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

• Pymol via the IMP::display::PymolWriter

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:

• See main IMP papers list.

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< Color >	Colors
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
SphereGeometry *	create_geometry (const algebra::Sphere3D &t, std::string name="algebra::Sphere3D"+"%1""%")
CylinderGeometry *	create_geometry (const algebra::Cylinder3D &t, std::string name="algebra::Cylinder3D"+"%1""%")
EllipsoidGeometry *	create_geometry (const algebra::Ellipsoid3D &t, std::string name="algebra::Ellipsoid3D"+"%1""%")
PointGeometry *	create_geometry (const algebra::Vector3D &t, std::string name="algebra::Vector3D"+"%1""%")
SegmentGeometry *	create_geometry (const algebra::Segment3D &t, std::string name="algebra::Segment3D"+"%1""%")
PolygonGeometry *	create_geometry (const algebra::Vector3Ds &t, std::string name="algebra::Vector3Ds"+"%1""%")
TriangleGeometry *	create_geometry (const algebra::Triangle3D &t, std::string name="algebra::Triangle3D"+"%1""%")
BoundingBoxGeometry *	create_geometry (const algebra::BoundingBoxD< 3 > &t, std::string name="algebra::BoundingBoxD<3>"+"%1""%")
ReferenceFrameGeometry *	create_geometry (const algebra::ReferenceFrame3D &t, std::string name="algebra::ReferenceFrame3D"+"%1""%")
Writer *	create_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

typedef IMP::base::Vector< Color > IMP::display::Colors

Pass or store a set of Color .

Definition at line 188 of file Color.h.

typedef IMP::base::Vector<IMP::base::Pointer< Geometry > > IMP::display::Geometries

Store a set of objects.

Definition at line 18 of file declare_Geometry.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< Geometry > > IMP::display::GeometriesTemp

Pass a set of objects.

See Also

Geometry

Definition at line 19 of file declare_Geometry.h.

typedef IMP::base::Vector<IMP::base::Pointer< TextWriter > > IMP::display::TextWriters

Store a set of objects.

Definition at line 136 of file Writer.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< TextWriter > > IMP::display::TextWritersTemp

Pass a set of objects.

See Also

TextWriter

Definition at line 137 of file Writer.h.

typedef IMP::base::Vector< WriterAdaptor > IMP::display::WriterAdaptors

Pass or store a set of WriterAdaptor .

Definition at line 158 of file Writer.h.

typedef IMP::base::Vector<IMP::base::Pointer< Writer > > IMP::display::Writers

Store a set of objects.

Definition at line 136 of file Writer.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< Writer > > IMP::display::WritersTemp

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

 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 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