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

#include <SpanningTopology.hh>

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, 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
	Show the current spans stored in this SpanningTopology Object. More...
void	write_spanfile (std::string output_filename)
utility::vector1< SpanOP >	get_spans ()
	Return Spanning Topology. More...
SpanOP	span (Size span_number)
	Return Transmembrane Span. More...
void	add_span (SpanOP span)
void	reorder_spans ()
	Sort Spans. More...
Size	total_spans ()
	Get total number of spans. More...
bool	in_span (Size residue)
	Is the residue in the membrane region? More...
bool	spanning (utility::vector1< Real > res_z_coord, SpanOP span)
	Does the span cross the membrane. More...
bool	is_valid ()
	Determine if this Spanning Topology Object is Valid. More...
Size	nres_topo ()
	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, Real 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

Referenced by operator=().

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,
		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

(

SpanOP

span

)

References 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 utility::io::izstream::clear(), utility::io::izstream::close(), core::sequence::end, getline(), utility::io::izstream::good(), is_valid(), l, nres_topo_, span(), start, topology_, core::conformation::TR, and utility_exit_with_message.

Referenced by SpanningTopology().

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

private

Create Transmembrane SPan OBject from structure.

References core::sequence::end, is_valid(), nres_topo_, span(), spanning(), start, core::conformation::membrane::thickness, topology_, core::conformation::TR, and utility_exit_with_message.

Referenced by SpanningTopology().

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

(

)

Return Spanning Topology.

return spanning topology as a vector1 of transmembrane spans

References topology_.

bool core::conformation::membrane::SpanningTopology::in_span

(

Size

resnum

)

Is the residue in the membrane region?

Return true if this residue is in a transmembrane span

References span(), and total_spans().

bool core::conformation::membrane::SpanningTopology::is_valid

(

)

Determine if this Spanning Topology Object is Valid.

Check that spans still span the membrane

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

Referenced by create_from_spanfile(), and create_from_structure().

Size core::conformation::membrane::SpanningTopology::nres_topo

(

)

Return the number of residues represented by this topology object.

References nres_topo_.

SpanningTopology & core::conformation::membrane::SpanningTopology::operator=

(

SpanningTopology const &

src

)

Assignment Operator.

Overload assignemnt operator - required Rosetta method

References SpanningTopology().

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

Show the current spans stored in this SpanningTopology Object.

Methods ///.

Generating a String Representation of Spanning Topology Object for debugging purposes

Show the current spans stored in this SpanningTopology Object

Generating a String Representation of Spanning Topology Object for debugging purposes

References topology_, and core::conformation::TR.

Referenced by core::membrane::geometry::Embedding::from_spans(), is_valid(), and core::conformation::membrane::MembraneInfo::show().

SpanOP core::conformation::membrane::SpanningTopology::span

(

Size

span_number

)

Return Transmembrane Span.

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

References topology_.

Referenced by create_from_spanfile(), create_from_structure(), core::membrane::geometry::Embedding::from_spans(), and in_span().

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

Does the span cross the membrane.

Determine if the membrane spanning region crosses the whole membrane

Referenced by create_from_structure().

Size core::conformation::membrane::SpanningTopology::total_spans

(

)

Get total number of spans.

Return the number of transmembrane spanning regions in this object

References topology_.

Referenced by core::membrane::geometry::Embedding::Embedding(), core::scoring::membrane::MPLipoEnergy::finalize_total_energy(), core::membrane::geometry::Embedding::from_spans(), in_span(), and core::scoring::membrane::MPCbetaEnergy::residue_energy().

void core::conformation::membrane::SpanningTopology::write_spanfile

(

std::string

output_filename

)

References utility::io::ozstream::close(), nres_topo_, utility::io::ozstream::open(), topology_, and core::conformation::TR.

Member Data Documentation

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

private

Referenced by create_from_spanfile(), create_from_structure(), nres_topo(), and write_spanfile().

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

private

Referenced by add_span(), create_from_spanfile(), create_from_structure(), get_spans(), is_valid(), reorder_spans(), show(), span(), total_spans(), 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