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Public Member Functions | Private Attributes | List of all members
protocols::dna::DNAParameters Class Reference

#include <DNAParameters.hh>

Inheritance diagram for protocols::dna::DNAParameters:
Inheritance graph
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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, DNABasepairbasepairs_
 
std::map< core::Size, DNABasestepbasesteps_
 
std::map< core::Size, DNABasebases_
 
utility::vector1< core::Sizepartners_
 
utility::vector1< core::Sizeunique_basepairs_
 
utility::vector1< core::Sizeunique_basestep_starts_
 
utility::vector1< core::Sizedna_base_positions_
 

Constructor & Destructor Documentation

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

References calculate().

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

Member Function Documentation

DNABase const & protocols::dna::DNAParameters::base ( core::Size  resid) const

References bases_.

DNABasepair const & protocols::dna::DNAParameters::basepair ( core::Size  resid) const

References basepairs_.

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

References basepairs_.

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

References basepairs_.

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

References bases_.

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

References bases_.

DNABasestep const & protocols::dna::DNAParameters::basestep ( core::Size  resid) const

References basesteps_.

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

References basesteps_.

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

References basesteps_.

void protocols::dna::DNAParameters::calculate ( core::pose::Pose const &  pose)
core::Size protocols::dna::DNAParameters::find_partner ( core::Size  resid) const

References partners_.

bool protocols::dna::DNAParameters::is_base_paired ( core::Size  resid) const

References basepairs_.

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

References dna_base_positions_.

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

References basepairs_.

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

References bases_.

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

References basesteps_.

core::Size protocols::dna::DNAParameters::random_basepair ( ) const
core::Size protocols::dna::DNAParameters::random_basestep ( ) const
bool protocols::dna::DNAParameters::valid_basestep_start ( core::Size  resid) const

References basesteps_.

Member Data Documentation

std::map< core::Size, DNABasepair > protocols::dna::DNAParameters::basepairs_
private
std::map< core::Size, DNABase > protocols::dna::DNAParameters::bases_
private
std::map< core::Size, DNABasestep > protocols::dna::DNAParameters::basesteps_
private
utility::vector1< core::Size > protocols::dna::DNAParameters::dna_base_positions_
private

Referenced by calculate(), and nth_dna_base().

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

Referenced by calculate(), and find_partner().

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

Referenced by calculate(), and random_basepair().

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

Referenced by calculate(), and random_basestep().


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