core::scoring::MembraneTopology Class Reference

#include <MembraneTopology.hh>

Public Member Functions
	MembraneTopology ()
	MembraneTopology (MembraneTopology const &src)
basic::datacache::CacheableDataOP	clone () const
bool	initialized () const
bool &	initialized ()
Size	tmhelix () const
Size	span_begin (Size n) const
Size	span_end (Size n) const
Size	helix_id (Size n) const
Size	relative_tmh_ori (Size const n, Size const m) 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
Public Member Functions inherited from basic::datacache::CacheableData
virtual	~CacheableData ()

Private Attributes
ObjexxFCL::FArray1D< Size >	helix_id_
ObjexxFCL::FArray2D< Size >	span_
ObjexxFCL::FArray2D< Size >	full_span_
ObjexxFCL::FArray2D< Size >	relative_tmh_ori_
Size	total_tmhelix_
utility::vector1< core::Real >	depth_
utility::vector1< core::Real >	LipidExposure_
utility::vector1< core::Real >	LipidBurial_
bool	LipoDefined_
bool	init_
bool	beta_barrel_
bool	N_term_inside_
bool	initialized_
utility::vector1< bool >	tmregion_
utility::vector1< bool >	allow_scoring_
utility::vector1< bool >	allow_tmh_scoring_
Size	tmh_inserted_

Constructor & Destructor Documentation

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

inline

Referenced by clone(), and core::scoring::nonconst_MembraneTopology_from_pose().

core::scoring::MembraneTopology::MembraneTopology

(

MembraneTopology const &

src

)

References allow_scoring_, allow_tmh_scoring_, beta_barrel_, depth_, full_span_, helix_id_, init_, initialized_, LipidBurial_, LipidExposure_, LipoDefined_, N_term_inside_, relative_tmh_ori_, span_, tmh_inserted_, tmregion_, and total_tmhelix_.

Member Function Documentation

bool core::scoring::MembraneTopology::allow_scoring ( Size const  seqpos ) const

inline

References allow_scoring_, and utility::to_string().

Referenced by core::scoring::methods::MembraneLipo::finalize_total_energy(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::scoring::methods::MembraneCbetaEnergy::residue_energy(), core::scoring::methods::MembraneEnvEnergy::residue_energy(), core::scoring::methods::MembraneCenPairEnergy::residue_pair_energy(), core::scoring::MembranePotential::score_normal_center(), and core::scoring::MembranePotential::termini_penalty().

bool core::scoring::MembraneTopology::allow_tmh_scoring ( Size const  tmh ) const

inline

References allow_tmh_scoring_.

Referenced by core::scoring::MembranePotential::check_spanning(), core::scoring::MembranePotential::init_membrane_center_normal(), and core::scoring::MembranePotential::tm_projection_penalty().

basic::datacache::CacheableDataOP core::scoring::MembraneTopology::clone ( ) const

inlinevirtual

Implements basic::datacache::CacheableData.

References MembraneTopology().

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
	)

References full_span_, helix_id_, j, relative_tmh_ori_, span_, total_tmhelix_, and utility_exit_with_message.

Size core::scoring::MembraneTopology::helix_id ( Size  n ) const

inline

References helix_id_.

Referenced by core::scoring::methods::ProQ_Energy::calculateZ(), core::scoring::MembranePotential::check_spanning(), and core::scoring::MembranePotential::init_membrane_center_normal().

void core::scoring::MembraneTopology::initialize

(

std::string const &

spanfile

)

References allow_scoring_, allow_tmh_scoring_, utility::io::izstream::clear(), utility::io::izstream::close(), depth_, utility::io::izstream::eof(), full_span_, getline(), helix_id_, init_, initialized_, l, LipidBurial_, LipidExposure_, LipoDefined_, in::file::lipofile, lipofile, utility::io::izstream::open(), option, relative_tmh_ori_, span_, tmh_inserted_, tmregion_, total_tmhelix_, core::scoring::TR, user, and utility_exit_with_message.

Referenced by core::scoring::MembranePotential::compute_membrane_embedding(), and core::scoring::methods::ProQ_Energy::initialize().

bool core::scoring::MembraneTopology::initialized ( ) const

inline

References initialized_.

Referenced by core::scoring::MembranePotential::compute_membrane_embedding().

bool& core::scoring::MembraneTopology::initialized ( )

inline

References initialized_.

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

inline

References LipidBurial_.

Referenced by core::scoring::methods::MembraneLipo::finalize_total_energy().

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

inline

References LipidExposure_.

Referenced by core::scoring::methods::MembraneLipo::finalize_total_energy().

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

inline

References LipoDefined_.

Referenced by core::scoring::methods::MembraneLipo::finalize_total_energy().

void core::scoring::MembraneTopology::print

(

)

const

References span_, total_tmhelix_, and core::scoring::TR.

Size core::scoring::MembraneTopology::relative_tmh_ori ( Size const  n, Size const  m  ) const

inline

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

inline

References allow_scoring_, allow_tmh_scoring_, and tmh_inserted_.

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_, total_tmhelix_, and utility_exit_with_message.

Size core::scoring::MembraneTopology::span_begin ( Size  n ) const

inline

References span_.

Referenced by core::scoring::methods::ProQ_Energy::calculateZ(), core::scoring::MembranePotential::check_spanning(), core::scoring::MembranePotential::init_membrane_center_normal(), and core::scoring::MembranePotential::tm_projection_penalty().

Size core::scoring::MembraneTopology::span_end ( Size  n ) const

inline

References span_.

Referenced by core::scoring::methods::ProQ_Energy::calculateZ(), core::scoring::MembranePotential::init_membrane_center_normal(), and core::scoring::MembranePotential::tm_projection_penalty().

Size core::scoring::MembraneTopology::tmh_inserted ( ) const

inline

References tmh_inserted_.

Referenced by core::scoring::methods::MembraneLipo::finalize_total_energy(), core::scoring::MembranePotential::init_membrane_center_normal(), and set_tmh_inserted().

Size core::scoring::MembraneTopology::tmhelix ( ) const

inline

References total_tmhelix_.

Referenced by core::scoring::methods::ProQ_Energy::calculateZ(), core::scoring::MembranePotential::check_spanning(), core::scoring::MembranePotential::init_membrane_center_normal(), and core::scoring::MembranePotential::tm_projection_penalty().

bool core::scoring::MembraneTopology::tmregion ( Size const  pos ) const

inline

References tmregion_.

Referenced by core::scoring::MembranePotential::non_helix_in_membrane_penalty(), and core::scoring::methods::ProQ_Energy::topology_feature().

Member Data Documentation

utility::vector1< bool > core::scoring::MembraneTopology::allow_scoring_

private

Referenced by allow_scoring(), initialize(), MembraneTopology(), reset_allowed_scoring(), and set_allow_scoring().

utility::vector1< bool > core::scoring::MembraneTopology::allow_tmh_scoring_

private

Referenced by allow_tmh_scoring(), initialize(), MembraneTopology(), reset_allowed_scoring(), and set_allow_tmh_scoring().

bool core::scoring::MembraneTopology::beta_barrel_

private

Referenced by MembraneTopology().

utility::vector1< core::Real > core::scoring::MembraneTopology::depth_

private

Referenced by depth(), initialize(), and MembraneTopology().

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

private

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

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

private

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

bool core::scoring::MembraneTopology::init_

private

Referenced by initialize(), and MembraneTopology().

bool core::scoring::MembraneTopology::initialized_

private

Referenced by initialize(), initialized(), and MembraneTopology().

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

private

Referenced by initialize(), LipidBurial(), and MembraneTopology().

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

private

Referenced by initialize(), LipidExposure(), and MembraneTopology().

bool core::scoring::MembraneTopology::LipoDefined_

private

Referenced by initialize(), LipoDefined(), and MembraneTopology().

bool core::scoring::MembraneTopology::N_term_inside_

private

Referenced by MembraneTopology().

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

private

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

ObjexxFCL::FArray2D< Size > core::scoring::MembraneTopology::span_

private

Referenced by get_subset(), initialize(), MembraneTopology(), print(), shift_span(), span_begin(), and span_end().

Size core::scoring::MembraneTopology::tmh_inserted_

private

Referenced by initialize(), MembraneTopology(), reset_allowed_scoring(), reset_tmh_insert(), set_tmh_inserted(), and tmh_inserted().

utility::vector1< bool > core::scoring::MembraneTopology::tmregion_

private

Referenced by initialize(), MembraneTopology(), and tmregion().

Size core::scoring::MembraneTopology::total_tmhelix_

private

Referenced by get_subset(), initialize(), MembraneTopology(), print(), shift_span(), and tmhelix().

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

• symlinks/rosetta/src/core/scoring/MembraneTopology.hh
• symlinks/rosetta/src/core/scoring/MembraneTopology.cc