IMP  2.1.0
The Integrative Modeling Platform
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  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)
 
FormFactorTabledefault_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

Store a set of objects.

Definition at line 299 of file Profile.h.

Pass a \ set of \ objects. \ See \ Profile

Definition at line 299 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 55 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

model));

This will ensure that the code works when IMP is installed or used via the setup_environment.sh script.