Rosetta: protocols::fldsgn::NcontactsCalculator Class Reference

#include <NcontactsCalculator.hh>

Inheritance diagram for protocols::fldsgn::NcontactsCalculator:

Inheritance graph

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_

Member Typedef Documentation

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

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

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

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

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

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

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

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

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

Constructor & Destructor Documentation

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

default constructor

Referenced by clone().

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

default constructor

protocols::fldsgn::NcontactsCalculator::NcontactsCalculator ( NcontactsCalculator const & rval )

copy constructor

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

virtual

destructor

Member Function Documentation

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

inlinevirtual

make clone

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

References NcontactsCalculator().

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

protectedvirtual

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

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.

References nc_allatm_, nc_hpatm_, nc_hpres_, ss_entrpy_, and core::id::to_string().

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

protectedvirtual

recomute ncontacts

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

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

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().

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:

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