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Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::simple_filters::ResidueDepthCalculator Class Reference

#include <ResidueDepthFilter.hh>

Public Member Functions

 ResidueDepthCalculator ()
 
 ~ResidueDepthCalculator ()
 
utility::vector1< core::Realestimate_sidechain_depth (core::pose::Pose const &pose) const
 
void report_crd (bool const value)
 
void niter (core::Size const value)
 
void set_dcut1 (core::Real const value)
 
void set_dcut2 (core::Real const value)
 
core::Real get_scdepth_avrg (core::Size const ires) const
 
core::Size nres () const
 These are only valid after the call to estimate_sidechain_depth() More...
 
utility::vector1< core::Realget_scdepth_avrg () const
 
utility::vector1< core::Realget_scdepth_sdev () const
 
utility::vector1< core::Realget_scdepth_fvar () const
 

Private Member Functions

void initialize ()
 
utility::vector1< core::Vectorread_unit_waterbox (core::Vector &boxwidth) const
 
void get_pose_crd_and_index (core::pose::Pose const &pose, utility::vector1< core::Vector > &protein_crd, utility::vector1< core::Size > &coarse_index, utility::vector1< core::Size > &res_id) const
 
utility::vector1< core::Vectorget_coarse_crd (utility::vector1< core::Vector > const &protein_crd, utility::vector1< core::Size > const &coarse_index) const
 
void duplicate_waterbox (utility::vector1< core::Vector > const &unit_waterbox_crd, core::Vector const boxwidth, core::Vector const mincrds, core::Vector const maxcrds) const
 
core::Vector bring_to_origin (utility::vector1< core::Vector > &protein_crd, core::Vector &maxcrds, core::Vector &mincrds) const
 
void append_unitbox (utility::vector1< core::Vector > const &unitbox, utility::vector1< core::Vector > &waterbox_dupl, core::Vector const boxwidth, int const i, int const j, int const k) const
 
void pert_protein (utility::vector1< core::Vector > &protein_crd) const
 
utility::vector1< core::Vectorquat2U (core::Vector const &quat3, core::Real const &quatw) const
 
utility::vector1< boolget_exclusion_index (utility::vector1< core::Vector > const &protein_crd, utility::vector1< core::Vector > const &protein_coarse_crd) const
 
utility::vector1< core::Realget_scdepth (utility::vector1< bool > const &excluded_wat, utility::vector1< core::Vector > const &protein_crd, utility::vector1< core::Size > const &res_id) const
 
bool stack_and_getaverage (utility::vector1< utility::vector1< core::Real > > &sc_depth_stack, utility::vector1< core::Real > const &sc_depth, core::Size const niter) const
 

Private Attributes

core::Size niter_
 
std::string waterbox_file_
 
core::Real dcut1_
 
core::Real dcut2_
 
bool use_bb_
 
bool use_sc_
 
bool report_crd_
 
core::Size nres_ = 0
 
utility::vector1< core::Vectorwaterbox_
 
utility::vector1< core::Realsc_depth_avrg_
 
utility::vector1< core::Realsc_depth_sdev_
 
utility::vector1< core::Realsc_depth_fvar_
 

Constructor & Destructor Documentation

protocols::simple_filters::ResidueDepthCalculator::ResidueDepthCalculator ( )
protocols::simple_filters::ResidueDepthCalculator::~ResidueDepthCalculator ( )
default

Member Function Documentation

void protocols::simple_filters::ResidueDepthCalculator::append_unitbox ( utility::vector1< core::Vector > const &  unitbox,
utility::vector1< core::Vector > &  waterbox_dupl,
core::Vector const  boxwidth,
int const  i,
int const  j,
int const  k 
) const
private
Vector protocols::simple_filters::ResidueDepthCalculator::bring_to_origin ( utility::vector1< core::Vector > &  protein_crd,
core::Vector maxcrds,
core::Vector mincrds 
) const
private
void protocols::simple_filters::ResidueDepthCalculator::duplicate_waterbox ( utility::vector1< core::Vector > const &  unit_waterbox_crd,
core::Vector const  boxwidth,
core::Vector const  mincrds,
core::Vector const  maxcrds 
) const
private
utility::vector1< core::Real > protocols::simple_filters::ResidueDepthCalculator::estimate_sidechain_depth ( core::pose::Pose const &  pose) const
utility::vector1< Vector > protocols::simple_filters::ResidueDepthCalculator::get_coarse_crd ( utility::vector1< core::Vector > const &  protein_crd,
utility::vector1< core::Size > const &  coarse_index 
) const
private
utility::vector1< bool > protocols::simple_filters::ResidueDepthCalculator::get_exclusion_index ( utility::vector1< core::Vector > const &  protein_crd,
utility::vector1< core::Vector > const &  protein_coarse_crd 
) const
private
void protocols::simple_filters::ResidueDepthCalculator::get_pose_crd_and_index ( core::pose::Pose const &  pose,
utility::vector1< core::Vector > &  protein_crd,
utility::vector1< core::Size > &  coarse_index,
utility::vector1< core::Size > &  res_id 
) const
private
utility::vector1< core::Real > protocols::simple_filters::ResidueDepthCalculator::get_scdepth ( utility::vector1< bool > const &  excluded_wat,
utility::vector1< core::Vector > const &  protein_crd,
utility::vector1< core::Size > const &  res_id 
) const
private
core::Real protocols::simple_filters::ResidueDepthCalculator::get_scdepth_avrg ( core::Size const  ires) const
inline
utility::vector1< core::Real > protocols::simple_filters::ResidueDepthCalculator::get_scdepth_avrg ( ) const
inline

References sc_depth_avrg_.

utility::vector1< core::Real > protocols::simple_filters::ResidueDepthCalculator::get_scdepth_fvar ( ) const
inline
utility::vector1< core::Real > protocols::simple_filters::ResidueDepthCalculator::get_scdepth_sdev ( ) const
inline
void protocols::simple_filters::ResidueDepthCalculator::initialize ( )
private
void protocols::simple_filters::ResidueDepthCalculator::niter ( core::Size const  value)
inline
core::Size protocols::simple_filters::ResidueDepthCalculator::nres ( ) const
inline

These are only valid after the call to estimate_sidechain_depth()

References nres_.

void protocols::simple_filters::ResidueDepthCalculator::pert_protein ( utility::vector1< core::Vector > &  protein_crd) const
private
utility::vector1< Vector > protocols::simple_filters::ResidueDepthCalculator::quat2U ( core::Vector const &  quat3,
core::Real const &  quatw 
) const
private
utility::vector1< Vector > protocols::simple_filters::ResidueDepthCalculator::read_unit_waterbox ( core::Vector boxwidth) const
private
void protocols::simple_filters::ResidueDepthCalculator::report_crd ( bool const  value)
inline
void protocols::simple_filters::ResidueDepthCalculator::set_dcut1 ( core::Real const  value)
inline
void protocols::simple_filters::ResidueDepthCalculator::set_dcut2 ( core::Real const  value)
inline
bool protocols::simple_filters::ResidueDepthCalculator::stack_and_getaverage ( utility::vector1< utility::vector1< core::Real > > &  sc_depth_stack,
utility::vector1< core::Real > const &  sc_depth,
core::Size const  niter 
) const
private

Member Data Documentation

core::Real protocols::simple_filters::ResidueDepthCalculator::dcut1_
private

Referenced by set_dcut1().

core::Real protocols::simple_filters::ResidueDepthCalculator::dcut2_
private

Referenced by set_dcut2().

core::Size protocols::simple_filters::ResidueDepthCalculator::niter_
private

Referenced by niter().

core::Size protocols::simple_filters::ResidueDepthCalculator::nres_ = 0
mutableprivate

Referenced by nres().

bool protocols::simple_filters::ResidueDepthCalculator::report_crd_
private

Referenced by report_crd().

utility::vector1< core::Real > protocols::simple_filters::ResidueDepthCalculator::sc_depth_avrg_
mutableprivate

Referenced by get_scdepth_avrg().

utility::vector1< core::Real > protocols::simple_filters::ResidueDepthCalculator::sc_depth_fvar_
mutableprivate

Referenced by get_scdepth_fvar().

utility::vector1< core::Real > protocols::simple_filters::ResidueDepthCalculator::sc_depth_sdev_
mutableprivate

Referenced by get_scdepth_sdev().

bool protocols::simple_filters::ResidueDepthCalculator::use_bb_
private
bool protocols::simple_filters::ResidueDepthCalculator::use_sc_
private
utility::vector1< core::Vector > protocols::simple_filters::ResidueDepthCalculator::waterbox_
mutableprivate
std::string protocols::simple_filters::ResidueDepthCalculator::waterbox_file_
private

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