protocols::dna::DNAParameters Class Reference

#include <DNAParameters.hh>

Inheritance diagram for protocols::dna::DNAParameters:

Public Member Functions
	DNAParameters ()
	DNAParameters (core::pose::Pose const &pose)
	~DNAParameters () override=default
core::Size	number_of_bases ()
core::Size	number_of_basepairs ()
core::Size	number_of_basesteps ()
core::Size	random_basepair () const
core::Size	random_basestep () const
core::Size const &	nth_dna_base (core::Size index) const
DNABase const &	base (core::Size resid) const
DNABasepair const &	basepair (core::Size resid) const
DNABasestep const &	basestep (core::Size resid) const
std::map< core::Size, DNABase >::const_iterator	bases_begin () const
std::map< core::Size, DNABase >::const_iterator	bases_end () const
std::map< core::Size, DNABasepair >::const_iterator	basepairs_begin () const
std::map< core::Size, DNABasepair >::const_iterator	basepairs_end () const
std::map< core::Size, DNABasestep >::const_iterator	basesteps_begin () const
std::map< core::Size, DNABasestep >::const_iterator	basesteps_end () const
core::Size	find_partner (core::Size resid) const
bool	is_base_paired (core::Size resid) const
bool	valid_basestep_start (core::Size resid) const
void	calculate (core::pose::Pose const &pose)

Private Attributes
std::map< core::Size, DNABasepair >	basepairs_
std::map< core::Size, DNABasestep >	basesteps_
std::map< core::Size, DNABase >	bases_
utility::vector1< core::Size >	partners_
utility::vector1< core::Size >	unique_basepairs_
utility::vector1< core::Size >	unique_basestep_starts_
utility::vector1< core::Size >	dna_base_positions_

Constructor & Destructor Documentation

DNAParameters() [1/2]

protocols::dna::DNAParameters::DNAParameters ( )

inline

DNAParameters() [2/2]

protocols::dna::DNAParameters::DNAParameters ( core::pose::Pose const &  pose )

inline

References calculate().

~DNAParameters()

protocols::dna::DNAParameters::~DNAParameters ( )

overridedefault

Member Function Documentation

base()

DNABase const & protocols::dna::DNAParameters::base

(

core::Size

resid

)

const

References bases_.

basepair()

DNABasepair const & protocols::dna::DNAParameters::basepair

(

core::Size

resid

)

const

References basepairs_.

basepairs_begin()

std::map< core::Size, DNABasepair >::const_iterator protocols::dna::DNAParameters::basepairs_begin ( ) const

inline

References basepairs_.

basepairs_end()

std::map< core::Size, DNABasepair >::const_iterator protocols::dna::DNAParameters::basepairs_end ( ) const

inline

References basepairs_.

bases_begin()

std::map< core::Size, DNABase >::const_iterator protocols::dna::DNAParameters::bases_begin ( ) const

inline

References bases_.

bases_end()

std::map< core::Size, DNABase >::const_iterator protocols::dna::DNAParameters::bases_end ( ) const

inline

References bases_.

basestep()

DNABasestep const & protocols::dna::DNAParameters::basestep

(

core::Size

resid

)

const

References basesteps_.

basesteps_begin()

std::map< core::Size, DNABasestep >::const_iterator protocols::dna::DNAParameters::basesteps_begin ( ) const

inline

References basesteps_.

basesteps_end()

std::map< core::Size, DNABasestep >::const_iterator protocols::dna::DNAParameters::basesteps_end ( ) const

inline

References basesteps_.

calculate()

void protocols::dna::DNAParameters::calculate

(

core::pose::Pose const &

pose

)

References basepairs_, bases_, basesteps_, dna_base_positions_, core::scoring::dna::find_basepairs(), core::conformation::Residue::is_DNA(), core::conformation::Residue::is_upper_terminus(), partners_, core::pose::Pose::residue(), core::pose::Pose::size(), unique_basepairs_, and unique_basestep_starts_.

Referenced by DNAParameters().

find_partner()

core::Size protocols::dna::DNAParameters::find_partner

(

core::Size

resid

)

const

References partners_.

Referenced by protocols::dna::make_base_pair_aware_fold_tree().

is_base_paired()

bool protocols::dna::DNAParameters::is_base_paired

(

core::Size

resid

)

const

References basepairs_.

nth_dna_base()

core::Size const& protocols::dna::DNAParameters::nth_dna_base ( core::Size  index ) const

inline

References dna_base_positions_.

number_of_basepairs()

core::Size protocols::dna::DNAParameters::number_of_basepairs ( )

inline

References basepairs_.

number_of_bases()

core::Size protocols::dna::DNAParameters::number_of_bases ( )

inline

References bases_.

number_of_basesteps()

core::Size protocols::dna::DNAParameters::number_of_basesteps ( )

inline

References basesteps_.

random_basepair()

core::Size protocols::dna::DNAParameters::random_basepair

(

)

const

References core::scoring::rg, and unique_basepairs_.

random_basestep()

core::Size protocols::dna::DNAParameters::random_basestep

(

)

const

References core::scoring::rg, and unique_basestep_starts_.

valid_basestep_start()

bool protocols::dna::DNAParameters::valid_basestep_start

(

core::Size

resid

)

const

References basesteps_.

Member Data Documentation

basepairs_

std::map< core::Size, DNABasepair > protocols::dna::DNAParameters::basepairs_

private

Referenced by basepair(), basepairs_begin(), basepairs_end(), calculate(), is_base_paired(), and number_of_basepairs().

bases_

std::map< core::Size, DNABase > protocols::dna::DNAParameters::bases_

private

Referenced by base(), bases_begin(), bases_end(), calculate(), and number_of_bases().

basesteps_

std::map< core::Size, DNABasestep > protocols::dna::DNAParameters::basesteps_

private

Referenced by basestep(), basesteps_begin(), basesteps_end(), calculate(), number_of_basesteps(), and valid_basestep_start().

dna_base_positions_

utility::vector1< core::Size > protocols::dna::DNAParameters::dna_base_positions_

private

Referenced by calculate(), and nth_dna_base().

partners_

utility::vector1< core::Size > protocols::dna::DNAParameters::partners_

private

Referenced by calculate(), and find_partner().

unique_basepairs_

utility::vector1< core::Size > protocols::dna::DNAParameters::unique_basepairs_

private

Referenced by calculate(), and random_basepair().

unique_basestep_starts_

utility::vector1< core::Size > protocols::dna::DNAParameters::unique_basestep_starts_

private

Referenced by calculate(), and random_basestep().

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

• src/protocols/dna/DNAParameters.hh
• src/protocols/dna/DNAParameters.cc