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

Classes

struct  BlockParam
 
struct  MyTemplatePointerHash1
 
class  PerResidueSapScoreMetric
 A per-residue metric that will calculate SASA for each residue given in a selector. More...
 
class  PerResidueSapScoreMetricCreator
 
struct  RotamerRotamerHasher
 
class  SapConstraint
 
class  SapConstraintEnergy
 
class  SapConstraintEnergyCreator
 
class  SapConstraintHelper
 
class  SapConstraintOptions
 
class  SapDatabase
 
class  SapMathConstraint
 
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
< 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.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)
 
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)
 
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)
 
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)
 
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

typedef utility::pointer::shared_ptr< PerResidueSapScoreMetric const > core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetricCOP
typedef utility::pointer::shared_ptr< PerResidueSapScoreMetric > core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetricOP
typedef utility::pointer::shared_ptr< SapConstraint const > core::pack::guidance_scoreterms::sap::SapConstraintCOP
typedef utility::pointer::shared_ptr< SapConstraintEnergy > core::pack::guidance_scoreterms::sap::SapConstraintEnergyOP
typedef utility::pointer::shared_ptr< SapConstraintHelper const > core::pack::guidance_scoreterms::sap::SapConstraintHelperCOP
typedef utility::pointer::shared_ptr< SapConstraintHelper > core::pack::guidance_scoreterms::sap::SapConstraintHelperOP
typedef utility::pointer::shared_ptr< SapConstraint > core::pack::guidance_scoreterms::sap::SapConstraintOP
typedef utility::pointer::shared_ptr< SapConstraintOptions const > core::pack::guidance_scoreterms::sap::SapConstraintOptionsCOP
typedef utility::pointer::shared_ptr< SapConstraintOptions > core::pack::guidance_scoreterms::sap::SapConstraintOptionsOP
typedef utility::pointer::shared_ptr< SapDatabase const > core::pack::guidance_scoreterms::sap::SapDatabaseCOP
typedef utility::pointer::shared_ptr< SapDatabase > core::pack::guidance_scoreterms::sap::SapDatabaseOP
typedef utility::pointer::shared_ptr< SapMathConstraint const > core::pack::guidance_scoreterms::sap::SapMathConstraintCOP
typedef utility::pointer::shared_ptr< SapMathConstraint > core::pack::guidance_scoreterms::sap::SapMathConstraintOP
typedef utility::pointer::shared_ptr< SapScoreMetric const > core::pack::guidance_scoreterms::sap::SapScoreMetricCOP
typedef utility::pointer::shared_ptr< SapScoreMetric > core::pack::guidance_scoreterms::sap::SapScoreMetricOP

Function Documentation

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 
)

References common_setup().

Referenced by 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 
)

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().

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 
)

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().

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 
)

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

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().

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().

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().

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().

static basic::Tracer core::pack::guidance_scoreterms::sap::TR ( "core.pack.guidance_scoreterms.sap.util"  )
static
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(), and core::pack::guidance_scoreterms::sap::SapConstraintHelper::setup_for_symmetry().

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

float const core::pack::guidance_scoreterms::sap::MAX_ATOMIC_RADIUS = 2.5
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().

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().

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

Referenced by sap_atom_sasa().

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