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protocols::fldsgn::NcontactsCalculator Class Reference

#include <NcontactsCalculator.hh>

Inheritance diagram for protocols::fldsgn::NcontactsCalculator:
Inheritance graph
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Public Types

typedef
core::pose::metrics::StructureDependentCalculator 
Super
 
typedef std::string String
 
typedef core::Size Size
 
typedef core::Real Real
 
typedef core::pose::Pose Pose
 
typedef core::conformation::Atom Atom
 
typedef core::conformation::Residue Residue
 
typedef
core::pose::metrics::PoseMetricCalculatorOP 
PoseMetricCalculatorOP
 
typedef basic::MetricValueBase MetricValueBase
 

Public Member Functions

 NcontactsCalculator ()
 default constructor More...
 
 NcontactsCalculator (Real const condist, core::Size const isep_sep)
 default constructor More...
 
PoseMetricCalculatorOP clone () const override
 make clone More...
 
void contact_distance (Real const r)
 set contact distance More...
 
void ignore_loops (bool const b)
 ignore loops for calculation More...
 
void ignore_same_sselement (bool const b)
 ignore residue pairs of which residue belong to same ss element More...
 
void ignore_same_sheet (bool const b)
 ignore residue pairs of which residue belong to same beta sheet ( default true ) More...
 
void use_only_calpha (bool const b)
 use only calpha for calculation More...
 
- 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 (String const &key, MetricValueBase *valptr) const override
 
std::string print (String const &key) const override
 
void recompute (Pose const &this_pose) override
 recomute ncontacts More...
 

Private Attributes

Real condist_
 distact used for juding contact pair ( default 6.0 ) More...
 
core::Size isep_residue_
 residue pairs of i < i+isep_residue_ are used for counting #countacts ( default 4 ) More...
 
bool ignore_loops_
 ignore loops for calculation ( default false ) More...
 
bool ignore_same_sselement_
 ignore residue pairs of which residue belong to same ss element ( default false ) More...
 
bool ignore_same_sheet_
 ignore residue pairs of which residue belong to same beta sheet ( default false ) More...
 
bool use_only_calpha_
 use only calpha atoms for calculation ( default false ) More...
 
Real nc_allatm_
 #atom-contacts among all heavy atoms More...
 
Real nc_hpatm_
 #atom-contacts among hydrophobic heavy atoms More...
 
Real nc_hpres_
 #atom-contacts among heavy atoms of sidechains of hydrophobic residues More...
 
Real ss_entrpy_
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::fldsgn::NcontactsCalculator::NcontactsCalculator ( )

default constructor

protocols::fldsgn::NcontactsCalculator::NcontactsCalculator ( Real const  condist,
core::Size const  isep_sep 
)

default constructor

Member Function Documentation

PoseMetricCalculatorOP protocols::fldsgn::NcontactsCalculator::clone ( ) const
inlineoverridevirtual
void protocols::fldsgn::NcontactsCalculator::contact_distance ( Real const  r)
inline

set contact distance

References condist_.

void protocols::fldsgn::NcontactsCalculator::ignore_loops ( bool const  b)
inline

ignore loops for calculation

References protocols::match::upstream::b, and ignore_loops_.

void protocols::fldsgn::NcontactsCalculator::ignore_same_sheet ( bool const  b)
inline

ignore residue pairs of which residue belong to same beta sheet ( default true )

References protocols::match::upstream::b, and ignore_same_sheet_.

void protocols::fldsgn::NcontactsCalculator::ignore_same_sselement ( bool const  b)
inline

ignore residue pairs of which residue belong to same ss element

References protocols::match::upstream::b, and ignore_same_sselement_.

void protocols::fldsgn::NcontactsCalculator::lookup ( String const &  key,
MetricValueBase valptr 
) const
overrideprotectedvirtual
std::string protocols::fldsgn::NcontactsCalculator::print ( String const &  key) const
overrideprotectedvirtual
void protocols::fldsgn::NcontactsCalculator::recompute ( Pose const &  this_pose)
overrideprotectedvirtual
void protocols::fldsgn::NcontactsCalculator::use_only_calpha ( bool const  b)
inline

use only calpha for calculation

References protocols::match::upstream::b, and use_only_calpha_.

Member Data Documentation

Real protocols::fldsgn::NcontactsCalculator::condist_
private

distact used for juding contact pair ( default 6.0 )

Referenced by contact_distance(), and recompute().

bool protocols::fldsgn::NcontactsCalculator::ignore_loops_
private

ignore loops for calculation ( default false )

Referenced by ignore_loops(), and recompute().

bool protocols::fldsgn::NcontactsCalculator::ignore_same_sheet_
private

ignore residue pairs of which residue belong to same beta sheet ( default false )

Referenced by ignore_same_sheet(), and recompute().

bool protocols::fldsgn::NcontactsCalculator::ignore_same_sselement_
private

ignore residue pairs of which residue belong to same ss element ( default false )

Referenced by ignore_same_sselement(), and recompute().

core::Size protocols::fldsgn::NcontactsCalculator::isep_residue_
private

residue pairs of i < i+isep_residue_ are used for counting #countacts ( default 4 )

Referenced by recompute().

Real protocols::fldsgn::NcontactsCalculator::nc_allatm_
private

#atom-contacts among all heavy atoms

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

Real protocols::fldsgn::NcontactsCalculator::nc_hpatm_
private

#atom-contacts among hydrophobic heavy atoms

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

Real protocols::fldsgn::NcontactsCalculator::nc_hpres_
private

#atom-contacts among heavy atoms of sidechains of hydrophobic residues

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

Real protocols::fldsgn::NcontactsCalculator::ss_entrpy_
private

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

bool protocols::fldsgn::NcontactsCalculator::use_only_calpha_
private

use only calpha atoms for calculation ( default false )

Referenced by recompute(), and use_only_calpha().


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