CountContact Class Reference

Inheritance diagram for CountContact:

Public Member Functions
	CountContact ()
	default constructor More...
	CountContact (Real const cdist, Size const sep)
	value constructor More...
virtual void	apply (core::pose::Pose &)
virtual	~CountContact ()

Private Types
typedef core::Real	Real
typedef core::Size	Size
typedef ObjexxFCL::FArray2D< Size >	FArray2D_Size
typedef core::conformation::Residue	Residue
typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP
typedef core::scoring::dssp::Dssp	Dssp
typedef protocols::fldsgn::sspot::SS_Info2	SS_Info2

Private Member Functions
void	initialize ()

Private Attributes
Real	condist_
	distact**2 used for juding contact pair More...
Size	isep_residue_
	residue pairs of i < i+isep_residue_ are used for counting #countacts More...
Size	ncontact_allatm_
	#atom-contacts among all heavy atoms More...
Size	ncontact_hpatm_
	#atom-contacts among hydrophobic heavy atoms More...
Size	ncontact_atm_hpres_
	#atom-contacts among heavy atoms of sidechains of hydrophobic residues More...
Size	ncontact_res_hh_
	residue-contacts among helices, defeined only by Ca More...
Size	ncontact_res_eh_
	residue-contacts between helices and strands, defeined only by Ca More...
ScoreFunctionOP	scorefxn_
	score function More...

Member Typedef Documentation

Dssp

typedef core::scoring::dssp::Dssp CountContact::Dssp

private

FArray2D_Size

typedef ObjexxFCL::FArray2D< Size > CountContact::FArray2D_Size

private

Real

typedef core::Real CountContact::Real

private

Residue

typedef core::conformation::Residue CountContact::Residue

private

ScoreFunctionOP

typedef core::scoring::ScoreFunctionOP CountContact::ScoreFunctionOP

private

Size

typedef core::Size CountContact::Size

private

SS_Info2

typedef protocols::fldsgn::sspot::SS_Info2 CountContact::SS_Info2

private

Constructor & Destructor Documentation

CountContact() [1/2]

CountContact::CountContact ( )

inline

default constructor

References basic::options::initialize().

CountContact() [2/2]

CountContact::CountContact ( Real const  cdist, Size const  sep  )

inline

value constructor

References basic::options::initialize().

~CountContact()

virtual CountContact::~CountContact ( )

inlinevirtual

Member Function Documentation

apply()

void CountContact::apply ( core::pose::Pose &  pose )

virtual

References numeric::distance_squared(), basic::options::OptionKeys::in::file::dssp, create_a3b_hbs::i, basic::options::initialize(), create_a3b_hbs::j, numeric::log(), beta_nonlocal::pose, and spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::prob.

Referenced by pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::execute().

initialize()

void CountContact::initialize ( )

inlineprivate

Member Data Documentation

condist_

Real CountContact::condist_

private

distact**2 used for juding contact pair

isep_residue_

Size CountContact::isep_residue_

private

residue pairs of i < i+isep_residue_ are used for counting #countacts

ncontact_allatm_

Size CountContact::ncontact_allatm_

private

#atom-contacts among all heavy atoms

ncontact_atm_hpres_

Size CountContact::ncontact_atm_hpres_

private

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

ncontact_hpatm_

Size CountContact::ncontact_hpatm_

private

#atom-contacts among hydrophobic heavy atoms

ncontact_res_eh_

Size CountContact::ncontact_res_eh_

private

residue-contacts between helices and strands, defeined only by Ca

ncontact_res_hh_

Size CountContact::ncontact_res_hh_

private

residue-contacts among helices, defeined only by Ca

scorefxn_

ScoreFunctionOP CountContact::scorefxn_

private

score function

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

• src/apps/pilot/nobuyasu/ncontact.cc