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Rosetta
2020.11
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Whole Pose Membrane Embedding. More...
#include <MembranePotential.hh>
Public Member Functions | |
MembraneEmbed () | |
Default Constructor. More... | |
basic::datacache::CacheableDataOP | clone () const override |
Clone Cacheable Data. More... | |
Size | size () const |
Compute Size of MP (??) More... | |
Real & | depth (Size const seqpos) |
Compute depth of residue in the membrane. More... | |
void | set_normal (Vector const &v) |
Set Pose Embedding Normal (should not use this method, deprecated 3/11/14) More... | |
void | set_center (Vector const &v) |
Set Pose Embedding Center (should not use this method, deprecated 3/11/14) More... | |
void | set_penalty (Real const &p) |
Set Penalty. More... | |
Real | depth (Size const seqpos) const |
Get NonConst Depth. More... | |
bool & | spanning () |
Return Ref Spanning Parameter. More... | |
bool | spanning () const |
Return Non_Ref Spanning Parameter. More... | |
bool | calculated () const |
Return Calculated (no idea what this does) More... | |
bool & | calculated () |
Return Non_Ref Calculated (no idea what this does - maybe observer) More... | |
Vector const & | normal () const |
Get Normal Parameter. More... | |
Vector const & | center () const |
Get Center Parameter. More... | |
Real const & | penalty () const |
Get MP Penalty. More... | |
void | initialize (pose::Pose const &pose) |
Initialize Membrane Embedding From Pose?? More... | |
Private Attributes | |
utility::vector1< Real > | depth_ |
Vector | normal_ |
Vector | center_ |
bool | calculated_ |
bool | spanning_ |
Real | penalty_ |
Whole Pose Membrane Embedding.
Define the embedding of the membrane pose based on computed normal and center parameters. These are initialzed in the membrane protein framework and then recomputed based upon the structured and stored in MP residues (see MP Framework code)
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Default Constructor.
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Return Calculated (no idea what this does)
References calculated_.
Referenced by core::scoring::Membrane_FAPotential::compute_fa_projection(), core::scoring::MembranePotential::compute_membrane_embedding(), core::scoring::Membrane_FAPotential::finalize(), and core::scoring::MembranePotential::finalize().
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Return Non_Ref Calculated (no idea what this does - maybe observer)
References calculated_.
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Get Center Parameter.
References center_.
Referenced by core::scoring::hbonds::get_membrane_depth_dependent_weight(), protocols::topology_broker::TMHTopologySamplerClaimer::output_membrane_vector(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), and core::scoring::hbonds::HBondEnergy::setup_for_scoring().
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Clone Cacheable Data.
Compute depth of residue in the membrane.
References depth_.
Referenced by core::scoring::MembranePotential::compute_membrane_embedding().
Get NonConst Depth.
References depth_.
void core::scoring::MembraneEmbed::initialize | ( | pose::Pose const & | pose | ) |
Initialize Membrane Embedding From Pose??
Initialize a Membrane Embedding Object.
References center_, depth_, normal_, and core::pose::Pose::size().
Referenced by core::scoring::MembranePotential::compute_membrane_embedding().
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Get Normal Parameter.
References normal_.
Referenced by core::scoring::ChemicalShiftAnisotropy::compute_csascore(), core::scoring::DipolarCoupling::compute_dcscore(), core::scoring::hbonds::get_membrane_depth_dependent_weight(), protocols::topology_broker::TMHTopologySamplerClaimer::output_membrane_vector(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), and core::scoring::hbonds::HBondEnergy::setup_for_scoring().
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Get MP Penalty.
References penalty_.
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Set Pose Embedding Center (should not use this method, deprecated 3/11/14)
References center_.
Referenced by core::scoring::MembranePotential::compute_membrane_embedding().
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Set Pose Embedding Normal (should not use this method, deprecated 3/11/14)
References normal_.
Referenced by core::scoring::MembranePotential::compute_membrane_embedding().
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Set Penalty.
References penalty_.
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Return Ref Spanning Parameter.
References spanning_.
Referenced by core::scoring::MembranePotential::compute_membrane_embedding().
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Return Non_Ref Spanning Parameter.
References spanning_.
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Referenced by calculated().
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Referenced by center(), initialize(), and set_center().
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Referenced by depth(), initialize(), and size().
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Referenced by initialize(), normal(), and set_normal().
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Referenced by penalty(), and set_penalty().
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Referenced by spanning().