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	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< Colored >	Coloreds
typedef IMP::Vector< Color >	Colors
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
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 ()
	Return the version of this module, as a string. More...
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

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

Pass or store a set of Color .

Definition at line 188 of file Color.h.

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

A vector of reference-counting object pointers.

Definition at line 18 of file declare_Geometry.h.

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

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

See Also

Geometry

Definition at line 19 of file declare_Geometry.h.

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

A vector of reference-counting object pointers.

Definition at line 136 of file Writer.h.

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

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

See Also

TextWriter

Definition at line 137 of file Writer.h.

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

Pass or store a set of WriterAdaptor .

Definition at line 158 of file Writer.h.

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

A vector of reference-counting object pointers.

Definition at line 136 of file Writer.h.

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

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).

std::string IMP::display::get_module_version

(

)

Return the version of this module, as a string.

Note

This function is only available in Python.

Definition at line 4 of file EMageFit/__init__.py.

Color IMP::display::get_rgb_color

(

double

f

)

Return the color for f from the RGB color map.

See Also

Color