IMP  2.0.1
The Integrative Modeling Platform
IMP::cnmultifit Namespace Reference

See IMP.cnmultifit Overview for more information.


class  AlignSymmetric
 A class for fast alignment of a cyclic model to its density. More...


typedef IMP::base::Vector
< AlignSymmetric
typedef IMP::base::Vector
< CnSymmAxisDetector > 
typedef IMP::base::Vector
< MolCnSymmAxisDetector > 


em::DensityMapbuild_cn_dens_assembly (em::DensityMap *subunit_dens, const em::DensityHeader &asmb_dens_header, algebra::Transformation3D monomer_t, int symm_deg)
algebra::Transformation3D calc_transformation_around_axis (algebra::Vector3D a, algebra::Vector3D b, float angle_rad)
float cn_symm_score (atom::Hierarchies mhs, const algebra::Vector3D &center, const algebra::Vector3D &direction, int symm_deg)
 scores an input vector as a symmetry axis
void do_all_fitting (const std::string param_filename, const std::string chimera_filename="")
 High level interface to build cyclic symmetric complexes. More...
em::FittingSolutions fit_cn_assembly (atom::Hierarchies mhs, int dn_symm_deg, em::DensityMap *dmap, float threshold, const AlignSymmetric &aligner, bool sample_translation=false, bool fine_rotational_sampling=true)
 Fit a symmetric model to its density.
em::FittingSolutions fit_cn_assembly (em::DensityMap *asmb_map, const MolCnSymmAxisDetector &symm_mol, em::DensityMap *dmap, const CnSymmAxisDetector &symm_map, int symm_deg, float threshold)
algebra::Transformation3Ds generate_cn_transformations (atom::Hierarchies mhs, int symm_deg)
algebra::Transformation3Ds generate_translations_along_symm_axis (atom::Hierarchies mhs, int symm_deg)
float get_cn_rmsd (atom::Hierarchies mh1, atom::Hierarchies mh2)
 Find correspondence between the two rings and calculate rmsd.
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...
Floats get_rmsd_for_models (const std::string param_filename, const std::string trans_filename, const std::string ref_filename, int start_model=0, int end_model=-1)
statistics::Histogram my_get_density_histogram (const em::DensityMap *dmap, float threshold, int num_bins)
bool pca_matching (const algebra::PrincipalComponentAnalysis &pca1, const algebra::PrincipalComponentAnalysis &pca2, float resolution)
multifit::FittingSolutionRecords prune_by_pca (const std::string &param_fn, const multifit::FittingSolutionRecords &sols, int dn=1)
em::FittingSolutions symmetry_local_fitting (atom::Hierarchies mhs, int cn_symm_deg, int dn_symm_deg, em::DensityMap *dmap, int num_of_trans_to_consider)
void transform_cn_assembly (atom::Hierarchies mhs, algebra::Transformation3D monomer_t)

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

Pass or store a set of AlignSymmetric .

Definition at line 63 of file AlignSymmetric.h.

Pass or store a set of CnSymmAxisDetector .

Definition at line 58 of file CnSymmAxisDetector.h.

Pass or store a set of MolCnSymmAxisDetector .

Definition at line 45 of file MolCnSymmAxisDetector.h.

Function Documentation

void IMP::cnmultifit::do_all_fitting ( const std::string  param_filename,
const std::string  chimera_filename = "" 

Given a parameter file, this function does all the work to build a number of fits of the monomer into a density map of the symmetric complex.

param_filenameName of a parameter file.
chimera_filenameIf not empty, the name of a file that will be generated containing Chimera-compatible fit information.
std::string IMP::cnmultifit::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 tools/ script.

std::string IMP::cnmultifit::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 tools/ script.