core::scoring::MembraneTopology Class Reference

#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

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

inline

Member Function Documentation

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

inline

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

Referenced by protocols::abinitio::MembraneAbinitio::move_all_inserted(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), protocols::abinitio::MembraneAbinitio::print_debug(), core::energy_methods::MembraneCbetaEnergy::residue_energy(), core::energy_methods::MembraneEnvEnergy::residue_energy(), core::energy_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(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::scoring::MembranePotential::init_membrane_center_normal(), and core::scoring::MembranePotential::tm_projection_penalty().

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
	)

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

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().

void core::scoring::MembraneTopology::initialize

(

std::string const &

spanfile

)

References allow_scoring_, allow_tmh_scoring_, depth_, full_span_, helix_id_, init_, initialized_, LipidBurial_, LipidExposure_, LipoDefined_, relative_tmh_ori_, span_, tmh_inserted_, tmregion_, total_tmhelix_, and core::scoring::TR().

Referenced by core::scoring::MembranePotential::compute_membrane_embedding(), core::energy_methods::ProQ_Energy::initialize(), protocols::topology_broker::MembraneTopologyClaimer::initialize_dofs(), protocols::topology_broker::MembraneTopologyClaimer::pre_process(), protocols::relax::setup_membrane_topology(), protocols::abinitio::AbrelaxApplication::setup_membrane_topology(), and protocols::jobdist::universal_main().

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_.

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

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

std::string core::scoring::MembraneTopology::read_in_spanfile

(

)

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

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

inline

References allow_scoring_, allow_tmh_scoring_, and tmh_inserted_.

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

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

References span_.

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

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

inline

References span_.

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

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

inline

References tmh_inserted_.

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

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

inline

References total_tmhelix_.

Referenced by 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(), 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::energy_methods::ProQ_Energy::topology_feature().

Member Data Documentation

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

private

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

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

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

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

private

Referenced by read_in_spanfile().

Size core::scoring::MembraneTopology::tmh_inserted_

private

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

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

private

Referenced by initialize(), and tmregion().

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