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IMP Reference Guide  develop.cd20b1e321,2019/12/14
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  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::Vector< ColoredColoreds
 
typedef IMP::Vector< ColorColors
 
typedef IMP::Vector
< IMP::Pointer< Geometry > > 
Geometries
 
typedef IMP::Vector
< IMP::WeakPointer< Geometry > > 
GeometriesTemp
 
typedef IMP::Vector
< IMP::Pointer< TextWriter > > 
TextWriters
 
typedef IMP::Vector
< IMP::WeakPointer< TextWriter > > 
TextWritersTemp
 
typedef IMP::Vector
< WriterAdaptor
WriterAdaptors
 
typedef IMP::Vector
< IMP::Pointer< Writer > > 
Writers
 
typedef IMP::Vector
< IMP::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 one of this module's data files. More...
 
std::string get_example_path (std::string file_name)
 Return the full path to one of this module's example files. More...
 

Typedef Documentation

Pass or store a set of Color .

Definition at line 188 of file Color.h.

A vector of reference-counting object pointers.

Definition at line 18 of file declare_Geometry.h.

A vector of weak (non reference-counting) pointers to specified objects.

See Also
Geometry

Definition at line 19 of file declare_Geometry.h.

A vector of reference-counting object pointers.

Definition at line 136 of file Writer.h.

A vector of weak (non reference-counting) pointers to specified 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.

A vector of reference-counting object pointers.

Definition at line 136 of file Writer.h.

A vector of weak (non reference-counting) pointers to specified 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 one of this module's data files.

To read the data file "data_library" that was placed in the data directory of this module, do something like

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

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

Note
Each module has its own data directory, so be sure to use this function from the correct module.
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 full path to one of this module's example files.

To read the example file "example_protein.pdb" that was placed in the examples directory of this module, do something like

std::ifstream in(IMP::display::get_example_path("example_protein.pdb"));

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

Note
Each module has its own example directory, so be sure to use this function from the correct module.
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