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core::scoring::MembraneTopology Class Reference

#include <MembraneTopology.hh>

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Public Member Functions

 MembraneTopology ()
 default ctor More...
 
 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
 

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_
 

Detailed Description

Definition at line 51 of file MembraneTopology.hh.

Constructor & Destructor Documentation

protocols::simple_moves::MembraneTopology::MembraneTopology ( )
inline

default ctor

Definition at line 54 of file MembraneTopology.hh.

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

core::scoring::MembraneTopology::MembraneTopology ( MembraneTopology const &  src)

Definition at line 55 of file MembraneTopology.cc.

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

Definition at line 131 of file MembraneTopology.hh.

References allow_scoring_.

Referenced by core::scoring::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::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

Definition at line 181 of file MembraneTopology.hh.

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
inline

Definition at line 59 of file MembraneTopology.hh.

References MembraneTopology().

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

Definition at line 103 of file MembraneTopology.hh.

References depth_.

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

Definition at line 108 of file MembraneTopology.hh.

References depth_.

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

Definition at line 253 of file MembraneTopology.cc.

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

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

Definition at line 93 of file MembraneTopology.hh.

References helix_id_.

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

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

Definition at line 78 of file MembraneTopology.cc.

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(), protocols::topology_broker::MembraneTopologyClaimer::initialize_dofs(), protocols::relax::setup_membrane_topology(), protocols::abinitio::AbrelaxApplication::setup_membrane_topology(), and protocols::jobdist::universal_main().

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

Definition at line 66 of file MembraneTopology.hh.

References initialized_.

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

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

Definition at line 72 of file MembraneTopology.hh.

References initialized_.

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

Definition at line 202 of file MembraneTopology.hh.

References LipidBurial_.

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

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

Definition at line 198 of file MembraneTopology.hh.

References LipidExposure_.

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

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

Definition at line 207 of file MembraneTopology.hh.

References LipoDefined_.

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

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

Definition at line 242 of file MembraneTopology.cc.

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

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

Definition at line 98 of file MembraneTopology.hh.

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

Definition at line 155 of file MembraneTopology.hh.

References allow_scoring_, allow_tmh_scoring_, and tmh_inserted_.

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

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

Definition at line 150 of file MembraneTopology.hh.

References tmh_inserted_.

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

Definition at line 192 of file MembraneTopology.hh.

References allow_scoring_.

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

Definition at line 187 of file MembraneTopology.hh.

References allow_tmh_scoring_.

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

Definition at line 169 of file MembraneTopology.hh.

References tmh_inserted(), and tmh_inserted_.

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

Definition at line 211 of file MembraneTopology.cc.

References full_span_, span_, and total_tmhelix_.

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

Definition at line 83 of file MembraneTopology.hh.

References span_.

Referenced by protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), 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().

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

Definition at line 88 of file MembraneTopology.hh.

References span_.

Referenced by protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), 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().

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

Definition at line 144 of file MembraneTopology.hh.

References tmh_inserted_.

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

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

Definition at line 78 of file MembraneTopology.hh.

References total_tmhelix_.

Referenced by protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::abinitio::MembraneAbinitio::apply(), 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().

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

Definition at line 175 of file MembraneTopology.hh.

References tmregion_.

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

Member Data Documentation

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

Definition at line 251 of file MembraneTopology.hh.

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

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

Definition at line 252 of file MembraneTopology.hh.

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

bool core::scoring::MembraneTopology::beta_barrel_
private

Definition at line 247 of file MembraneTopology.hh.

Referenced by MembraneTopology().

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

Definition at line 242 of file MembraneTopology.hh.

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

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

Definition at line 239 of file MembraneTopology.hh.

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

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

Definition at line 237 of file MembraneTopology.hh.

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

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

Definition at line 246 of file MembraneTopology.hh.

Referenced by initialize(), and MembraneTopology().

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

Definition at line 249 of file MembraneTopology.hh.

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

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

Definition at line 244 of file MembraneTopology.hh.

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

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

Definition at line 243 of file MembraneTopology.hh.

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

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

Definition at line 245 of file MembraneTopology.hh.

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

bool core::scoring::MembraneTopology::N_term_inside_
private

Definition at line 248 of file MembraneTopology.hh.

Referenced by MembraneTopology().

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

Definition at line 240 of file MembraneTopology.hh.

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

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

Definition at line 238 of file MembraneTopology.hh.

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

Size core::scoring::MembraneTopology::tmh_inserted_
private

Definition at line 253 of file MembraneTopology.hh.

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

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

Definition at line 250 of file MembraneTopology.hh.

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

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

Definition at line 241 of file MembraneTopology.hh.

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

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