IMP::saxs Namespace Reference

See IMP.saxs for more information.

Classes
class	ChiFreeScore
class	ChiScore
class	ChiScoreLog
class	DeltaDistributionFunction
class	DerivativeCalculator
class	Distribution
class	FormFactorTable
class	Profile
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

Functions
Float	compute_max_distance (const kernel::Particles &particles)
	compute max distance
Float	compute_max_distance (const kernel::Particles &particles1, const kernel::Particles &particles2)
FormFactorTable *	default_form_factor_table ()
void	get_coordinates (const kernel::Particles &particles, std::vector< algebra::Vector3D > &coordinates)
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...
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

Standard module methods
All IMP modules have a set of standard methods to help get information about the module and about files associated with the module.
std::string	get_module_version ()
std::string	get_module_name ()

Typedef Documentation

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

Store a set of objects.

Definition at line 283 of file Profile.h.

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

Pass a set of objects. See Profile

Definition at line 283 of file Profile.h.

Function Documentation

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 53 of file saxs/utility.h.

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FormFactorTable* IMP::saxs::default_form_factor_table

(

)

Get the default table.

std::string IMP::saxs::get_data_path

(

std::string

file_name

)

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.

std::string IMP::saxs::get_example_path

(

std::string

file_name

)

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.