Support for small angle X-ray scattering (SAXS) data. More...

Detailed Description

Support for small angle X-ray scattering (SAXS) data.

Small angle X-ray scattering (SAXS) is an experimental technique that uses scattering of X-rays at low angles to determine structural information about proteins in solution. This has the advantage that a crystal is not required; however, the information is rotationally averaged.

This module provides a number of classes to handle SAXS profiles. For example, Restraint includes the fit to a SAXS profile as an IMP restraint.

See also IMP::foxs for a command line tool to generate a SAXS profile for a protein and fit it against an experimental profile, or IMP::saxs_merge for a tool to combine multiple experimental profiles.

We provide a number of command line tools to handle SAXS profiles:

cluster_profiles

Cluster SAXS profiles.

compute_chi

Calculate chi value for SAXS profiles.

rg

Compute radius of gyration from SAXS profiles.

validate_profile

Validate SAXS profiles.

Info

Author(s): Dina Schneidman, Seung Joong Kim, Yannick Spill

Maintainer: duhovka

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.
D. Schneidman-Duhovny, M. Hammel, A. Sali, "FoXS: A Web server for Rapid Computation and Fitting of SAXS Profiles", Nucleic Acids Res 38, 2010.
D. Schneidman-Duhovny, M. Hammel, A. Sali, "Macromolecular docking restrained by a small angle X-ray scattering profile", J Struct Biol 173(3), 2011.
D. Schneidman-Duhovny, M. Hammel, J. A. Tainer, A. Sali, "Accurate SAXS profile computation and its assessment by contrast variation experiments", Biophys J 105(4), 2013.

Classes
class	ChiFreeScore

class	ChiScore

class	ChiScoreLog

class	DeltaDistributionFunction

class	DerivativeCalculator

class	Distribution

class	FormFactorTable

class	Profile

class	ProfileClustering

class	ProfileFitter

class	RadialDistributionFunction

class	RadiusOfGyrationRestraint
	Calculate score based on radius of gyration, taken from saxs profile. More...

class	Restraint
	Calculate score based on fit to SAXS profile. More...

class	RigidBodiesProfileHandler
	Handle the profile for a set of particles, which may include rigid bodies. More...

class	SolventAccessibleSurface

class	WeightedProfileFitter

Typedefs
typedef IMP::base::Vector < IMP::base::Pointer< Profile > >	Profiles

typedef IMP::base::Vector < IMP::base::WeakPointer < Profile > >	ProfilesTemp

Enumerations
enum	FormFactorType { ALL_ATOMS, HEAVY_ATOMS, CA_ATOMS }
	type of the form factors for profile calculations More...

Functions
Float	compute_max_distance (const kernel::Particles &particles)
	compute max distance More...

Float	compute_max_distance (const kernel::Particles &particles1, const kernel::Particles &particles2)

Profile *	compute_profile (IMP::kernel::Particles particles, float min_q=0.0, float max_q=0.5, float delta_q=0.001, FormFactorTable *ft=get_default_form_factor_table(), FormFactorType ff_type=HEAVY_ATOMS, float water_layer_c2=4.0, bool fit=true, bool reciprocal=false, bool ab_initio=false, bool vacuum=false, std::string beam_profile_file="")
	profile calculation for particles and a given set of options More...

void	get_coordinates (const kernel::Particles &particles, std::vector< algebra::Vector3D > &coordinates)

FormFactorTable *	get_default_form_factor_table ()

void	get_form_factors (const kernel::Particles &particles, FormFactorTable *ff_table, Floats &form_factors, FormFactorType ff_type)

Float	radius_of_gyration (const kernel::Particles &particles)
	compute radius_of_gyration 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<IMP::base::Pointer< Profile > > IMP::saxs::Profiles

Store a set of objects.

Definition at line 290 of file Profile.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< Profile > > IMP::saxs::ProfilesTemp

Pass a set of objects.

See Also: Profile

Definition at line 290 of file Profile.h.

Enumeration Type Documentation

enum IMP::saxs::FormFactorType

type of the form factors for profile calculations

Definition at line 32 of file FormFactorTable.h.

Function Documentation

Float IMP::saxs::compute_max_distance ( const kernel::Particles & particles )

compute max distance

Definition at line 39 of file saxs/utility.h.

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Float IMP::saxs::compute_max_distance	(	const kernel::Particles &	particles1,
		const kernel::Particles &	particles2
	)

compute max distance between pairs of particles one from particles1 and the other from particles2

Definition at line 55 of file saxs/utility.h.

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Profile* IMP::saxs::compute_profile	(	IMP::kernel::Particles	particles,
		float	min_q = `0.0`,
		float	max_q = `0.5`,
		float	delta_q = `0.001`,
		FormFactorTable *	ft = `get_default_form_factor_table()`,
		FormFactorType	ff_type = `HEAVY_ATOMS`,
		float	water_layer_c2 = `4.0`,
		bool	fit = `true`,
		bool	reciprocal = `false`,
		bool	ab_initio = `false`,
		bool	vacuum = `false`,
		std::string	beam_profile_file = `""`
	)

profile calculation for particles and a given set of options

std::string IMP::saxs::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.

FormFactorTable* IMP::saxs::get_default_form_factor_table ( )

Get the default table.

std::string IMP::saxs::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.

Float IMP::saxs::radius_of_gyration ( const kernel::Particles & particles )

compute radius_of_gyration

Definition at line 73 of file saxs/utility.h.

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Detailed Description

cluster_profiles

compute_chi

rg

validate_profile

Info

Classes

Typedefs

Enumerations

Functions

Standard module functions

Typedef Documentation

Enumeration Type Documentation

Function Documentation