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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< Realcalculate_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< Realcalculate_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< Realsap_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< SapConstraint const > core::pack::guidance_scoreterms::sap::SapConstraintCOP
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< SapScoreMetric const > core::pack::guidance_scoreterms::sap::SapScoreMetricCOP

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

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
float const core::pack::guidance_scoreterms::sap::SAP_BLOCK_STORE_SCALE = 2.2
Real const core::pack::guidance_scoreterms::sap::SAP_PROBE_SIZE = 1.1

Referenced by sap_atom_sasa().