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Public Member Functions | Private Attributes | List of all members
core::scoring::MembraneTopology Class Reference

#include <MembraneTopology.hh>

Inheritance diagram for core::scoring::MembraneTopology:
Inheritance graph
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Public Member Functions

 MembraneTopology ()
 
basic::datacache::CacheableDataOP clone () const override
 
std::string read_in_spanfile ()
 
bool initialized () const
 
boolinitialized ()
 
Size tmhelix () const
 
Size span_begin (Size n) const
 
Size span_end (Size n) const
 
Size helix_id (Size n) const
 
Real depth (Size const seqpos)
 
utility::vector1< core::Real > & depth ()
 
void initialize (std::string const &spanfile)
 
void print () const
 
void shift_span (Size shift)
 
void get_subset (utility::vector1< Size > &TMH_list, MembraneTopology &src)
 
bool allow_scoring (Size const seqpos) const
 
Size tmh_inserted () const
 
void reset_tmh_insert ()
 
void reset_allowed_scoring ()
 
void set_tmh_inserted (Size tmh_inserted)
 
bool tmregion (Size const pos) const
 
bool allow_tmh_scoring (Size const tmh) const
 
void set_allow_tmh_scoring (Size const tmh, bool setting)
 
void set_allow_scoring (Size const pos, bool setting)
 
Real LipidExposure (Size const n) const
 
Real LipidBurial (Size const n) const
 
bool LipoDefined () const
 

Private Attributes

std::string spanfile_
 
ObjexxFCL::FArray1D< Sizehelix_id_
 
ObjexxFCL::FArray2D< Sizespan_
 
ObjexxFCL::FArray2D< Sizefull_span_
 
ObjexxFCL::FArray2D< Sizerelative_tmh_ori_
 
Size total_tmhelix_
 
utility::vector1< core::Realdepth_
 
utility::vector1< core::RealLipidExposure_
 
utility::vector1< core::RealLipidBurial_
 
bool LipoDefined_
 
bool init_
 
bool initialized_
 
utility::vector1< booltmregion_
 
utility::vector1< boolallow_scoring_
 
utility::vector1< boolallow_tmh_scoring_
 
Size tmh_inserted_
 

Constructor & Destructor Documentation

core::scoring::MembraneTopology::MembraneTopology ( )
inline

Member Function Documentation

bool core::scoring::MembraneTopology::allow_scoring ( Size const  seqpos) const
inline
bool core::scoring::MembraneTopology::allow_tmh_scoring ( Size const  tmh) const
inline
basic::datacache::CacheableDataOP core::scoring::MembraneTopology::clone ( ) const
inlineoverride
Real core::scoring::MembraneTopology::depth ( Size const  seqpos)
inline

References depth_.

utility::vector1< core::Real >& core::scoring::MembraneTopology::depth ( )
inline

References depth_.

void core::scoring::MembraneTopology::get_subset ( utility::vector1< Size > &  TMH_list,
MembraneTopology src 
)
Size core::scoring::MembraneTopology::helix_id ( Size  n) const
inline
void core::scoring::MembraneTopology::initialize ( std::string const &  spanfile)
bool core::scoring::MembraneTopology::initialized ( ) const
inline
bool& core::scoring::MembraneTopology::initialized ( )
inline

References initialized_.

Real core::scoring::MembraneTopology::LipidBurial ( Size const  n) const
inline

References LipidBurial_.

Real core::scoring::MembraneTopology::LipidExposure ( Size const  n) const
inline

References LipidExposure_.

bool core::scoring::MembraneTopology::LipoDefined ( ) const
inline

References LipoDefined_.

void core::scoring::MembraneTopology::print ( ) const
std::string core::scoring::MembraneTopology::read_in_spanfile ( )

References spanfile_, and core::scoring::TR().

void core::scoring::MembraneTopology::reset_allowed_scoring ( )
inline
void core::scoring::MembraneTopology::reset_tmh_insert ( )
inline

References tmh_inserted_.

void core::scoring::MembraneTopology::set_allow_scoring ( Size const  pos,
bool  setting 
)
inline

References allow_scoring_.

void core::scoring::MembraneTopology::set_allow_tmh_scoring ( Size const  tmh,
bool  setting 
)
inline

References allow_tmh_scoring_.

void core::scoring::MembraneTopology::set_tmh_inserted ( Size  tmh_inserted)
inline

References tmh_inserted(), and tmh_inserted_.

void core::scoring::MembraneTopology::shift_span ( Size  shift)

References full_span_, span_, and total_tmhelix_.

Size core::scoring::MembraneTopology::span_begin ( Size  n) const
inline
Size core::scoring::MembraneTopology::span_end ( Size  n) const
inline
Size core::scoring::MembraneTopology::tmh_inserted ( ) const
inline
Size core::scoring::MembraneTopology::tmhelix ( ) const
inline
bool core::scoring::MembraneTopology::tmregion ( Size const  pos) const
inline

Member Data Documentation

utility::vector1< bool > core::scoring::MembraneTopology::allow_scoring_
private
utility::vector1< bool > core::scoring::MembraneTopology::allow_tmh_scoring_
private
utility::vector1< core::Real > core::scoring::MembraneTopology::depth_
private

Referenced by depth(), and initialize().

ObjexxFCL::FArray2D< Size > core::scoring::MembraneTopology::full_span_
private

Referenced by get_subset(), initialize(), and shift_span().

ObjexxFCL::FArray1D< Size > core::scoring::MembraneTopology::helix_id_
private

Referenced by get_subset(), helix_id(), and initialize().

bool core::scoring::MembraneTopology::init_
private

Referenced by initialize().

bool core::scoring::MembraneTopology::initialized_
private

Referenced by initialize(), and initialized().

utility::vector1< core::Real > core::scoring::MembraneTopology::LipidBurial_
private

Referenced by initialize(), and LipidBurial().

utility::vector1< core::Real > core::scoring::MembraneTopology::LipidExposure_
private

Referenced by initialize(), and LipidExposure().

bool core::scoring::MembraneTopology::LipoDefined_
private

Referenced by initialize(), and LipoDefined().

ObjexxFCL::FArray2D< Size > core::scoring::MembraneTopology::relative_tmh_ori_
private

Referenced by get_subset(), and initialize().

ObjexxFCL::FArray2D< Size > core::scoring::MembraneTopology::span_
private
std::string core::scoring::MembraneTopology::spanfile_
private

Referenced by read_in_spanfile().

Size core::scoring::MembraneTopology::tmh_inserted_
private
utility::vector1< bool > core::scoring::MembraneTopology::tmregion_
private

Referenced by initialize(), and tmregion().

Size core::scoring::MembraneTopology::total_tmhelix_
private

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