IMP::display Namespace Reference

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Detailed Description

This module provides support for displaying and exporting IMP data in various ways.

Author:

Daniel Russel

Version:

1.0

Overview:

This module provides code to write various file formats for displaying data from IMP optimizations. The display::Writer classes provides the base class for objects which write to specific file formats and the display::Geometry provide means of describing geometry. Currently it supports output to

• Chimera via the IMP::display::ChimeraWriter
• Pymol via the IMP::display::PymolWriter
• VRML via the IMP::display::VRMLWriter

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

Examples

Examples can be found on the IMP.display examples page.

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:

• Daniel Russel, Keren Lasker, Ben Webb, Dina Schneidman, Javier Velazquez-Muriel, Andrej Sali, “Integrative assembly modeling using IMP”, submitted, 2010. This paper provides an overview of the key concepts in IMP and how to apply them to biological problems.
• Frank Alber, Friedrich Foerster, Dmitry Korkin, Maya Topf, Andrej Sali, “Integrating diverse data for structure determination of macromolecular assemblies”, Annual Review of Biochemistry, 2008. This paper provides a review of the integrative structure determination methodology and various data sources that can be used.

Data Structures
class	BildWriter
	Write a Bild file with the geometry. 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	DisplayModelOnFailure
	Dump the state of the model to a file on an error and then go on the the other handlers. 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	LogOptimizerState
	Write geometry to a container periodically. 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	PDBOptimizerState
	Write molecules in pdb format periodically. More...
class	PymolWriter
	Write a CGO file with the geometry. 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	Writer
	Base class for writing geometry to a file. More...
Typedefs
typedef VectorOfRefCounted < Geometry * >	Geometries
typedef std::vector< Geometry * >	GeometriesTemp
Functions
Writer *	create_writer (std::string filename)
std::string	get_data_path (std::string file_name)
	Return the path to installed data for this module.
std::string	get_example_path (std::string file_name)
	Return the path to installed example data for this module.
std::string	get_module_name ()
const VersionInfo &	get_module_version_info ()

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Function Documentation

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 path to installed data for this module.

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.

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 tools/imppy.sh script.