#include <SpanningTopology.hh>

Inheritance diagram for core::conformation::membrane::SpanningTopology:

Public Member Functions
	SpanningTopology ()
	Default Constructor (Private) More...

	SpanningTopology (std::string spanfile, Size total_residues=0)
	Custom Constructor - Transmembrane Spans from Spanfile. More...

	SpanningTopology (utility::vector1< Real > res_z_coord, utility::vector1< Size > chainID, utility::vector1< char > secstruct, Real thickness)
	Custom Constructor - Transmembrane Spans from xyz coords. More...

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

SpanningTopology &	operator= (SpanningTopology const &src)
	Assignment Operator. More...

	~SpanningTopology ()
	Destructor. More...

virtual void	show (std::ostream &output=std::cout) const
	Generate string representation of Spanning Topology Object for debugging purposes. More...

void	write_spanfile (std::string output_filename) const

utility::vector1< SpanOP >	get_spans () const
	Return Spanning Topology. More...

Size	nspans () const
	Get total number of spans. More...

SpanOP	span (Size span_number) const
	Return Transmembrane Span. More...

void	fill_from_spanfile (std::string spanfile, Size total_residues=0)
	Methods ///. More...

void	fill_from_structure (utility::vector1< Real > res_z_coord, utility::vector1< Size > chainID, utility::vector1< char > secstruct, Real thickness)

SpanningTopology &	concatenate_topology (SpanningTopology const &topo)

void	add_span (Span const &span, Size offset=0)

void	add_span (Size start, Size end, Size offset=0)

void	reorder_spans ()
	Sort Spans. More...

bool	in_span (Size residue) const
	Is the residue in the membrane region? More...

bool	spanning (utility::vector1< Real > res_z_coord, Span const &span) const
	Does the span cross the membrane. More...

bool	is_valid () const
	Determine if this Spanning Topology Object is Valid. More...

Size	nres_topo () const
	Return the number of residues represented by this topology object. More...

Private Member Functions
SpanningTopology	create_from_spanfile (std::string spanfile, Size nres)
	Create spanning topology object from spanfile. More...

SpanningTopology	create_from_structure (utility::vector1< Real > res_z_coord, utility::vector1< Size > chainID, utility::vector1< char > secstruct, Real thickness=mem_thickness)
	Create Transmembrane SPan OBject from structure. More...

Private Attributes
utility::vector1< SpanOP >	topology_

Size	nres_topo_

Constructor & Destructor Documentation

core::conformation::membrane::SpanningTopology::SpanningTopology ( )

Default Constructor (Private)

Constructors ///.

Construct an Empty Spanning Topology Object

Default Constructor (Private)

Construct an Empty Spanning Topology Object

References nres_topo_.

core::conformation::membrane::SpanningTopology::SpanningTopology	(	std::string	spanfile,
		Size	total_residues = `0`
	)

Custom Constructor - Transmembrane Spans from Spanfile.

Use transmembrane spans provided to consturct a spanning topology object

References create_from_spanfile().

core::conformation::membrane::SpanningTopology::SpanningTopology	(	utility::vector1< Real >	res_z_coord,
		utility::vector1< Size >	chainID,
		utility::vector1< char >	secstruct,
		Real	thickness
	)

Custom Constructor - Transmembrane Spans from xyz coords.

Use coordinates of residue CA and thickness to determine the spanning regions in the pose

References create_from_structure().

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

Copy Constructor.

Create a deep copy of this object copying over all private fields

core::conformation::membrane::SpanningTopology::~SpanningTopology ( )

Destructor.

Member Function Documentation

void core::conformation::membrane::SpanningTopology::add_span	(	Span const &	span,
		Size	offset = `0`
	)

References core::conformation::membrane::Span::end(), nres_topo_, core::conformation::membrane::Span::start(), and topology_.

Referenced by create_from_structure(), and protocols::membrane::split_topology_by_jump().

void core::conformation::membrane::SpanningTopology::add_span	(	Size	start,
		Size	end,
		Size	offset = `0`
	)

References nres_topo_, span(), and topology_.

SpanningTopology & core::conformation::membrane::SpanningTopology::concatenate_topology ( SpanningTopology const & topo )

References nres_topo(), nres_topo_, nspans(), span(), and topology_.

SpanningTopology core::conformation::membrane::SpanningTopology::create_from_spanfile	(	std::string	spanfile,
		Size	nres
	)

private

Create spanning topology object from spanfile.

Helper Methods ///.

Create spanning topology object from spanfile

References core::sequence::end, is_valid(), nres_topo(), nres_topo_, show(), span(), protocols::loops::start, topology_, and core::conformation::TR().

Referenced by fill_from_spanfile(), and SpanningTopology().

SpanningTopology core::conformation::membrane::SpanningTopology::create_from_structure	(	utility::vector1< Real >	res_z_coord,
		utility::vector1< Size >	chainID,
		utility::vector1< char >	secstruct,
		Real	thickness = `mem_thickness`
	)

private

Create Transmembrane SPan OBject from structure.

Create span object from structure.

References add_span(), core::sequence::end, is_valid(), nres_topo_, nspans(), show(), protocols::loops::start, topology_, and core::conformation::TR().

Referenced by fill_from_structure(), and SpanningTopology().

void core::conformation::membrane::SpanningTopology::fill_from_spanfile	(	std::string	spanfile,
		Size	total_residues = `0`
	)

Methods ///.

fill from spanfile

fill object from spanfile, can be used after creating empty object

References create_from_spanfile(), and core::conformation::TR().

void core::conformation::membrane::SpanningTopology::fill_from_structure	(	utility::vector1< Real >	res_z_coord,
		utility::vector1< Size >	chainID,
		utility::vector1< char >	secstruct,
		Real	thickness
	)

References create_from_structure(), show(), core::conformation::TR(), and write_spanfile().

utility::vector1< SpanOP > core::conformation::membrane::SpanningTopology::get_spans ( ) const

Return Spanning Topology.

return spanning topology as a vector1 of transmembrane spans

References topology_.

Referenced by core::conformation::membrane::operator<<().

bool core::conformation::membrane::SpanningTopology::in_span ( Size resnum ) const

Is the residue in the membrane region?

Return true if this residue is in a transmembrane span

References nspans(), and span().

bool core::conformation::membrane::SpanningTopology::is_valid ( ) const

Determine if this Spanning Topology Object is Valid.

Check that spans still span the membrane

References core::sequence::end, show(), protocols::loops::start, topology_, and core::conformation::TR().

Referenced by create_from_spanfile(), and create_from_structure().

Size core::conformation::membrane::SpanningTopology::nres_topo ( ) const

Return the number of residues represented by this topology object.

References nres_topo_.

Referenced by concatenate_topology(), and create_from_spanfile().

Size core::conformation::membrane::SpanningTopology::nspans ( ) const

Get total number of spans.

Return the number of transmembrane spanning regions in this object

References topology_.

Referenced by protocols::membrane::compute_structure_based_embedding(), concatenate_topology(), create_from_structure(), protocols::membrane::geometry::Embedding::Embedding(), protocols::membrane::geometry::Embedding::from_spans(), in_span(), core::conformation::membrane::operator<<(), protocols::membrane::split_topology_by_jump(), and protocols::membrane::symmetry::symmetrize_spans().

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

Assignment Operator.

Overload assignemnt operator - required Rosetta method

References topology_.

void core::conformation::membrane::SpanningTopology::reorder_spans ( )

Sort Spans.

Sort spans in ascending order from begin to end anchor

References topology_.

void core::conformation::membrane::SpanningTopology::show ( std::ostream & output = std::cout ) const

virtual

Generate string representation of Spanning Topology Object for debugging purposes.

Generating a String Representation of Spanning Topology Object for debugging purposes.

References nres_topo_, topology_, and core::conformation::TR().

Referenced by create_from_spanfile(), create_from_structure(), fill_from_structure(), is_valid(), and protocols::membrane::split_topology_by_jump().

SpanOP core::conformation::membrane::SpanningTopology::span ( Size span_number ) const

Return Transmembrane Span.

Return transmembrane span by it's index in the spanning topology object

References topology_.

Referenced by add_span(), concatenate_topology(), create_from_spanfile(), protocols::membrane::geometry::Embedding::from_spans(), in_span(), protocols::membrane::split_topology_by_jump(), and protocols::membrane::symmetry::symmetrize_spans().

bool core::conformation::membrane::SpanningTopology::spanning	(	utility::vector1< Real >	res_z_coord,
		Span const &	span
	)		const

Does the span cross the membrane.

Determine if the membrane spanning region crosses the whole membrane

References core::conformation::membrane::Span::end(), and core::conformation::membrane::Span::start().

void core::conformation::membrane::SpanningTopology::write_spanfile ( std::string output_filename ) const

References nres_topo_, topology_, and core::conformation::TR().

Referenced by fill_from_structure().

Member Data Documentation

Size core::conformation::membrane::SpanningTopology::nres_topo_

private

Referenced by add_span(), concatenate_topology(), create_from_spanfile(), create_from_structure(), nres_topo(), show(), SpanningTopology(), and write_spanfile().

utility::vector1< SpanOP > core::conformation::membrane::SpanningTopology::topology_

private

Referenced by add_span(), concatenate_topology(), create_from_spanfile(), create_from_structure(), get_spans(), is_valid(), nspans(), operator=(), reorder_spans(), show(), span(), and write_spanfile().

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

src/core/conformation/membrane/SpanningTopology.hh
src/core/conformation/membrane/SpanningTopology.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation