IMP  2.0.1
The Integrative Modeling Platform
IMP::display Namespace Reference

See IMP.display Overview for more information.

Classes

class  BildWriter
 Write a Bild file with the geometry. More...
 
class  BoundingBoxGeometry
 Display a bounding box. More...
 
class  ChimeraWriter
 Write geometry to a python file for Chimera to read. More...
 
class  CMMWriter
 Write a CMM file with the geometry. More...
 
class  Color
 Represent an RGB color. More...
 
class  Colored
 A particle with a color. More...
 
class  CylinderGeometry
 Display a cylinder. More...
 
class  EllipsoidGeometry
 Display a ellipsoid. More...
 
class  FilterGeometry
 Remove geometry which is not above a plane. More...
 
class  Geometry
 The base class for geometry. More...
 
class  GeometryProcessor
 Provide a standard geometry processing framework. More...
 
class  GeometrySet
 Group of set of geometric elements. More...
 
class  IsosurfaceGeometry
 Display an isosurface of a density map. More...
 
class  LabelGeometry
 A text label for a ball in space. More...
 
class  PairGeometry
 A base class for geometry contained in particles. More...
 
class  PairsGeometry
 A base class for geometry from a set of particles. More...
 
class  PivyWriter
 
class  PlaneGeometry
 Display a plane as truncated to a bounding box. More...
 
class  PointGeometry
 Display a point. More...
 
class  PolygonGeometry
 
class  PymolWriter
 Write a CGO file with the geometry. More...
 
class  ReferenceFrameGeometry
 Display a reference frame. More...
 
class  RestraintGeometry
 Try to draw some stuff for a generic restraint. More...
 
class  RestraintSetGeometry
 Geometry for a whole set of restraints. More...
 
class  SegmentGeometry
 Display a segment. More...
 
class  SingletonGeometry
 A base class for geometry contained in particles. More...
 
class  SingletonsGeometry
 A base class for geometry from a set of particles. More...
 
class  SkinSurfaceGeometry
 Display an isosurface of a density map. More...
 
class  SphereGeometry
 Display a sphere. More...
 
class  SurfaceMeshGeometry
 Display a surface mesh. More...
 
class  TextWriter
 
class  TriangleGeometry
 Display a triangule. More...
 
class  WriteOptimizerState
 
class  Writer
 Base class for writing geometry to a file. More...
 
class  WriterAdaptor
 

Typedefs

typedef IMP::base::Vector< ColorColors
 
typedef IMP::base::Vector
< IMP::base::Pointer< Geometry > > 
Geometries
 
typedef IMP::base::Vector
< IMP::base::Pointer
< TextWriter > > 
TextWriters
 
typedef IMP::base::Vector
< IMP::base::Pointer
< WriteOptimizerState > > 
WriteOptimizerStates
 
typedef IMP::base::Vector
< WriterAdaptor
WriterAdaptors
 
typedef IMP::base::Vector
< IMP::base::Pointer< Writer > > 
Writers
 

Functions

SphereGeometrycreate_geometry (const algebra::Sphere3D &t, std::string name="algebra::Sphere3D"+"%1%")
 
CylinderGeometrycreate_geometry (const algebra::Cylinder3D &t, std::string name="algebra::Cylinder3D"+"%1%")
 
EllipsoidGeometrycreate_geometry (const algebra::Ellipsoid3D &t, std::string name="algebra::Ellipsoid3D"+"%1%")
 
PointGeometrycreate_geometry (const algebra::Vector3D &t, std::string name="algebra::Vector3D"+"%1%")
 
SegmentGeometrycreate_geometry (const algebra::Segment3D &t, std::string name="algebra::Segment3D"+"%1%")
 
PolygonGeometrycreate_geometry (const algebra::Vector3Ds &t, std::string name="algebra::Vector3Ds"+"%1%")
 
TriangleGeometrycreate_geometry (const algebra::Triangle3D &t, std::string name="algebra::Triangle3D"+"%1%")
 
BoundingBoxGeometrycreate_geometry (const algebra::BoundingBoxD< 3 > &t, std::string name="algebra::BoundingBoxD<3>"+"%1%")
 
ReferenceFrameGeometrycreate_geometry (const algebra::ReferenceFrame3D &t, std::string name="algebra::ReferenceFrame3D"+"%1%")
 
Writercreate_writer (std::string filename)
 
std::string get_data_path (std::string file_name)
 Return the full path to installed data. More...
 
Color get_display_color (unsigned int i)
 
std::string get_example_path (std::string file_name)
 Return the path to installed example data for this module. More...
 
Color get_interpolated_rgb (const Color &a, const Color &b, double f)
 Return a color interpolated between a and b in RGB space. More...
 
double get_linear_color_map_value (double min, double max, double value)
 

Colormaps

These functions map a number in the interval [0,1] to a color using some color map.

Color get_jet_color (double f)
 Return the color for f from the jet color map.
 
Color get_hot_color (double f)
 Return the color for f from the hot color map.
 
Color get_rgb_color (double f)
 Return the color for f from the rgb color map.
 
Color get_grey_color (double f)
 Return the a greyscale value for f.
 
Color get_gnuplot_color (double f)
 Return colors using the gnuplot default color map.
 

Standard module methods

All IMP modules have a set of standard methods to help get information about the module and about files associated with the module.

std::string get_module_version ()
 
std::string get_module_name ()
 

Typedef Documentation

Pass or store a set of Color .

Definition at line 211 of file Color.h.

Store a set of objects.

Definition at line 18 of file declare_Geometry.h.

Store a set of objects.

Definition at line 149 of file Writer.h.

Pass or store a set of WriterAdaptor .

Definition at line 177 of file Writer.h.

Store a set of objects.

Definition at line 149 of file Writer.h.

Function Documentation

SphereGeometry* IMP::display::create_geometry ( const algebra::Sphere3D &  t,
std::string  name = "algebra::Sphere3D"+"%1%" 
)

Create a Geometry with the passed primitive.

CylinderGeometry* IMP::display::create_geometry ( const algebra::Cylinder3D &  t,
std::string  name = "algebra::Cylinder3D"+"%1%" 
)

Create a Geometry with the passed primitive.

EllipsoidGeometry* IMP::display::create_geometry ( const algebra::Ellipsoid3D &  t,
std::string  name = "algebra::Ellipsoid3D"+"%1%" 
)

Create a Geometry with the passed primitive.

PointGeometry* IMP::display::create_geometry ( const algebra::Vector3D &  t,
std::string  name = "algebra::Vector3D"+"%1%" 
)

Create a Geometry with the passed primitive.

SegmentGeometry* IMP::display::create_geometry ( const algebra::Segment3D &  t,
std::string  name = "algebra::Segment3D"+"%1%" 
)

Create a Geometry with the passed primitive.

PolygonGeometry* IMP::display::create_geometry ( const algebra::Vector3Ds &  t,
std::string  name = "algebra::Vector3Ds"+"%1%" 
)

Create a Geometry with the passed primitive.

TriangleGeometry* IMP::display::create_geometry ( const algebra::Triangle3D &  t,
std::string  name = "algebra::Triangle3D"+"%1%" 
)

Create a Geometry with the passed primitive.

BoundingBoxGeometry* IMP::display::create_geometry ( const algebra::BoundingBoxD< 3 > &  t,
std::string  name = "algebra::BoundingBoxD<3>"+"%1%" 
)

Create a Geometry with the passed primitive.

ReferenceFrameGeometry* IMP::display::create_geometry ( const algebra::ReferenceFrame3D &  t,
std::string  name = "algebra::ReferenceFrame3D"+"%1%" 
)

Create a Geometry with the passed primitive.

Writer* IMP::display::create_writer ( std::string  filename)

Create an appropriate writer based on the file suffix.

std::string IMP::display::get_data_path ( std::string  file_name)

Each module has its own data directory, so be sure to use the version of this function in the correct module. To read the data file "data_library" that was placed in the data directory of module "mymodule", do something like

std::ifstream in(IMP::mymodule::get_data_path("data_library"));

This will ensure that the code works when IMP is installed or used via the tools/imppy.sh script.

Color IMP::display::get_display_color ( unsigned int  i)

Produce a color that is attempted to be contrasting with the i-1 previous colors. Currently, they recycle after 11, but they can be darkened instead. Just ask.

std::string IMP::display::get_example_path ( std::string  file_name)

Each module has its own example directory, so be sure to use the version of this function in the correct module. For example to read the file example_protein.pdb located in the examples directory of the IMP::atom module, do

IMP::atom::read_pdb(IMP::atom::get_example_path("example_protein.pdb", model));

This will ensure that the code works when IMP is installed or used via the tools/imppy.sh script.

Color get_interpolated_rgb ( const Color &  a,
const Color &  b,
double  f 
)

If f is 0, then a is returned, if f is 1, b is returned.

Definition at line 162 of file Color.h.

double IMP::display::get_linear_color_map_value ( double  min,
double  max,
double  value 
)

Return a number suitable for being passed to a color map that is gotten by linearly scaling between the passed min and max (and truncating values that are out of range).