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protocols::vardist_solaccess::VarSolDistSasaCalculator Class Reference

#include <VarSolDRotamerDots.hh>

Inheritance diagram for protocols::vardist_solaccess::VarSolDistSasaCalculator:
Inheritance graph
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Public Member Functions

 VarSolDistSasaCalculator ()
 
VarSolDistSasaCalculatorCOP get_self_ptr () const
 
VarSolDistSasaCalculatorOP get_self_ptr ()
 
VarSolDistSasaCalculatorCAP get_self_weak_ptr () const
 
VarSolDistSasaCalculatorAP get_self_weak_ptr ()
 
core::pose::metrics::PoseMetricCalculatorOP clone () const override
 
void set_element_radii (std::string atype_name, core::Real coll_radius, core::Real int_radius, core::Size nshells)
 
void set_atom_type_radii (std::string atype_name, core::Real coll_radius, core::Real int_radius, core::Size nshells)
 
core::id::AtomID_Map< core::Realcalculate (const core::pose::Pose &pose)
 
- Public Member Functions inherited from core::pose::metrics::StructureDependentCalculator
 StructureDependentCalculator ()
 
void notify_structure_change () override
 
void get (std::string const &key, basic::MetricValueBase &val, Pose const &this_pose) override
 
std::string get (std::string const &key, Pose const &this_pose) override
 
- Public Member Functions inherited from core::pose::metrics::PoseMetricCalculator
 PoseMetricCalculator ()
 
virtual void notify_energy_change ()
 

Protected Member Functions

void lookup (const std::string &key, basic::MetricValueBase *valptr) const override
 
std::string print (const std::string &key) const override
 
void recompute (const core::pose::Pose &this_pose) override
 

Private Member Functions

void initialize_sasa_arrays ()
 Initializes the pointers to the angles and masks FArrays used by sasa.cc and inits the dot sphere coordinates. More...
 
core::Real interaction_radii_squared (core::Size attype1, core::Size attype2) const
 

Private Attributes

core::Real probe_radius_
 
core::Real wobble_
 
core::Real total_sasa_
 
core::id::AtomID_Map< core::Realatom_sasa_
 
utility::vector1< core::Realresidue_sasa_
 
utility::vector1
< VarSolDRotamerDotsOP
rotamer_dots_vec_
 
utility::vector1
< utility::vector1< core::Real > > 
radii_
 
utility::vector1< core::Realmsas_radii_
 
utility::vector1< core::Realcoll_radii_
 
utility::vector1< core::Realint_radii_
 
utility::vector1
< utility::vector1< core::Real > > 
int_radii_sum_
 
utility::vector1
< utility::vector1< core::Real > > 
int_radii_sum2_
 
core::Size const num_bytes_
 
const ObjexxFCL::FArray2D_ubyte * lg_masks_
 
const ObjexxFCL::FArray2D_int * lg_angles_
 
core::Real polar_expansion_radius_
 
bool up_to_date
 

Friends

class VarSolDRotamerDots
 

Constructor & Destructor Documentation

protocols::vardist_solaccess::VarSolDistSasaCalculator::VarSolDistSasaCalculator ( )

Member Function Documentation

id::AtomID_Map< core::Real > protocols::vardist_solaccess::VarSolDistSasaCalculator::calculate ( const core::pose::Pose pose)

References atom_sasa_, and recompute().

core::pose::metrics::PoseMetricCalculatorOP protocols::vardist_solaccess::VarSolDistSasaCalculator::clone ( ) const
overridevirtual
VarSolDistSasaCalculatorCOP protocols::vardist_solaccess::VarSolDistSasaCalculator::get_self_ptr ( ) const
inline

Referenced by recompute().

VarSolDistSasaCalculatorOP protocols::vardist_solaccess::VarSolDistSasaCalculator::get_self_ptr ( )
inline
VarSolDistSasaCalculatorCAP protocols::vardist_solaccess::VarSolDistSasaCalculator::get_self_weak_ptr ( ) const
inline
VarSolDistSasaCalculatorAP protocols::vardist_solaccess::VarSolDistSasaCalculator::get_self_weak_ptr ( )
inline
void protocols::vardist_solaccess::VarSolDistSasaCalculator::initialize_sasa_arrays ( )
private

Initializes the pointers to the angles and masks FArrays used by sasa.cc and inits the dot sphere coordinates.

This call should only occur once (when the first RotamerDots object get constructed) and never again.

References core::chemical::AtomType::atom_type_name(), coll_radii_, core::chemical::AtomType::element(), core::chemical::AtomType::extra_parameter(), core::chemical::FA_STANDARD, core::scoring::sasa::get_legrand_sasa_angles(), core::scoring::sasa::get_legrand_sasa_masks(), int_radii_, int_radii_sum2_, int_radii_sum_, lg_angles_, lg_masks_, protocols::mean_field::max(), msas_radii_, and radii_.

Referenced by VarSolDistSasaCalculator().

core::Real protocols::vardist_solaccess::VarSolDistSasaCalculator::interaction_radii_squared ( core::Size  attype1,
core::Size  attype2 
) const
private
void protocols::vardist_solaccess::VarSolDistSasaCalculator::lookup ( const std::string &  key,
basic::MetricValueBase *  valptr 
) const
overrideprotectedvirtual
std::string protocols::vardist_solaccess::VarSolDistSasaCalculator::print ( const std::string &  key) const
overrideprotectedvirtual
void protocols::vardist_solaccess::VarSolDistSasaCalculator::recompute ( const core::pose::Pose this_pose)
overrideprotectedvirtual
void protocols::vardist_solaccess::VarSolDistSasaCalculator::set_atom_type_radii ( std::string  atype_name,
core::Real  coll_radius,
core::Real  int_radius,
core::Size  nshells 
)
void protocols::vardist_solaccess::VarSolDistSasaCalculator::set_element_radii ( std::string  atype_name,
core::Real  coll_radius,
core::Real  int_radius,
core::Size  nshells 
)

Friends And Related Function Documentation

friend class VarSolDRotamerDots
friend

Member Data Documentation

core::id::AtomID_Map< core::Real > protocols::vardist_solaccess::VarSolDistSasaCalculator::atom_sasa_
private

Referenced by calculate(), lookup(), and recompute().

utility::vector1< core::Real > protocols::vardist_solaccess::VarSolDistSasaCalculator::coll_radii_
private
utility::vector1< core::Real > protocols::vardist_solaccess::VarSolDistSasaCalculator::int_radii_
private
utility::vector1< utility::vector1< core::Real > > protocols::vardist_solaccess::VarSolDistSasaCalculator::int_radii_sum2_
private
utility::vector1< utility::vector1< core::Real > > protocols::vardist_solaccess::VarSolDistSasaCalculator::int_radii_sum_
private
const ObjexxFCL::FArray2D_int* protocols::vardist_solaccess::VarSolDistSasaCalculator::lg_angles_
private

Referenced by initialize_sasa_arrays().

const ObjexxFCL::FArray2D_ubyte* protocols::vardist_solaccess::VarSolDistSasaCalculator::lg_masks_
private

Referenced by initialize_sasa_arrays().

utility::vector1< core::Real > protocols::vardist_solaccess::VarSolDistSasaCalculator::msas_radii_
private
core::Size const protocols::vardist_solaccess::VarSolDistSasaCalculator::num_bytes_
private
core::Real protocols::vardist_solaccess::VarSolDistSasaCalculator::polar_expansion_radius_
private
core::Real protocols::vardist_solaccess::VarSolDistSasaCalculator::probe_radius_
private
utility::vector1< utility::vector1< core::Real > > protocols::vardist_solaccess::VarSolDistSasaCalculator::radii_
private
utility::vector1< core::Real > protocols::vardist_solaccess::VarSolDistSasaCalculator::residue_sasa_
private

Referenced by lookup(), print(), and recompute().

utility::vector1< VarSolDRotamerDotsOP > protocols::vardist_solaccess::VarSolDistSasaCalculator::rotamer_dots_vec_
private

Referenced by recompute().

core::Real protocols::vardist_solaccess::VarSolDistSasaCalculator::total_sasa_
private

Referenced by lookup(), print(), and recompute().

bool protocols::vardist_solaccess::VarSolDistSasaCalculator::up_to_date
private
core::Real protocols::vardist_solaccess::VarSolDistSasaCalculator::wobble_
private

The documentation for this class was generated from the following files: