A Membrane conformation: Additional data for maintaining a mebrane. More...

#include <MembraneInfo.hh>

Public Member Functions
	MembraneInfo (ConformationOP conf_in, utility::vector1< std::pair< int, int > > embres_map, int membrane)
	Standard Constructor. More...

	MembraneInfo (MembraneInfo const &src)
	Copy Constructor. More...

utility::vector1< std::pair < int, int > >	embres_map () const
	Return Membrane Embedding Map. More...

int	membrane () const
	Return Membrane root. More...

bool	is_membrane () const
	Assert Membrane Conformation Invariants. More...

core::Vector	membrane_center () const
	Membrane Postion Info ///////////. More...

core::Vector	membrane_normal () const
	Get Membrane Normal Coords. More...

core::Real	membrane_thickness () const
	Get Membrane Thickness Parameter. More...

core::Vector	embedding_center (core::Size chain) const
	Chain-Specific Kinematic Embedding Info ///////////. More...

core::Vector	embedding_normal (core::Size chain) const
	Get Chain Embedding Normal coords. More...

core::Real	embedding_depth (core::Size chain) const
	Get Chain Embedding Depth Parameter. More...

core::Vector	pose_embedding_center ()
	Whole-Chain Non-Kinematic Embedding Info ////////////////. More...

core::Vector	pose_embedding_normal ()
	WHole Pose Normal. More...

core::Real	residue_depth (core::Size seqpos)
	Depth. More...

core::Real	pose_embedding_steepness ()
	Fullatom Whole-Chain Non-Kinematic Membrane Info ///////////////. More...

core::Real	fa_proj (core::Size seqpos, core::Size atom)
	Get Fullatom TM Projection at Seqpos and Atom Pos. More...

core::Real	fa_depth (core::Size seqpos, core::Size atom)
	Get Depth of FA Coordinate. More...

core::Real	fa_proj_deriv (core::Size seqpos, core::Size atom)
	Get Fullatom Projection Derivative. More...

core::Vector	fa_proj_coord (core::Size seqpos, core::Size atom)
	Return Coordinate of the FA Proj. More...

void	update_fullatom_info ()
	Update Fullatom or Centroid Info Set ///////////////. More...

void	update_lowres_info ()
	Update HWole Pose Embedding Info for Low Resolution Typesets. More...

core::Size	total_polymer_residue () const
	Return the total number of polymer reisdues in the pose (no mp residues) More...

core::Size	num_polymer_chains () const
	Return the total number of polymer chains in the pose (no mp chain) More...

void	add_topology_by_chain (SpanningTopology sp, core::Size chain)
	Add Spanning Topology. More...

utility::vector1 < SpanningTopology >	spanning_topology () const

void	add_lips_by_chain (LipidAccInfo const &sp, core::Size chain)
	Add Lipid Accessibility Info. More...

utility::vector1< LipidAccInfo >	lipid_acc_data () const

Private Member Functions
void	init ()
	Initialize Membrane Info Class. More...

void	init_for_lowres ()
	Compute WHole Pose Centroid Embedding Parameters. More...

void	init_for_highres ()
	Compute Whole Pose Fullatom Embedding Parameters. More...

bool	conformation_changed ()
	Watch for Membrane Relevant changes in the conformation every time membrane info is updated. More...

	MembraneInfo ()
	Default Constructor. More...

void	build_membrane_foldtree ()
	Build Membrane FoldTree. More...

Private Attributes
ConformationOP	conf_

core::Vector	center_
	Non-Kinematic Embedding Parameters /////////////. More...

core::Vector	normal_

core::Real	steepness_

utility::vector1< core::Real >	depth_

utility::vector1 < utility::vector1< core::Real > >	fa_proj_

utility::vector1 < utility::vector1< core::Real > >	fa_depth_

utility::vector1 < utility::vector1 < core::Vector > >	fa_proj_coord_

utility::vector1 < utility::vector1< core::Real > >	fa_proj_deriv_

bool	fullatom_
	Data for Object Syncrhonization ////////////////. More...

core::Size	nres_

utility::vector1< std::pair < int, int > >	embres_map_
	Kinematic Embedding Info //////////////////. More...

int	membrane_

utility::vector1< LipidAccInfo >	lipid_acc_data_
	Membrane Conformation Info ///////////////. More...

utility::vector1 < SpanningTopology >	spanning_topology_

Detailed Description

A Membrane conformation: Additional data for maintaining a mebrane.

Handles membrane proteins

Constructor & Destructor Documentation

core::conformation::membrane::MembraneInfo::MembraneInfo	(	ConformationOP	conf_in,
		utility::vector1< std::pair< int, int > >	embres_map,
		int	membrane
	)

Standard Constructor.

References init().

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

Copy Constructor.

References init().

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

private

Default Constructor.

References init().

Member Function Documentation

void core::conformation::membrane::MembraneInfo::add_lips_by_chain	(	LipidAccInfo const &	sp,
		core::Size	chain
	)

Add Lipid Accessibility Info.

References lipid_acc_data_.

void core::conformation::membrane::MembraneInfo::add_topology_by_chain	(	SpanningTopology	sp,
		core::Size	chain
	)

Add Spanning Topology.

References spanning_topology_.

void core::conformation::membrane::MembraneInfo::build_membrane_foldtree ( )

private

Build Membrane FoldTree.

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), conf_, embres_map_, core::conformation::Conformation::fold_tree(), membrane_, and core::conformation::Conformation::num_chains().

Referenced by init().

bool core::conformation::membrane::MembraneInfo::conformation_changed ( )

private

Watch for Membrane Relevant changes in the conformation every time membrane info is updated.

References conf_, fullatom_, init_for_highres(), init_for_lowres(), core::conformation::Conformation::is_fullatom(), nres_, and core::conformation::Conformation::size().

Referenced by init().

core::Vector core::conformation::membrane::MembraneInfo::embedding_center ( core::Size chain ) const

Chain-Specific Kinematic Embedding Info ///////////.

Get Chain Embedding Center Coords.

Get Chain Embedding Center Coords

References core::conformation::Residue::atom(), conf_, embres_map_, core::conformation::Conformation::residue(), and core::conformation::Atom::xyz().

core::Real core::conformation::membrane::MembraneInfo::embedding_depth ( core::Size chain ) const

Get Chain Embedding Depth Parameter.

References core::conformation::Residue::atom(), conf_, embres_map_, core::conformation::Conformation::residue(), core::conformation::Atom::xyz(), and numeric::xyzVector< class >::y().

core::Vector core::conformation::membrane::MembraneInfo::embedding_normal ( core::Size chain ) const

Get Chain Embedding Normal coords.

References core::conformation::Residue::atom(), conf_, embres_map_, core::conformation::Conformation::residue(), and core::conformation::Atom::xyz().

utility::vector1< std::pair< int, int > > core::conformation::membrane::MembraneInfo::embres_map ( ) const

Return Membrane Embedding Map.

References embres_map_.

core::Real core::conformation::membrane::MembraneInfo::fa_depth	(	core::Size	seqpos,
		core::Size	atom
	)

Get Depth of FA Coordinate.

References fa_depth_, fullatom_, and core::conformation::TR.

core::Real core::conformation::membrane::MembraneInfo::fa_proj	(	core::Size	seqpos,
		core::Size	atom
	)

Get Fullatom TM Projection at Seqpos and Atom Pos.

References fa_proj_, fullatom_, and core::conformation::TR.

core::Vector core::conformation::membrane::MembraneInfo::fa_proj_coord	(	core::Size	seqpos,
		core::Size	atom
	)

Return Coordinate of the FA Proj.

References fa_proj_coord_, fullatom_, and core::conformation::TR.

core::Real core::conformation::membrane::MembraneInfo::fa_proj_deriv	(	core::Size	seqpos,
		core::Size	atom
	)

Get Fullatom Projection Derivative.

References fa_proj_deriv_, fullatom_, and core::conformation::TR.

void core::conformation::membrane::MembraneInfo::init ( )

private

Initialize Membrane Info Class.

References build_membrane_foldtree(), conf_, conformation_changed(), depth_, fa_depth_, fa_proj_, fa_proj_coord_, fa_proj_deriv_, fullatom_, core::conformation::Conformation::is_fullatom(), is_membrane(), nres_, and core::conformation::Conformation::size().

Referenced by MembraneInfo().

void core::conformation::membrane::MembraneInfo::init_for_highres ( )

private

Compute Whole Pose Fullatom Embedding Parameters.

Referenced by conformation_changed().

void core::conformation::membrane::MembraneInfo::init_for_lowres ( )

private

Compute WHole Pose Centroid Embedding Parameters.

Referenced by conformation_changed().

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

Assert Membrane Conformation Invariants.

References core::kinematics::FoldTree::check_fold_tree(), conf_, embres_map_, core::conformation::Conformation::fold_tree(), core::kinematics::FoldTree::is_root(), membrane_, core::conformation::Conformation::num_chains(), core::conformation::Conformation::size(), and core::conformation::TR.

Referenced by init().

utility::vector1< LipidAccInfo > core::conformation::membrane::MembraneInfo::lipid_acc_data ( ) const

References lipid_acc_data_.

int core::conformation::membrane::MembraneInfo::membrane ( ) const

Return Membrane root.

References membrane_.

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

Membrane Postion Info ///////////.

Get Membrane Center Coords

References core::conformation::Residue::atom(), conf_, membrane_, core::conformation::Conformation::residue(), and core::conformation::Atom::xyz().

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

Get Membrane Normal Coords.

References core::conformation::Residue::atom(), conf_, membrane_, core::conformation::Conformation::residue(), and core::conformation::Atom::xyz().

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

Get Membrane Thickness Parameter.

References core::conformation::Residue::atom(), conf_, membrane_, core::conformation::Conformation::residue(), core::conformation::Atom::xyz(), and numeric::xyzVector< class >::y().

core::Size core::conformation::membrane::MembraneInfo::num_polymer_chains ( ) const

Return the total number of polymer chains in the pose (no mp chain)

Return the total number of polymer chains in the pose (excluding mp residues)

References conf_, and core::conformation::Conformation::num_chains().

core::Vector core::conformation::membrane::MembraneInfo::pose_embedding_center ( )

Whole-Chain Non-Kinematic Embedding Info ////////////////.

WHole Pose Center

References center_.

core::Vector core::conformation::membrane::MembraneInfo::pose_embedding_normal ( )

WHole Pose Normal.

References normal_.

core::Real core::conformation::membrane::MembraneInfo::pose_embedding_steepness ( )

Fullatom Whole-Chain Non-Kinematic Membrane Info ///////////////.

WHole Pose Steepness

References fullatom_, steepness_, and core::conformation::TR.

core::Real core::conformation::membrane::MembraneInfo::residue_depth ( core::Size seqpos )

Depth.

References depth_.

utility::vector1< SpanningTopology > core::conformation::membrane::MembraneInfo::spanning_topology ( ) const

References spanning_topology_.

core::Size core::conformation::membrane::MembraneInfo::total_polymer_residue ( ) const

Return the total number of polymer reisdues in the pose (no mp residues)

Return the total number of polymer residues in the pose (excluding mp residues)

References conf_, nres, core::conformation::Conformation::num_chains(), and core::conformation::Conformation::size().

void core::conformation::membrane::MembraneInfo::update_fullatom_info ( )

Update Fullatom or Centroid Info Set ///////////////.

Update Whole Pose for High Resolution Typesets

void core::conformation::membrane::MembraneInfo::update_lowres_info ( )

Update HWole Pose Embedding Info for Low Resolution Typesets.

Member Data Documentation

core::Vector core::conformation::membrane::MembraneInfo::center_

private

Non-Kinematic Embedding Parameters /////////////.

Referenced by pose_embedding_center().

ConformationOP core::conformation::membrane::MembraneInfo::conf_

private

Referenced by build_membrane_foldtree(), conformation_changed(), embedding_center(), embedding_depth(), embedding_normal(), init(), is_membrane(), membrane_center(), membrane_normal(), membrane_thickness(), num_polymer_chains(), and total_polymer_residue().

utility::vector1< core::Real > core::conformation::membrane::MembraneInfo::depth_

private

Referenced by init(), and residue_depth().

utility::vector1< std::pair< int, int > > core::conformation::membrane::MembraneInfo::embres_map_

private

Kinematic Embedding Info //////////////////.

Referenced by build_membrane_foldtree(), embedding_center(), embedding_depth(), embedding_normal(), embres_map(), and is_membrane().

utility::vector1< utility::vector1 < core::Real > > core::conformation::membrane::MembraneInfo::fa_depth_

private

Referenced by fa_depth(), and init().

utility::vector1< utility::vector1 < core::Real > > core::conformation::membrane::MembraneInfo::fa_proj_

private

Referenced by fa_proj(), and init().

utility::vector1< utility::vector1 < core::Vector > > core::conformation::membrane::MembraneInfo::fa_proj_coord_

private

Referenced by fa_proj_coord(), and init().

utility::vector1< utility::vector1 < core::Real > > core::conformation::membrane::MembraneInfo::fa_proj_deriv_

private

Referenced by fa_proj_deriv(), and init().

bool core::conformation::membrane::MembraneInfo::fullatom_

private

Data for Object Syncrhonization ////////////////.

Referenced by conformation_changed(), fa_depth(), fa_proj(), fa_proj_coord(), fa_proj_deriv(), init(), and pose_embedding_steepness().

utility::vector1< LipidAccInfo > core::conformation::membrane::MembraneInfo::lipid_acc_data_

private

Membrane Conformation Info ///////////////.

Referenced by add_lips_by_chain(), and lipid_acc_data().

int core::conformation::membrane::MembraneInfo::membrane_

private

Referenced by build_membrane_foldtree(), is_membrane(), membrane(), membrane_center(), membrane_normal(), and membrane_thickness().

core::Vector core::conformation::membrane::MembraneInfo::normal_

private

Referenced by pose_embedding_normal().

core::Size core::conformation::membrane::MembraneInfo::nres_

private

Referenced by conformation_changed(), and init().

utility::vector1< SpanningTopology > core::conformation::membrane::MembraneInfo::spanning_topology_

private

Referenced by add_topology_by_chain(), and spanning_topology().

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

private

Referenced by pose_embedding_steepness().

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

symlinks/rosetta/src/core/conformation/membrane/MembraneInfo.hh
symlinks/rosetta/src/core/conformation/membrane/MembraneInfo.cc

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation