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

#include <SpanningTopology.hh>

Inheritance diagram for core::conformation::membrane::SpanningTopology:
Inheritance graph
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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...
 
SpanningTopologyoperator= (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< SpanOPget_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)
 
SpanningTopologyconcatenate_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< SpanOPtopology_
 
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 
)
void core::conformation::membrane::SpanningTopology::add_span ( core::Size  start,
core::Size  end,
core::Size  offset = 0 
)
SpanningTopology & core::conformation::membrane::SpanningTopology::concatenate_topology ( SpanningTopology const &  topo)
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 
)
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
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
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

Member Data Documentation

core::Size core::conformation::membrane::SpanningTopology::nres_topo_
private
bool core::conformation::membrane::SpanningTopology::structure_based_
private

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

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

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