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.

compute_vr

Calculate volatility ratio for SAXS profiles.

rg

Compute radius of gyration from SAXS profiles.

validate_profile

Validate SAXS profiles.

weight_profiles

Weighting of the 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	FitParameters
	Parameters of a fit, from ProfileFitter. More...

class	FormFactorTable

class	Profile

class	ProfileClustering

class	ProfileFitter
	Fit two profiles with user-defined scoring function as a template parameter. More...

class	RadialDistributionFunction

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

class	RatioVolatilityScore

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	WeightedFitParameters
	Parameters of a weighted fit, from WeightedProfileFitter. More...

class	WeightedProfileFitter
	Fitting of multiple profiles to the experimental one. More...

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

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

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

Functions
double	compute_max_distance (const Particles &particles)
	compute max distance More...

double	compute_max_distance (const Particles &particles1, const Particles &particles2)

Profile *	compute_profile (Particles particles, double min_q=0.0, double max_q=0.5, double delta_q=0.001, FormFactorTable *ft=get_default_form_factor_table(), FormFactorType ff_type=HEAVY_ATOMS, bool hydration_layer=true, 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 Particles &particles, std::vector< algebra::Vector3D > &coordinates)

FormFactorTable *	get_default_form_factor_table ()

void	get_form_factors (const Particles &particles, FormFactorTable *ff_table, Vector< double > &form_factors, FormFactorType ff_type)

IMP_Eigen::VectorXf	NNLS (const IMP_Eigen::MatrixXf &A, const IMP_Eigen::VectorXf &b)
	non-negative least square fitting for profile weight solving problem More...

double	radius_of_gyration (const Particles &particles)
	compute radius_of_gyration More...

void	read_files (Model *m, const std::vector< std::string > &files, std::vector< std::string > &pdb_file_names, std::vector< std::string > &dat_files, std::vector< IMP::Particles > &particles_vec, Profiles &exp_profiles, bool residue_level=false, bool heavy_atoms_only=true, int multi_model_pdb=2, bool explicit_water=false, float max_q=0.0)
	Parse PDB and profile files. More...

void	read_files (const std::vector< std::string > &files, std::vector< std::string > &pdb_file_names, std::vector< std::string > &dat_files, std::vector< IMP::Particles > &particles_vec, Profiles &exp_profiles, bool residue_level=false, bool heavy_atoms_only=true, int multi_model_pdb=2, bool explicit_water=false, float max_q=0.0)

void	read_pdb (Model *m, const std::string file, std::vector< std::string > &pdb_file_names, std::vector< IMP::Particles > &particles_vec, bool residue_level=false, bool heavy_atoms_only=true, int multi_model_pdb=2, bool explicit_water=false)
	Read PDB files. More...

void	read_pdb (const std::string file, std::vector< std::string > &pdb_file_names, std::vector< IMP::Particles > &particles_vec, bool residue_level=false, bool heavy_atoms_only=true, int multi_model_pdb=2, bool explicit_water=false)

std::string	trim_extension (const std::string file_name)

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

typedef IMP::Vector<IMP::Pointer< Profile > > IMP::saxs::Profiles

A vector of reference-counting object pointers.

Definition at line 295 of file Profile.h.

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

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

See Also: Profile

Definition at line 295 of file Profile.h.

Enumeration Type Documentation

enum IMP::saxs::FormFactorType

type of the form factors for profile calculations

Definition at line 33 of file FormFactorTable.h.

Function Documentation

double IMP::saxs::compute_max_distance ( const Particles & particles )

compute max distance

Definition at line 40 of file saxs/utility.h.

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

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

Definition at line 56 of file saxs/utility.h.

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Profile* IMP::saxs::compute_profile	(	Particles	particles,
		double	min_q = `0.0`,
		double	max_q = `0.5`,
		double	delta_q = `0.001`,
		FormFactorTable *	ft = `get_default_form_factor_table()`,
		FormFactorType	ff_type = `HEAVY_ATOMS`,
		bool	hydration_layer = `true`,
		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 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::saxs::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.

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 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::saxs::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.

IMP_Eigen::VectorXf IMP::saxs::NNLS	(	const IMP_Eigen::MatrixXf &	A,
		const IMP_Eigen::VectorXf &	b
	)

non-negative least square fitting for profile weight solving problem

Definition at line 21 of file nnls.h.

double IMP::saxs::radius_of_gyration ( const Particles & particles )

compute radius_of_gyration

Definition at line 74 of file saxs/utility.h.

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void IMP::saxs::read_files	(	Model *	m,
		const std::vector< std::string > &	files,
		std::vector< std::string > &	pdb_file_names,
		std::vector< std::string > &	dat_files,
		std::vector< IMP::Particles > &	particles_vec,
		Profiles &	exp_profiles,
		bool	residue_level = `false`,
		bool	heavy_atoms_only = `true`,
		int	multi_model_pdb = `2`,
		bool	explicit_water = `false`,
		float	max_q = `0.0`
	)

Parse PDB and profile files.

void IMP::saxs::read_pdb	(	Model *	m,
		const std::string	file,
		std::vector< std::string > &	pdb_file_names,
		std::vector< IMP::Particles > &	particles_vec,
		bool	residue_level = `false`,
		bool	heavy_atoms_only = `true`,
		int	multi_model_pdb = `2`,
		bool	explicit_water = `false`
	)

Read PDB files.

Detailed Description

cluster_profiles

compute_chi

compute_vr

rg

validate_profile

weight_profiles

Info

Classes

Typedefs

Enumerations

Functions

Standard module functions

Typedef Documentation

Enumeration Type Documentation

Function Documentation