core::conformation::membrane::SpanningTopology Class Reference

#include <SpanningTopology.hh>

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

Public Member Functions
	SpanningTopology ()
	Default Constructor (Private) More...
	SpanningTopology (std::string spanfile, std::map< std::string, core::Size > pdb2pose_map, core::Size total_residues=0)
	Custom Constructor - Transmembrane Spans from Spanfile. More...
	SpanningTopology (utility::vector1< core::Real > res_z_coord, utility::vector1< core::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 () override
	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...
core::Size	nspans () const
	Get total number of spans. More...
SpanOP	span (core::Size span_number) const
	Return Transmembrane Span. More...
void	fill_from_spanfile (std::string spanfile, std::map< std::string, core::Size > pdb2pose_map, core::Size total_residues=0)
	Methods ///. More...
void	fill_from_structure (utility::vector1< core::Real > res_z_coord, utility::vector1< core::Size > chainID, utility::vector1< char > secstruct, Real thickness)
SpanningTopology &	concatenate_topology (SpanningTopology const &topo)
void	add_span (Span const &span, core::Size offset=0)
void	add_span (core::Size start, core::Size end, core::Size offset=0)
void	reorder_spans ()
	Sort Spans. More...
bool	in_span (core::Size residue) const
	Is the residue in the membrane region? More...
bool	spanning (utility::vector1< core::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...
core::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, std::map< std::string, core::Size > pdb2pose_map, core::Size nres)
	Create spanning topology object from spanfile. More...
SpanningTopology	create_from_structure (utility::vector1< core::Real > res_z_coord, utility::vector1< core::Size > chainID, utility::vector1< char > secstruct, core::Real thickness=15)
	Create Transmembrane SPan OBject from structure. More...

Private Attributes
utility::vector1< SpanOP >	topology_
core::Size	nres_topo_
bool	structure_based_

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

core::conformation::membrane::SpanningTopology::SpanningTopology	(	std::string	spanfile,
		std::map< std::string, core::Size >	pdb2pose_map,
		core::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< core::Real >	res_z_coord,
		utility::vector1< core::Size >	chainID,
		utility::vector1< char >	secstruct,
		core::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 )

default

Copy Constructor.

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

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

overridedefault

Destructor.

Member Function Documentation

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

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

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

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

References nres_topo_, span(), structure_based_, 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, std::map< std::string, core::Size >  pdb2pose_map, core::Size  nres  )

private

Create spanning topology object from spanfile.

Helper Methods ///.

Create spanning topology object from spanfile

References core::sequence::end, is_valid(), protocols::antibody::l2, 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< core::Real >  res_z_coord, utility::vector1< core::Size >  chainID, utility::vector1< char >  secstruct, core::Real  thickness = 15  )

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,
		std::map< std::string, core::Size >	pdb2pose_map,
		core::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< core::Real >	res_z_coord,
		utility::vector1< core::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

(

core::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 nres_topo_, structure_based_, and 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

(

core::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< core::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

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

private

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

bool core::conformation::membrane::SpanningTopology::structure_based_

private

Referenced by add_span(), and operator=().

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().

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

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