#include <MembraneTopology.hh>

Inheritance diagram for core::scoring::MembraneTopology:

Public Member Functions
	MembraneTopology ()

basic::datacache::CacheableDataOP	clone () const override

std::string	read_in_spanfile ()

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

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< 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	initialized_

utility::vector1< bool >	tmregion_

utility::vector1< bool >	allow_scoring_

utility::vector1< bool >	allow_tmh_scoring_

Size	tmh_inserted_

Constructor & Destructor Documentation

◆ MembraneTopology()

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

inline

Member Function Documentation

◆ allow_scoring()

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

inline

References allow_scoring_, and core::id::to_string().

Referenced by core::energy_methods::MembraneLipo::finalize_total_energy(), protocols::abinitio::MembraneAbinitio::move_all_inserted(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), protocols::abinitio::MembraneAbinitio::print_debug(), core::scoring::MembranePotential::score_normal_center(), and core::scoring::MembranePotential::termini_penalty().

◆ allow_tmh_scoring()

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

inline

References allow_tmh_scoring_.

Referenced by protocols::abinitio::MembraneAbinitio::add_spanning_region(), core::scoring::MembranePotential::check_spanning(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::scoring::MembranePotential::init_membrane_center_normal(), and core::scoring::MembranePotential::tm_projection_penalty().

◆ clone()

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

inlineoverride

◆ depth() [1/2]

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

inline

References depth_.

◆ depth() [2/2]

Real core::scoring::MembraneTopology::depth ( Size const seqpos )

inline

References depth_.

◆ get_subset()

void core::scoring::MembraneTopology::get_subset	(	utility::vector1< Size > &	TMH_list,
		MembraneTopology &	src
	)

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

◆ helix_id()

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

inline

References helix_id_.

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

◆ initialize()

void core::scoring::MembraneTopology::initialize ( std::string const & spanfile )

◆ initialized() [1/2]

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

inline

References initialized_.

◆ initialized() [2/2]

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

inline

References initialized_.

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

◆ LipidBurial()

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

inline

References LipidBurial_.

Referenced by core::energy_methods::MembraneLipo::finalize_total_energy().

◆ LipidExposure()

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

inline

References LipidExposure_.

Referenced by core::energy_methods::MembraneLipo::finalize_total_energy().

◆ LipoDefined()

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

inline

References LipoDefined_.

Referenced by core::energy_methods::MembraneLipo::finalize_total_energy().

◆ print()

void core::scoring::MembraneTopology::print ( ) const

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

◆ read_in_spanfile()

std::string core::scoring::MembraneTopology::read_in_spanfile ( )

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

◆ reset_allowed_scoring()

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

inline

References allow_scoring_, allow_tmh_scoring_, and tmh_inserted_.

Referenced by protocols::abinitio::MembraneAbinitio::apply().

◆ reset_tmh_insert()

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

inline

References tmh_inserted_.

◆ set_allow_scoring()

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

inline

References allow_scoring_.

Referenced by protocols::abinitio::MembraneAbinitio::add_spanning_region().

◆ set_allow_tmh_scoring()

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

inline

References allow_tmh_scoring_.

Referenced by protocols::abinitio::MembraneAbinitio::add_spanning_region().

◆ set_tmh_inserted()

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

inline

References tmh_inserted(), and tmh_inserted_.

Referenced by protocols::abinitio::MembraneAbinitio::add_spanning_region().

◆ shift_span()

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

References full_span_, span_, and total_tmhelix_.

◆ span_begin()

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

inline

References span_.

Referenced by protocols::abinitio::MembraneAbinitio::add_spanning_region(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), core::energy_methods::ProQ_Energy::calculateZ(), core::scoring::MembranePotential::check_spanning(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::scoring::MembranePotential::init_membrane_center_normal(), protocols::abinitio::MembraneAbinitio::print_debug(), protocols::jumping::MembraneJump::setup_fold_tree(), and core::scoring::MembranePotential::tm_projection_penalty().

◆ span_end()

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

inline

References span_.

Referenced by protocols::abinitio::MembraneAbinitio::add_spanning_region(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), core::energy_methods::ProQ_Energy::calculateZ(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::scoring::MembranePotential::init_membrane_center_normal(), protocols::abinitio::MembraneAbinitio::print_debug(), protocols::jumping::MembraneJump::setup_fold_tree(), and core::scoring::MembranePotential::tm_projection_penalty().

◆ tmh_inserted()

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

inline

References tmh_inserted_.

Referenced by protocols::abinitio::MembraneAbinitio::add_spanning_region(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::energy_methods::MembraneLipo::finalize_total_energy(), protocols::abinitio::MembraneAbinitio::get_tmh_inserted(), core::scoring::MembranePotential::init_membrane_center_normal(), and set_tmh_inserted().

◆ tmhelix()

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

inline

References total_tmhelix_.

Referenced by protocols::abinitio::MembraneAbinitio::add_spanning_region(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::abinitio::MembraneAbinitio::apply(), core::energy_methods::ProQ_Energy::calculateZ(), core::scoring::MembranePotential::check_spanning(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::scoring::MembranePotential::init_membrane_center_normal(), protocols::abinitio::MembraneAbinitio::print_debug(), protocols::jumping::MembraneJump::setup_fold_tree(), and core::scoring::MembranePotential::tm_projection_penalty().

◆ tmregion()

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

inline

References tmregion_.

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

Member Data Documentation

◆ allow_scoring_

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

private

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

◆ allow_tmh_scoring_

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

private

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

◆ depth_

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

private

Referenced by depth(), and initialize().

◆ full_span_

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

private

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

◆ helix_id_

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

private

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

◆ init_

bool core::scoring::MembraneTopology::init_

private

Referenced by initialize().

◆ initialized_

bool core::scoring::MembraneTopology::initialized_

private

Referenced by initialize(), and initialized().

◆ LipidBurial_

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

private

Referenced by initialize(), and LipidBurial().

◆ LipidExposure_

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

private

Referenced by initialize(), and LipidExposure().

◆ LipoDefined_

bool core::scoring::MembraneTopology::LipoDefined_

private

Referenced by initialize(), and LipoDefined().

◆ relative_tmh_ori_

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

private

Referenced by get_subset(), and initialize().

◆ span_

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

private

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

◆ spanfile_

std::string core::scoring::MembraneTopology::spanfile_

private

Referenced by read_in_spanfile().

◆ tmh_inserted_

Size core::scoring::MembraneTopology::tmh_inserted_

private

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

◆ tmregion_

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

private

Referenced by initialize(), and tmregion().

◆ total_tmhelix_

Size core::scoring::MembraneTopology::total_tmhelix_

private

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

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

src/core/scoring/MembraneTopology.hh
src/core/scoring/MembraneTopology.cc

Public Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ MembraneTopology()

Member Function Documentation

◆ allow_scoring()

◆ allow_tmh_scoring()

◆ clone()

◆ depth() [1/2]

◆ depth() [2/2]

◆ get_subset()

◆ helix_id()

◆ initialize()

◆ initialized() [1/2]

◆ initialized() [2/2]

◆ LipidBurial()

◆ LipidExposure()

◆ LipoDefined()

◆ print()

◆ read_in_spanfile()

◆ reset_allowed_scoring()

◆ reset_tmh_insert()

◆ set_allow_scoring()

◆ set_allow_tmh_scoring()

◆ set_tmh_inserted()

◆ shift_span()

◆ span_begin()

◆ span_end()

◆ tmh_inserted()

◆ tmhelix()

◆ tmregion()

Member Data Documentation

◆ allow_scoring_

◆ allow_tmh_scoring_

◆ depth_

◆ full_span_

◆ helix_id_

◆ init_

◆ initialized_

◆ LipidBurial_

◆ LipidExposure_

◆ LipoDefined_

◆ relative_tmh_ori_

◆ span_

◆ spanfile_

◆ tmh_inserted_

◆ tmregion_

◆ total_tmhelix_