protocols::fldsgn::NcontactsCalculator Class Reference

#include <NcontactsCalculator.hh>

Inheritance diagram for protocols::fldsgn::NcontactsCalculator:

Collaboration diagram for protocols::fldsgn::NcontactsCalculator:

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, Size const isep_sep)
	default constructor More...
	NcontactsCalculator (NcontactsCalculator const &rval)
	copy constructor More...
virtual	~NcontactsCalculator ()
	destructor More...
PoseMetricCalculatorOP	clone () const
	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 ()
void	get (std::string const &key, basic::MetricValueBase &val, Pose const &this_pose)
std::string	get (std::string const &key, Pose const &this_pose)
Public Member Functions inherited from core::pose::metrics::PoseMetricCalculator
	PoseMetricCalculator ()
virtual void	notify_energy_change ()

Protected Member Functions
virtual void	lookup (String const &key, MetricValueBase *valptr) const
virtual std::string	print (String const &key) const
virtual void	recompute (Pose const &this_pose)
	recomute ncontacts More...

Private Attributes
Real	condist_
	distact used for juding contact pair ( default 6.0 ) More...
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_

Detailed Description

Definition at line 37 of file NcontactsCalculator.hh.

Member Typedef Documentation

typedef core::conformation::Atom protocols::fldsgn::NcontactsCalculator::Atom

Definition at line 46 of file NcontactsCalculator.hh.

typedef basic::MetricValueBase protocols::fldsgn::NcontactsCalculator::MetricValueBase

Definition at line 49 of file NcontactsCalculator.hh.

typedef core::pose::Pose protocols::fldsgn::NcontactsCalculator::Pose

Definition at line 45 of file NcontactsCalculator.hh.

typedef core::pose::metrics::PoseMetricCalculatorOP protocols::fldsgn::NcontactsCalculator::PoseMetricCalculatorOP

Definition at line 48 of file NcontactsCalculator.hh.

typedef core::Real protocols::fldsgn::NcontactsCalculator::Real

Definition at line 44 of file NcontactsCalculator.hh.

typedef core::conformation::Residue protocols::fldsgn::NcontactsCalculator::Residue

Definition at line 47 of file NcontactsCalculator.hh.

typedef core::Size protocols::fldsgn::NcontactsCalculator::Size

Definition at line 43 of file NcontactsCalculator.hh.

typedef std::string protocols::fldsgn::NcontactsCalculator::String

Definition at line 42 of file NcontactsCalculator.hh.

typedef core::pose::metrics::StructureDependentCalculator protocols::fldsgn::NcontactsCalculator::Super

Definition at line 41 of file NcontactsCalculator.hh.

Constructor & Destructor Documentation

protocols::fldsgn::NcontactsCalculator::NcontactsCalculator

(

)

default constructor

Definition at line 71 of file NcontactsCalculator.cc.

Referenced by clone().

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

default constructor

Definition at line 81 of file NcontactsCalculator.cc.

protocols::fldsgn::NcontactsCalculator::NcontactsCalculator

(

NcontactsCalculator const &

rval)

copy constructor

Definition at line 93 of file NcontactsCalculator.cc.

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

virtual

destructor

Definition at line 104 of file NcontactsCalculator.cc.

Member Function Documentation

PoseMetricCalculatorOP protocols::fldsgn::NcontactsCalculator::clone ( ) const

inlinevirtual

make clone

Implements core::pose::metrics::PoseMetricCalculator.

Definition at line 75 of file NcontactsCalculator.hh.

References NcontactsCalculator().

void protocols::fldsgn::NcontactsCalculator::contact_distance ( Real const  r)

inline

set contact distance

Definition at line 81 of file NcontactsCalculator.hh.

References condist_.

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

inline

ignore loops for calculation

Definition at line 84 of file NcontactsCalculator.hh.

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 )

Definition at line 90 of file NcontactsCalculator.hh.

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

Definition at line 87 of file NcontactsCalculator.hh.

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

void protocols::fldsgn::NcontactsCalculator::lookup ( String const &  key, MetricValueBase *  valptr  ) const

protectedvirtual

Implements core::pose::metrics::StructureDependentCalculator.

Definition at line 108 of file NcontactsCalculator.cc.

References nc_allatm_, nc_hpatm_, nc_hpres_, ss_entrpy_, and tr().

std::string protocols::fldsgn::NcontactsCalculator::print ( String const &  key) const

protectedvirtual

Implements core::pose::metrics::StructureDependentCalculator.

Definition at line 140 of file NcontactsCalculator.cc.

References nc_allatm_, nc_hpatm_, nc_hpres_, and ss_entrpy_.

void protocols::fldsgn::NcontactsCalculator::recompute ( Pose const &  this_pose)

protectedvirtual

recomute ncontacts

Implements core::pose::metrics::StructureDependentCalculator.

Definition at line 164 of file NcontactsCalculator.cc.

References protocols::fldsgn::topology::calc_strand_pairing_set(), condist_, ignore_loops_, ignore_same_sheet_, ignore_same_sselement_, protocols::fldsgn::MyAtom::is_hydrophobic(), isep_residue_, nc_allatm_, nc_hpatm_, nc_hpres_, core::pose::Pose::residue(), core::pose::Pose::secstruct(), core::scoring::electron_density::square(), ss_entrpy_, core::pose::Pose::total_residue(), and use_only_calpha_.

void protocols::fldsgn::NcontactsCalculator::use_only_calpha ( bool const  b)

inline

use only calpha for calculation

Definition at line 93 of file NcontactsCalculator.hh.

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 )

Definition at line 106 of file NcontactsCalculator.hh.

Referenced by contact_distance(), and recompute().

bool protocols::fldsgn::NcontactsCalculator::ignore_loops_

private

ignore loops for calculation ( default false )

Definition at line 112 of file NcontactsCalculator.hh.

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 )

Definition at line 118 of file NcontactsCalculator.hh.

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 )

Definition at line 115 of file NcontactsCalculator.hh.

Referenced by ignore_same_sselement(), and recompute().

Size protocols::fldsgn::NcontactsCalculator::isep_residue_

private

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

Definition at line 109 of file NcontactsCalculator.hh.

Referenced by recompute().

Real protocols::fldsgn::NcontactsCalculator::nc_allatm_

private

#atom-contacts among all heavy atoms

Definition at line 124 of file NcontactsCalculator.hh.

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

Real protocols::fldsgn::NcontactsCalculator::nc_hpatm_

private

#atom-contacts among hydrophobic heavy atoms

Definition at line 127 of file NcontactsCalculator.hh.

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

Real protocols::fldsgn::NcontactsCalculator::nc_hpres_

private

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

Definition at line 130 of file NcontactsCalculator.hh.

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

Real protocols::fldsgn::NcontactsCalculator::ss_entrpy_

private

Definition at line 133 of file NcontactsCalculator.hh.

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

bool protocols::fldsgn::NcontactsCalculator::use_only_calpha_

private

use only calpha atoms for calculation ( default false )

Definition at line 121 of file NcontactsCalculator.hh.

Referenced by recompute(), and use_only_calpha().

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

• src/protocols/fldsgn/NcontactsCalculator.hh
• src/protocols/fldsgn/NcontactsCalculator.cc