Rosetta Core  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
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...
 
SpanningTopologyoperator= (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< SpanOPget_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< SpanOPtopology_
 
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
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 ( )
void core::conformation::membrane::SpanningTopology::write_spanfile ( std::string  output_filename)

Member Data Documentation

Size core::conformation::membrane::SpanningTopology::nres_topo_
private
utility::vector1< SpanOP > core::conformation::membrane::SpanningTopology::topology_
private

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