IMP Reference Guide
2.20.0
The Integrative Modeling Platform
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Restraints for handling electron microscopy maps. More...
Restraints for handling electron microscopy maps.
First, import the module:
``` import IMP.bayesianem import IMP.bayesianem.restraint ```
Then, select the model densities that you want to assign to the EM:
``` sel = IMP.atom.Selection(hierarchy=hier, representation_type=IMP.atom.DENSITIES) densities=sel.get_selected_particles() ```
Finally, create the restraint (replace gmm.txt by your target gmm), and add it to the model.
``` gem = IMP.bayesianem.restraint.GaussianEMRestraintWrapper(densities, target_fn=‘gmm.txt', scale_target_to_mass=True, slope=0.01, target_radii_scale=3.0, target_is_rigid_body=False) gem.add_to_model() gem.set_label("Total") output_objects.append(gem) ```
Author(s): Samuel Hanot, Massimiliano Bonomi, Riccardo Pellarin
Maintainer: Riccardo Pellarin
License: LGPL
Publications: Bayesian multi-scale modeling of macromolecular structures based on cryo-electron microscopy density maps Samuel Hanot, Massimiliano Bonomi, Charles H Greenberg, Andrej Sali, Michael Nilges, Michele Vendruscolo, Riccardo Pellarin bioRxiv 113951; doi: https://doi.org/10.1101/113951 (submitted)
Classes | |
class | GaussianEMRestraint |
Creates a restraint between two Gaussian Mixture Models, "model" and "density". More... | |
Typedefs | |
typedef IMP::algebra::DenseGrid3D < double > | DensityGrid |
Functions | |
double | gem_score_cc (Particles model_ps, Particles density_ps) |
DensityGrid | get_grid (IMP::em::DensityMap *in) |
Return a dense grid containing the voxels of the passed density map. More... | |
IMP::em::DensityMap * | get_masked_map (const IMP::algebra::Gaussian3Ds &gmm, const Floats &weights, IMP::em::DensityMap *densitymap, double threshold) |
IMP::algebra::Vector3Ds | get_overlap_binned (const IMP::algebra::Gaussian3Ds &gmm, const Floats &weights, IMP::em::DensityMap *dm, double factor=2.5, int Nbin=100) |
double | get_overlap_fast (const IMP::algebra::Gaussian3Ds &gmm, const Floats &weights, IMP::em::DensityMap *dm, double factor=2.5) |
double | get_percentage_closer_than (const IMP::core::XYZs &m1, const IMP::core::XYZs &m2, const double t) |
double | get_rmsd_excluding_higher_than (const IMP::core::XYZs &m1, const IMP::core::XYZs &m2, const double t) |
double | get_rmsd_of_best_population (const IMP::core::XYZs &m1, const IMP::core::XYZs &m2, const double percentage) |
double | get_rmsd_of_best_population (const IMP::atom::Selection &s1, const IMP::atom::Selection &s2, const double percentage) |
double | get_rmsd_of_best_population (const IMP::algebra::Vector3Ds &m1, const IMP::algebra::Vector3Ds &m2, const double percentage) |
IMP::algebra::Rotation3D | get_rotation_matrix (const IMP::algebra::Vector3D &x, const IMP::algebra::Vector3D &y) |
IMP::em::DensityMap * | get_sub_map (const IMP::em::DensityMap *dm, const IMP::em::DensityMap *sub_gmm, const IMP::em::DensityMap *gmm) |
IMP::algebra::Transformation3D | get_transformation_aligning_first_to_second (const IMP::atom::Selection &s1, const IMP::atom::Selection &s2) |
Get the transformation to align two selections. More... | |
IMP::algebra::PrincipalComponentAnalysis | NormalizePCA (const IMP::algebra::PrincipalComponentAnalysis &pca, const IMP::Particles &ps) |
IMP::algebra::Transformation3Ds | PCAalign (const IMP::algebra::PrincipalComponentAnalysis &pca1, const IMP::algebra::PrincipalComponentAnalysis &pca2) |
float | sgn (double v) |
Standard module functions | |
All | |
std::string | get_module_version () |
Return the version of this module, as a string. More... | |
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... | |
std::string IMP::bayesianem::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
This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh
script.
std::string IMP::bayesianem::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
This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh
script.
DensityGrid IMP::bayesianem::get_grid | ( | DensityMap * | in_map | ) |
Return a dense grid containing the voxels of the passed density map.
The returned grid has the same bounding box as the map.
Definition at line 182 of file bayesianem/utilities.h.
std::string IMP::bayesianem::get_module_version | ( | ) |
Return the version of this module, as a string.
Definition at line 5 of file EMageFit/__init__.py.
IMP::algebra::Transformation3D IMP::bayesianem::get_transformation_aligning_first_to_second | ( | const IMP::atom::Selection & | s1, |
const IMP::atom::Selection & | s2 | ||
) |
Get the transformation to align two selections.
Definition at line 95 of file bayesianem/utilities.h.