Rosetta Core  2014.35
Public Member Functions | Private Attributes | List of all members
core::conformation::membrane::MembraneInfo Class Reference

Membrane Info Object - Contains information for describing a membrane protein in Rosetta, including the position of the membrane virtual residue, spanning topology, and lips acc data. More...

#include <MembraneInfo.hh>

Public Member Functions

 MembraneInfo ()
 Constructors ///. More...
 
 MembraneInfo (Conformation &conformation, core::Size membrane_pos, SpanningTopologyOP topology, core::SSize membrane_jump=2, bool view_in_pymol=false)
 Custom Constructor - Membrane pos & topology. More...
 
 MembraneInfo (Conformation &conformation, core::Size membrane_pos, SpanningTopologyOP topology, LipidAccInfoOP lips, core::SSize membrane_jump=2, bool view_in_pymol=false)
 Custom Constructor - Membrane pos, topology & lips. More...
 
 MembraneInfo (MembraneInfo const &src)
 Copy Constructor. More...
 
MembraneInfooperator= (MembraneInfo const &src)
 Assignment Operator. More...
 
 ~MembraneInfo ()
 Destructor. More...
 
virtual void show (std::ostream &output=std::cout) const
 Generate string representation of MembraneInfo for debugging purposes. More...
 
Vector membrane_center () const
 Coordinate Derived Membrane Info ///. More...
 
Vector membrane_normal () const
 Returns the normal of the membrane. More...
 
Real residue_z_position (core::Size resnum) const
 Compute Residue Z Position relative to mem. More...
 
Real atom_z_position (core::Size resnum, core::Size atomnum) const
 Compute atom Z Position relative to mem. More...
 
core::Size membrane_rsd_num () const
 Non-Coordinate Derived Membrane Data ///. More...
 
core::Real membrane_thickness () const
 Return membrane thickness. More...
 
core::Real membrane_steepness () const
 Return the membrane transition steepness. More...
 
SpanningTopologyOP spanning_topology ()
 Return a list of membrane spanning topology objects. More...
 
LipidAccInfoOP lipid_acc_data () const
 Return a list of lipid accessibility objects. More...
 
core::SSize membrane_jump () const
 Membrane Base Fold Tree Info ///. More...
 
bool check_membrane_fold_tree (FoldTree const &ft_in) const
 Check membrane fold tree. More...
 
bool view_in_pymol () const
 Visualizaiton ///. More...
 
void setup_plane_visualization (utility::vector1< Size > top_points, utility::vector1< Size > bottom_points)
 Setup Planes Info Object. More...
 
MembranePlanesOP plane_info ()
 Membrane Planes Points. More...
 

Private Attributes

Conformationconformation_
 
core::Real thickness_
 
core::Real steepness_
 
core::Size membrane_rsd_num_
 
core::Size anchoring_rsd_num_
 
core::SSize membrane_jump_
 
LipidAccInfoOP lipid_acc_data_
 
SpanningTopologyOP spanning_topology_
 
bool view_in_pymol_
 
MembranePlanesOP plane_info_
 

Detailed Description

Membrane Info Object - Contains information for describing a membrane protein in Rosetta, including the position of the membrane virtual residue, spanning topology, and lips acc data.

Constructor & Destructor Documentation

core::conformation::membrane::MembraneInfo::MembraneInfo ( )

Constructors ///.

Default Constructor

Creates a default copy of the membrane info object with the membrane virtual at nres = 1, thicnkess = 15A, steepenss of fullatom membrane transition = 10A and no spanning topology or lips info defined

Referenced by operator=().

core::conformation::membrane::MembraneInfo::MembraneInfo ( Conformation conformation,
core::Size  membrane_pos,
SpanningTopologyOP  topology,
core::SSize  membrane_jump = 2,
bool  view_in_pymol = false 
)

Custom Constructor - Membrane pos & topology.

Creates a default copy of the membrane info object with the membrane virtual at nres = membrane_pos, thicnkess = 15A, steepenss of fullatom membrane transition = 10A and spanning topology defined by API provided vector1 of spanning topology obejcts (by chain)

core::conformation::membrane::MembraneInfo::MembraneInfo ( Conformation conformation,
core::Size  membrane_pos,
SpanningTopologyOP  topology,
LipidAccInfoOP  lips,
core::SSize  membrane_jump = 2,
bool  view_in_pymol = false 
)

Custom Constructor - Membrane pos, topology & lips.

Creates a default copy of the membrane info object with the membrane virtual at nres = membrane_pos, thicnkess = 15A, steepenss of fullatom membrane transition = 10A, spanning topology defined by API provided vector1 of spanning topology obejcts (by chain), and lipid accessibility defined by a vector1 of lipid acc objects.

core::conformation::membrane::MembraneInfo::MembraneInfo ( MembraneInfo const &  src)

Copy Constructor.

Create a deep copy of this object

core::conformation::membrane::MembraneInfo::~MembraneInfo ( )

Destructor.

Member Function Documentation

Real core::conformation::membrane::MembraneInfo::atom_z_position ( core::Size  resnum,
core::Size  atomnum 
) const

Compute atom Z Position relative to mem.

Compute the z position of an atom relative to the pre-defined layers in the membrane. Maintians the relative coordinate frame

References core::conformation::Residue::atom(), conformation_, dot(), membrane_center(), membrane_normal(), core::conformation::Conformation::residue(), xyz, and core::conformation::Atom::xyz().

Referenced by core::scoring::membrane::FaMPEnvEnergy::init(), and core::scoring::membrane::FaMPSolvEnergy::init().

bool core::conformation::membrane::MembraneInfo::check_membrane_fold_tree ( FoldTree const &  ft_in) const

Check membrane fold tree.

Check that the membrane jump num is a jump point and located at the root of the fold tree in addition to maintaining a reasonable fold tree

References core::kinematics::FoldTree::check_fold_tree(), core::kinematics::FoldTree::is_jump_point(), and membrane_rsd_num_.

LipidAccInfoOP core::conformation::membrane::MembraneInfo::lipid_acc_data ( ) const

Return a list of lipid accessibility objects.

Return a vector1 of lipid accessibility info objects describing lipid exposre of individual residues in the pose

References lipid_acc_data_.

Referenced by core::scoring::membrane::MPLipoEnergy::finalize_total_energy().

Vector core::conformation::membrane::MembraneInfo::membrane_center ( ) const
core::SSize core::conformation::membrane::MembraneInfo::membrane_jump ( ) const

Membrane Base Fold Tree Info ///.

Get the number of the membrane jump

Get a core::SSize (int) denoting the number of the fold tree jump relating the membrane residue to the rest of the pose

References membrane_jump_.

Referenced by core::conformation::Conformation::check_valid_membrane().

Vector core::conformation::membrane::MembraneInfo::membrane_normal ( ) const
core::Size core::conformation::membrane::MembraneInfo::membrane_rsd_num ( ) const

Non-Coordinate Derived Membrane Data ///.

Membrane Data Access ///.

Return position of membrane residue

Return the residue number of the membrane virtual residue in the pose

References membrane_rsd_num_.

Referenced by membrane_center(), membrane_normal(), and core::conformation::Conformation::update_membrane_position().

core::Real core::conformation::membrane::MembraneInfo::membrane_steepness ( ) const

Return the membrane transition steepness.

Return the steepness betwen isotropic and ansitropic layers of the membrane used by the fullatom energy methods

References steepness_.

Referenced by core::scoring::membrane::FaMPEnvEnergy::init(), core::scoring::membrane::FaMPSolvEnergy::init(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), and core::scoring::hbonds::HBondEnergy::setup_for_scoring().

core::Real core::conformation::membrane::MembraneInfo::membrane_thickness ( ) const

Return membrane thickness.

Return the membrane thicnkess used by the fullatom energy method (centroid is hard coded for now)

Return the membrane thicnkess used by the fullatom energy method (centroid is hard coded for now

References thickness_.

Referenced by core::scoring::membrane::FaMPEnvEnergy::init(), core::scoring::membrane::FaMPSolvEnergy::init(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), and core::scoring::hbonds::HBondEnergy::setup_for_scoring().

MembraneInfo & core::conformation::membrane::MembraneInfo::operator= ( MembraneInfo const &  src)

Assignment Operator.

Create a deep copy of this object while overloading the assignemnt operator "="

References MembraneInfo().

MembranePlanesOP core::conformation::membrane::MembraneInfo::plane_info ( )

Membrane Planes Points.

Return object containing membrane planes info. Initialized at setup

References plane_info_.

Real core::conformation::membrane::MembraneInfo::residue_z_position ( core::Size  resnum) const
void core::conformation::membrane::MembraneInfo::setup_plane_visualization ( utility::vector1< Size top_points,
utility::vector1< Size bottom_points 
)

Setup Planes Info Object.

References plane_info_.

void core::conformation::membrane::MembraneInfo::show ( std::ostream &  output = std::cout) const
virtual
SpanningTopologyOP core::conformation::membrane::MembraneInfo::spanning_topology ( )

Return a list of membrane spanning topology objects.

Return a vector1 of spanning topology objects defining the starting and ending position of membrane spans per chain.

References spanning_topology_.

Referenced by core::scoring::membrane::MPLipoEnergy::finalize_total_energy(), core::scoring::membrane::MPTMProjPenalty::finalize_total_energy(), core::scoring::membrane::MPCbetaEnergy::residue_energy(), and core::scoring::membrane::MPNonHelixPenalty::residue_energy().

bool core::conformation::membrane::MembraneInfo::view_in_pymol ( ) const

Visualizaiton ///.

Check Membrane Planes initialized for visualization

Check membrane planes are initialized for visualization

References plane_info_.

Member Data Documentation

core::Size core::conformation::membrane::MembraneInfo::anchoring_rsd_num_
private
Conformation& core::conformation::membrane::MembraneInfo::conformation_
private
LipidAccInfoOP core::conformation::membrane::MembraneInfo::lipid_acc_data_
private

Referenced by lipid_acc_data().

core::SSize core::conformation::membrane::MembraneInfo::membrane_jump_
private

Referenced by membrane_jump(), and show().

core::Size core::conformation::membrane::MembraneInfo::membrane_rsd_num_
private
MembranePlanesOP core::conformation::membrane::MembraneInfo::plane_info_
private
SpanningTopologyOP core::conformation::membrane::MembraneInfo::spanning_topology_
private

Referenced by show(), and spanning_topology().

core::Real core::conformation::membrane::MembraneInfo::steepness_
private

Referenced by membrane_steepness(), and show().

core::Real core::conformation::membrane::MembraneInfo::thickness_
private

Referenced by membrane_thickness(), and show().

bool core::conformation::membrane::MembraneInfo::view_in_pymol_
private

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