapConstraintCOP
typedef utility::pointer::shared_ptr< SapConstraintEnergy >	SapConstraintEnergyOP
typedef utility::pointer::shared_ptr< SapConstraintHelper >	SapConstraintHelperOP
typedef utility::pointer::shared_ptr< SapConstraintHelper const >	SapConstraintHelperCOP
typedef utility::pointer::shared_ptr< SapConstraintOptions >	SapConstraintOptionsOP
typedef utility::pointer::shared_ptr< SapConstraintOptions const >	SapConstraintOptionsCOP
typedef utility::pointer::shared_ptr< SapDatabase >	SapDatabaseOP
typedef utility::pointer::shared_ptr< SapDatabase const >	SapDatabaseCOP
typedef utility::pointer::shared_ptr< SapMathConstraint >	SapMathConstraintOP
typedef utility::pointer::shared_ptr< SapMathConstraint const >	SapMathConstraintCOP
typedef utility::pointer::shared_ptr< SapParameterOptions >	SapParameterOptionsOP
typedef utility::pointer::shared_ptr< SapParameterOptions const >	SapParameterOptionsCOP
typedef utility::pointer::shared_ptr< SapScoreMetric >	SapScoreMetricOP
typedef utility::pointer::shared_ptr< SapScoreMetric const >	SapScoreMetricCOP

Functions
static basic::Tracer	TR ("core.pack.guidance_scoreterms.sap.SapConstraint")
static basic::Tracer	TR ("core.pack.guidance_scoreterms.sap.SapConstraintEnergy")
void	find_mismatch (select::residue_selector::ResidueSubset const &small_sub, select::residue_selector::ResidueSubset const &big_sub, std::string const &small_name, std::string const &big_name)
Size	upper_triangle_offset (Size y, Size x, Size size)
static basic::Tracer	TR ("core.pack.guidance_scoreterms.sap.SapConstraintOptions")
static basic::Tracer	TR ("core.pack.guidance_scoreterms.sap.SapMathConstraint")
static basic::Tracer	TR ("core.pack.guidance_scoreterms.sap.SapParameterOptions")
static basic::Tracer	TR ("core.pack.guidance_scoreterms.sap.util")
pack::rotamer_set::RotamerSetsOP	rotamer_sets_from_pose (pose::Pose const &pose, utility::vector1< core::conformation::ResidueCOP > &res_vector)
SapConstraintHelperOP	common_setup (SapConstraintOptionsOP const &options, pose::Pose const &pose, select::residue_selector::ResidueSelectorCOP const &score_sel, select::residue_selector::ResidueSelectorCOP const &sap_calculate_sel, select::residue_selector::ResidueSelectorCOP const &sasa_sel, utility::vector1< core::conformation::ResidueCOP > &res_vector)
Real	calculate_sap (pose::Pose const &pose, select::residue_selector::ResidueSelectorCOP const &score_sel, select::residue_selector::ResidueSelectorCOP const &sap_calculate_sel, select::residue_selector::ResidueSelectorCOP const &sasa_sel, SapParameterOptions const &sap_parameter_options)
core::id::AtomID_Map< Real >	calculate_per_atom_sap (pose::Pose const &pose, select::residue_selector::ResidueSelectorCOP const &score_sel, select::residue_selector::ResidueSelectorCOP const &sap_calculate_sel, select::residue_selector::ResidueSelectorCOP const &sasa_sel, SapParameterOptions const &sap_parameter_options)
utility::vector1< Real >	calculate_per_res_sap (pose::Pose const &pose, select::residue_selector::ResidueSelectorCOP const &score_sel, select::residue_selector::ResidueSelectorCOP const &sap_calculate_sel, select::residue_selector::ResidueSelectorCOP const &sasa_sel, SapParameterOptions const &sap_parameter_options)
Real	calculate_slow_approx_sap (pose::Pose const &pose, select::residue_selector::ResidueSelectorCOP const &score_sel, select::residue_selector::ResidueSelectorCOP const &sap_calculate_sel, select::residue_selector::ResidueSelectorCOP const &sasa_sel, SapParameterOptions const &sap_parameter_options)
core::id::AtomID_Map< Real >	sap_atom_sasa (core::pose::Pose const &pose, select::residue_selector::ResidueSubset const &sasa_sub)

Variables
float const	SAP_BLOCK_STORE_SCALE = 2.2
float const	MAX_ATOMIC_RADIUS = 2.5
float const	MAX_BLOCK_INTERACTION = MAX_ATOMIC_RADIUS*2 + 3
Real const	SAP_PROBE_SIZE = 1.1

Typedef Documentation

PerResidueSapScoreMetricCOP

typedef utility::pointer::shared_ptr< PerResidueSapScoreMetric const > core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetricCOP

PerResidueSapScoreMetricOP

typedef utility::pointer::shared_ptr< PerResidueSapScoreMetric > core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetricOP

SapConstraintCOP

typedef utility::pointer::shared_ptr< SapConstraint const > core::pack::guidance_scoreterms::sap::SapConstraintCOP

SapConstraintEnergyOP

typedef utility::pointer::shared_ptr< SapConstraintEnergy > core::pack::guidance_scoreterms::sap::SapConstraintEnergyOP

SapConstraintHelperCOP

typedef utility::pointer::shared_ptr< SapConstraintHelper const > core::pack::guidance_scoreterms::sap::SapConstraintHelperCOP

SapConstraintHelperOP

typedef utility::pointer::shared_ptr< SapConstraintHelper > core::pack::guidance_scoreterms::sap::SapConstraintHelperOP

SapConstraintOP

typedef utility::pointer::shared_ptr< SapConstraint > core::pack::guidance_scoreterms::sap::SapConstraintOP

SapConstraintOptionsCOP

typedef utility::pointer::shared_ptr< SapConstraintOptions const > core::pack::guidance_scoreterms::sap::SapConstraintOptionsCOP

SapConstraintOptionsOP

typedef utility::pointer::shared_ptr< SapConstraintOptions > core::pack::guidance_scoreterms::sap::SapConstraintOptionsOP

SapDatabaseCOP

typedef utility::pointer::shared_ptr< SapDatabase const > core::pack::guidance_scoreterms::sap::SapDatabaseCOP

SapDatabaseOP

typedef utility::pointer::shared_ptr< SapDatabase > core::pack::guidance_scoreterms::sap::SapDatabaseOP

SapMathConstraintCOP

typedef utility::pointer::shared_ptr< SapMathConstraint const > core::pack::guidance_scoreterms::sap::SapMathConstraintCOP

SapMathConstraintOP

typedef utility::pointer::shared_ptr< SapMathConstraint > core::pack::guidance_scoreterms::sap::SapMathConstraintOP

SapParameterOptionsCOP

typedef utility::pointer::shared_ptr< SapParameterOptions const > core::pack::guidance_scoreterms::sap::SapParameterOptionsCOP

SapParameterOptionsOP

typedef utility::pointer::shared_ptr< SapParameterOptions > core::pack::guidance_scoreterms::sap::SapParameterOptionsOP

SapScoreMetricCOP

typedef utility::pointer::shared_ptr< SapScoreMetric const > core::pack::guidance_scoreterms::sap::SapScoreMetricCOP

SapScoreMetricOP

typedef utility::pointer::shared_ptr< SapScoreMetric > core::pack::guidance_scoreterms::sap::SapScoreMetricOP

Function Documentation

calculate_per_atom_sap()

core::id::AtomID_Map< Real > core::pack::guidance_scoreterms::sap::calculate_per_atom_sap	(	pose::Pose const &	pose,
		select::residue_selector::ResidueSelectorCOP const &	score_sel,
		select::residue_selector::ResidueSelectorCOP const &	sap_calculate_sel,
		select::residue_selector::ResidueSelectorCOP const &	sasa_sel,
		SapParameterOptions const &	sap_parameter_options
	)

References common_setup().

Referenced by calculate_per_res_sap().

calculate_per_res_sap()

utility::vector1< Real > core::pack::guidance_scoreterms::sap::calculate_per_res_sap	(	pose::Pose const &	pose,
		select::residue_selector::ResidueSelectorCOP const &	score_sel,
		select::residue_selector::ResidueSelectorCOP const &	sap_calculate_sel,
		select::residue_selector::ResidueSelectorCOP const &	sasa_sel,
		SapParameterOptions const &	sap_parameter_options
	)

References calculate_per_atom_sap(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetric::calculate().

calculate_sap()

Real core::pack::guidance_scoreterms::sap::calculate_sap	(	pose::Pose const &	pose,
		select::residue_selector::ResidueSelectorCOP const &	score_sel,
		select::residue_selector::ResidueSelectorCOP const &	sap_calculate_sel,
		select::residue_selector::ResidueSelectorCOP const &	sasa_sel,
		SapParameterOptions const &	sap_parameter_options
	)

References common_setup(), and protocols::hybridization::score.

Referenced by core::pack::guidance_scoreterms::sap::SapScoreMetric::calculate(), and core::pack::guidance_scoreterms::sap::SapConstraintEnergy::clean_up_residuearrayannealableenergy_after_packing().

calculate_slow_approx_sap()

Real core::pack::guidance_scoreterms::sap::calculate_slow_approx_sap	(	pose::Pose const &	pose,
		select::residue_selector::ResidueSelectorCOP const &	score_sel,
		select::residue_selector::ResidueSelectorCOP const &	sap_calculate_sel,
		select::residue_selector::ResidueSelectorCOP const &	sasa_sel,
		SapParameterOptions const &	sap_parameter_options
	)

References common_setup(), and protocols::hybridization::score.

common_setup()

SapConstraintHelperOP core::pack::guidance_scoreterms::sap::common_setup	(	SapConstraintOptionsOP const &	options,
		pose::Pose const &	pose,
		select::residue_selector::ResidueSelectorCOP const &	score_sel,
		select::residue_selector::ResidueSelectorCOP const &	sap_calculate_sel,
		select::residue_selector::ResidueSelectorCOP const &	sasa_sel,
		utility::vector1< core::conformation::ResidueCOP > &	res_vector
	)

References rotamer_sets_from_pose().

Referenced by calculate_per_atom_sap(), calculate_sap(), and calculate_slow_approx_sap().

find_mismatch()

void core::pack::guidance_scoreterms::sap::find_mismatch	(	select::residue_selector::ResidueSubset const &	small_sub,
		select::residue_selector::ResidueSubset const &	big_sub,
		std::string const &	small_name,
		std::string const &	big_name
	)

References TR().

Referenced by core::pack::guidance_scoreterms::sap::SapConstraintHelper::resize_arrays().

rotamer_sets_from_pose()

pack::rotamer_set::RotamerSetsOP core::pack::guidance_scoreterms::sap::rotamer_sets_from_pose	(	pose::Pose const &	pose,
		utility::vector1< core::conformation::ResidueCOP > &	res_vector
	)

References core::pack::task::TaskFactory::create_packer_task(), core::conformation::Residue::get_self_ptr(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by common_setup(), and core::pack::guidance_scoreterms::sap::SapConstraintEnergy::finalize_total_energy().

sap_atom_sasa()

core::id::AtomID_Map< Real > core::pack::guidance_scoreterms::sap::sap_atom_sasa	(	core::pose::Pose const &	pose,
		select::residue_selector::ResidueSubset const &	sasa_sub
	)

References core::scoring::calc_per_atom_sasa(), core::id::AtomID_Map< T >::fill_with(), core::scoring::packing::get_surf_vol(), core::pose::initialize_atomid_map(), SAP_PROBE_SIZE, core::pose::Pose::size(), core::scoring::packing::SurfVol::surf, and core::scoring::packing::surf_vol_available().

Referenced by core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa(), and core::pack::guidance_scoreterms::sap::SapConstraintHelper::set_accurate_sasa_and_recalc().

TR() [1/6]

static basic::Tracer core::pack::guidance_scoreterms::sap::TR ( "core.pack.guidance_scoreterms.sap.SapConstraint"  )

static

Referenced by core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_block_params(), core::pack::guidance_scoreterms::sap::SapConstraintEnergy::finalize_after_minimizing(), find_mismatch(), core::pack::guidance_scoreterms::sap::SapDatabase::get_name1_name3(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::report_final_score(), core::pack::guidance_scoreterms::sap::SapConstraintEnergy::setup_for_minimizing(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::setup_for_symmetry(), and core::pack::guidance_scoreterms::sap::SapConstraintHelper::setup_lightning().

TR() [2/6]

static basic::Tracer core::pack::guidance_scoreterms::sap::TR ( "core.pack.guidance_scoreterms.sap.SapConstraintEnergy"  )

static

TR() [3/6]

static basic::Tracer core::pack::guidance_scoreterms::sap::TR ( "core.pack.guidance_scoreterms.sap.SapConstraintOptions"  )

static

TR() [4/6]

static basic::Tracer core::pack::guidance_scoreterms::sap::TR ( "core.pack.guidance_scoreterms.sap.SapMathConstraint"  )

static

TR() [5/6]

static basic::Tracer core::pack::guidance_scoreterms::sap::TR ( "core.pack.guidance_scoreterms.sap.SapParameterOptions"  )

static

TR() [6/6]

static basic::Tracer core::pack::guidance_scoreterms::sap::TR ( "core.pack.guidance_scoreterms.sap.util"  )

static

upper_triangle_offset()

Size core::pack::guidance_scoreterms::sap::upper_triangle_offset	(	Size	y,
		Size	x,
		Size	size
	)

Referenced by core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_2b_lookup().

Variable Documentation

MAX_ATOMIC_RADIUS

float const core::pack::guidance_scoreterms::sap::MAX_ATOMIC_RADIUS = 2.5

MAX_BLOCK_INTERACTION

float const core::pack::guidance_scoreterms::sap::MAX_BLOCK_INTERACTION = MAX_ATOMIC_RADIUS*2 + 3

Referenced by core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_atom_neighbor_stuff(), and core::pack::guidance_scoreterms::sap::SapConstraintHelper::init().

SAP_BLOCK_STORE_SCALE

float const core::pack::guidance_scoreterms::sap::SAP_BLOCK_STORE_SCALE = 2.2

Referenced by core::pack::guidance_scoreterms::sap::SapConstraintHelper::convert_block_sasa_to_sasa_score(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_atom_neighbor_stuff(), and core::pack::guidance_scoreterms::sap::SapDatabase::load_block_data().

SAP_PROBE_SIZE

Real const core::pack::guidance_scoreterms::sap::SAP_PROBE_SIZE = 1.1

Referenced by sap_atom_sasa().