IMP  2.3.0
The Integrative Modeling Platform
IMP::display Namespace Reference

Output IMP model data in various file formats. More...

Detailed Description

Output IMP model data in various file formats.

The IMP::display::Writer class provides the base class for objects which write to specific file formats and the IMP::display::Geometry class provides a means of describing geometry. Currently it supports output to

And display of boxes, points, spheres, segments, ellipsoids are supported.

You should probably check out IMP::rmf for a more general file format and one that is read natively by both IMP and Chimera.

Info

Author(s): Daniel Russel

Maintainer: benmwebb

License: LGPL This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Publications:

Classes

class  BoundingBoxGeometry
 Display a bounding box. More...
 
class  ChimeraWriter
 Write geometry to a Python file for Chimera to read. 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 triangle. More...
 
class  WriteOptimizerState
 
class  Writer
 Base class for writing geometry to a file. More...
 
class  WriterAdaptor
 

Typedefs

typedef IMP::base::Vector
< Colored
Coloreds
 
typedef IMP::base::Vector< ColorColors
 
typedef IMP::base::Vector
< IMP::base::Pointer< Geometry > > 
Geometries
 
typedef IMP::base::Vector
< IMP::base::WeakPointer
< Geometry > > 
GeometriesTemp
 
typedef IMP::base::Vector
< IMP::base::Pointer
< TextWriter > > 
TextWriters
 
typedef IMP::base::Vector
< IMP::base::WeakPointer
< TextWriter > > 
TextWritersTemp
 
typedef IMP::base::Vector
< WriterAdaptor
WriterAdaptors
 
typedef IMP::base::Vector
< IMP::base::Pointer< Writer > > 
Writers
 
typedef IMP::base::Vector
< IMP::base::WeakPointer
< Writer > > 
WritersTemp
 

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)
 
Color get_display_color (unsigned int i)
 
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. More...
 
Color get_hot_color (double f)
 Return the color for f from the hot color map. More...
 
Color get_rgb_color (double f)
 Return the color for f from the RGB color map. More...
 
Color get_gray_color (double f)
 Return the a grayscale value for f. More...
 
Color get_gnuplot_color (double f)
 Return colors using the gnuplot default color map. More...
 

Standard module functions

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

std::string get_module_version ()
 
std::string get_module_name ()
 
std::string get_data_path (std::string file_name)
 Return the full path to installed data. More...
 
std::string get_example_path (std::string file_name)
 Return the path to installed example data for this module. More...
 

Typedef Documentation

Pass or store a set of Color .

Definition at line 188 of file Color.h.

Store a set of objects.

Definition at line 18 of file declare_Geometry.h.

Pass a set of objects.

See Also
Geometry

Definition at line 19 of file declare_Geometry.h.

Store a set of objects.

Definition at line 136 of file Writer.h.

Pass a set of objects.

See Also
TextWriter

Definition at line 137 of file Writer.h.

Pass or store a set of WriterAdaptor .

Definition at line 158 of file Writer.h.

Store a set of objects.

Definition at line 136 of file Writer.h.

Pass a set of objects.

See Also
Writer

Definition at line 136 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)

Return the full path to installed data.

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 setup_environment.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)

Return the path to installed example data for this module.

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

model));

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

Color IMP::display::get_gnuplot_color ( double  f)

Return colors using the gnuplot default color map.

See Also
Color
Color IMP::display::get_gray_color ( double  f)

Return the a grayscale value for f.

See Also
Color
Color IMP::display::get_hot_color ( double  f)

Return the color for f from the hot color map.

See Also
Color
Color IMP::display::get_interpolated_rgb ( const Color &  a,
const Color &  b,
double  f 
)

Return a color interpolated between a and b in RGB space.

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

See Also
Color

Definition at line 143 of file Color.h.

Color IMP::display::get_jet_color ( double  f)

Return the color for f from the jet color map.

See Also
Color
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).

Color IMP::display::get_rgb_color ( double  f)

Return the color for f from the RGB color map.

See Also
Color