Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
VMD_viewer Class Reference

Viewer writing in VMD file format. More...

#include <VMD_viewer.hpp>

Public Types

typedef T_VMD_viewer Base
 
typedef T_VMD_viewer< Dummy > Self
 

Public Member Functions

 VMD_viewer (std::ostream &out=std::cout)
 

Parameters

unsigned get_color_id (const std::string &color) const
 Returns the index associated to a given color. More...
 
unsigned get_color_id (void) const
 Returns the current color index. More...
 
void set_color_id (unsigned color_id)
 Sets the current color index. More...
 
bool is_transparent (void) const
 Checks that the next object will be viewn using transparent material. More...
 
void set_transparent (bool is_transparent)
 Sets the transparent tag. More...
 
bool is_visible (void) const
 Checks that the next object will be visible. More...
 
void set_visible (bool is_visible)
 Sets the visible tag. More...
 
bool is_cloning (void) const
 Checks that the next object will copy the last molecule if any. More...
 
void set_cloning (bool is_cloning)
 Sets the cloning tag. More...
 
unsigned get_vertex_resolution (void) const
 Returns the number of facets around a sphere representing a vertex. More...
 
void set_vertex_resolution (unsigned resolution)
 Sets the number of facets around a sphere representing a vertex. More...
 
unsigned get_circle_resolution (void) const
 Returns the number of segments around a circular arc. More...
 
void set_circle_resolution (unsigned resolution)
 Sets the number of segments around a circular arc. More...
 
double get_vertex_radius (void) const
 Returns the radius of a sphere representing a vertex. More...
 
void set_vertex_radius (double radius)
 Sets the radius of a sphere representing a vertex. More...
 
double get_edge_radius (void) const
 Returns the radius of a cylinder representing an edge. More...
 
void set_edge_radius (double radius)
 Sets the radius of a cylinder representing an edge. More...
 
double get_infinite_factor (void) const
 Returns the multiplicative factor used for representing infinite objects (e.g a line). More...
 
void set_infinite_factor (double factor)
 Sets the multiplicative factor used for representing infinite objects (e.g a line). More...
 

Viewings

void add_new_representation (void)
 Creates a new representation of the current molecule in VMD. More...
 
void delete_first_representation (void)
 Deletes the first representation of the current molecule in VMD. More...
 
void set_representation (const std::string &rep)
 Sets the mode of the current representation of the current molecule in VMD. More...
 
void set_color (const std::string &color)
 Sets the color of the current representation of the current molecule in VMD. More...
 
void set_color (std::size_t color_id)
 Sets the current color index. More...
 
void set_graphics_color (const std::string &color)
 Sets the color of the current representation of the current molecule in VMD. More...
 
void set_graphics_transparent (bool is_transparent)
 Sets the type of material to use (opaque or transparent) for the current molecule in VMD. More...
 
void set_top_molecule (const std::string &mol_name)
 Sets the molecule with the input name as the current molecule in VMD. More...
 
void make_new_molecule (const std::string &mol_name)
 Creates a new molecule in VMD. More...
 
void make_add_molecule (const std::string &filename)
 Loads a molecule to the top molecule in VMD. More...
 
void make_add_molecules_with_index (const std::string &prefix, const std::string &extension, unsigned index)
 Loads a list of molecules to the top molecule in VMD, from the index represented by the number of loaded frames to the input index. The filename of molecules is built as : <prefix><index><extension> More...
 
void finalize_molecule (void)
 Finalizes the molecule: here it does nothing. More...
 

Detailed Description

Viewer writing in VMD file format.

Constructed with an output stream, it uses the output stream operator for writing in a file the corresponding objects in VMD format. For each object passed to the operator, the VMD_view method or struct should be defined.

Member Typedef Documentation

◆ Base

typedef T_VMD_viewer Base

◆ Self

typedef T_VMD_viewer<Dummy> Self
inherited

Constructor & Destructor Documentation

◆ VMD_viewer()

VMD_viewer ( std::ostream &  out = std::cout)
inline

Member Function Documentation

◆ add_new_representation()

void add_new_representation ( void  )
inlineinherited

Creates a new representation of the current molecule in VMD.

◆ delete_first_representation()

void delete_first_representation ( void  )
inlineinherited

Deletes the first representation of the current molecule in VMD.

◆ finalize_molecule()

void finalize_molecule ( void  )
inlineinherited

Finalizes the molecule: here it does nothing.

◆ get_circle_resolution()

unsigned get_circle_resolution ( void  ) const
inlineinherited

Returns the number of segments around a circular arc.

◆ get_color_id() [1/2]

unsigned get_color_id ( const std::string &  color) const
inlineinherited

Returns the index associated to a given color.

If the string does not represent a known color, it returns 0 (blue).

◆ get_color_id() [2/2]

unsigned get_color_id ( void  ) const
inlineinherited

Returns the current color index.

◆ get_edge_radius()

double get_edge_radius ( void  ) const
inlineinherited

Returns the radius of a cylinder representing an edge.

◆ get_infinite_factor()

double get_infinite_factor ( void  ) const
inlineinherited

Returns the multiplicative factor used for representing infinite objects (e.g a line).

◆ get_vertex_radius()

double get_vertex_radius ( void  ) const
inlineinherited

Returns the radius of a sphere representing a vertex.

◆ get_vertex_resolution()

unsigned get_vertex_resolution ( void  ) const
inlineinherited

Returns the number of facets around a sphere representing a vertex.

◆ is_cloning()

bool is_cloning ( void  ) const
inlineinherited

Checks that the next object will copy the last molecule if any.

◆ is_transparent()

bool is_transparent ( void  ) const
inlineinherited

Checks that the next object will be viewn using transparent material.

◆ is_visible()

bool is_visible ( void  ) const
inlineinherited

Checks that the next object will be visible.

◆ make_add_molecule()

void make_add_molecule ( const std::string &  filename)
inlineinherited

Loads a molecule to the top molecule in VMD.

◆ make_add_molecules_with_index()

void make_add_molecules_with_index ( const std::string &  prefix,
const std::string &  extension,
unsigned  index 
)
inlineinherited

Loads a list of molecules to the top molecule in VMD, from the index represented by the number of loaded frames to the input index. The filename of molecules is built as : <prefix><index><extension>

◆ make_new_molecule()

void make_new_molecule ( const std::string &  mol_name)
inlineinherited

Creates a new molecule in VMD.

◆ set_circle_resolution()

void set_circle_resolution ( unsigned  resolution)
inlineinherited

Sets the number of segments around a circular arc.

◆ set_cloning()

void set_cloning ( bool  is_cloning)
inlineinherited

Sets the cloning tag.

◆ set_color() [1/2]

void set_color ( const std::string &  color)
inlineinherited

Sets the color of the current representation of the current molecule in VMD.

◆ set_color() [2/2]

void set_color ( std::size_t  color_id)
inlineinherited

Sets the current color index.

◆ set_color_id()

void set_color_id ( unsigned  color_id)
inlineinherited

Sets the current color index.

◆ set_edge_radius()

void set_edge_radius ( double  radius)
inlineinherited

Sets the radius of a cylinder representing an edge.

◆ set_graphics_color()

void set_graphics_color ( const std::string &  color)
inlineinherited

Sets the color of the current representation of the current molecule in VMD.

◆ set_graphics_transparent()

void set_graphics_transparent ( bool  is_transparent)
inlineinherited

Sets the type of material to use (opaque or transparent) for the current molecule in VMD.

◆ set_infinite_factor()

void set_infinite_factor ( double  factor)
inlineinherited

Sets the multiplicative factor used for representing infinite objects (e.g a line).

◆ set_representation()

void set_representation ( const std::string &  rep)
inlineinherited

Sets the mode of the current representation of the current molecule in VMD.

◆ set_top_molecule()

void set_top_molecule ( const std::string &  mol_name)
inlineinherited

Sets the molecule with the input name as the current molecule in VMD.

◆ set_transparent()

void set_transparent ( bool  is_transparent)
inlineinherited

Sets the transparent tag.

◆ set_vertex_radius()

void set_vertex_radius ( double  radius)
inlineinherited

Sets the radius of a sphere representing a vertex.

◆ set_vertex_resolution()

void set_vertex_resolution ( unsigned  resolution)
inlineinherited

Sets the number of facets around a sphere representing a vertex.

◆ set_visible()

void set_visible ( bool  is_visible)
inlineinherited

Sets the visible tag.