IMP  2.2.0
The Integrative Modeling Platform
pca_based_rigid_fitting.h
Go to the documentation of this file.
1 /**
2  * \file IMP/multifit/pca_based_rigid_fitting.h
3  * \brief preforms rigid fitting between a set of particles and a density map
4  *
5  * Copyright 2007-2014 IMP Inventors. All rights reserved.
6  */
7 
8 #ifndef IMPMULTIFIT_PCA_BASED_RIGID_FITTING_H
9 #define IMPMULTIFIT_PCA_BASED_RIGID_FITTING_H
10 
11 #include <IMP/core/XYZR.h>
12 #include <IMP/algebra/Transformation3D.h>
13 #include <IMP/kernel/Particle.h>
14 #include <IMP/kernel/Model.h>
15 #include <IMP/em/DensityMap.h>
16 #include <IMP/em/rigid_fitting.h>
17 #include <IMP/multifit/multifit_config.h>
18 #include <IMP/atom/Mass.h>
19 #include <IMP/ScoreState.h>
20 #include <IMP/container/ListSingletonContainer.h>
21 #include <IMP/algebra/eigen_analysis.h>
22 #include <algorithm>
23 IMPMULTIFIT_BEGIN_NAMESPACE
24 
25 //! Compute fitting scores for a given set of rigid transformations
26 /**
27 \brief Fit a protein to its density by principal component matching
28 \param[in] rb The rigid body to be fitted
29 \param[in] rb_refiner The rigid body refiner
30 \param[in] em_map The density map to fit to
31 \param[in] threshold Use voxels above this threshold for PCA calculations
32 \param[in] wei_key The weight key of the particles in the rigid body
33 \param[in] dens_pca_input provide precalculated em_map PCA is available
34 \return fitting solutions
35 \note the function assumes the density map holds its density
36 */
37 IMPMULTIFITEXPORT em::FittingSolutions pca_based_rigid_fitting(
38  core::RigidBody rb, Refiner *rb_refiner, em::DensityMap *em_map,
39  Float threshold, FloatKey wei_key = atom::Mass::get_mass_key(),
40  algebra::PrincipalComponentAnalysis dens_pca_input =
41  algebra::PrincipalComponentAnalysis());
42 
43 //! Compute fitting scores for a given set of rigid transformations
44 /**
45 \brief Fit a protein to its density by principal component matching
46 \param[in] ps The particles to fit (treated as rigid)
47 \param[in] em_map The density map to fit to
48 \param[in] threshold Use voxels above this threshold for PCA calculations
49 \param[in] wei_key The weight key of the particles in the rigid body
50 \param[in] dens_pca_input precalculated em_map PCA
51 \return fitting solutions
52 \note the function assumes the density map holds its density
53 */
54 IMPMULTIFITEXPORT em::FittingSolutions pca_based_rigid_fitting(
55  kernel::ParticlesTemp ps, em::DensityMap *em_map, Float threshold,
56  FloatKey wei_key = atom::Mass::get_mass_key(),
57  algebra::PrincipalComponentAnalysis dens_pca_input =
58  algebra::PrincipalComponentAnalysis());
59 
60 IMPMULTIFITEXPORT
61 void write_markers(const algebra::PrincipalComponentAnalysisD<3> &pca,
62  std::ostream &out);
63 
64 IMPMULTIFIT_END_NAMESPACE
65 #endif /* IMPMULTIFIT_PCA_BASED_RIGID_FITTING_H */
Mass.h
A decorator for particles with mass.
ListSingletonContainer.h
Store a list of kernel::ParticlesTemp.
DensityMap.h
Class for handling density maps.
IMP::Refiner
IMP::kernel::Refiner Refiner
Definition: kernel/doxygen.h:166
ScoreState.h
Import IMP/kernel/ScoreState.h in the namespace.
Model.h
Storage of a model, its restraints, constraints and particles.
Particle.h
Classes to handle individual model particles.
Transformation3D.h
Simple 3D transformation class.
IMP::multifit::pca_based_rigid_fitting
em::FittingSolutions pca_based_rigid_fitting(kernel::ParticlesTemp ps, em::DensityMap *em_map, Float threshold, FloatKey wei_key=atom::Mass::get_mass_key(), algebra::PrincipalComponentAnalysis dens_pca_input=algebra::PrincipalComponentAnalysis())
Compute fitting scores for a given set of rigid transformations.
IMP::Float
double Float
Basic floating-point value (could be float, double...)
Definition: base/types.h:20
eigen_analysis.h
Principal component analysis of a set of points.
XYZR.h
Decorator for a sphere-like particle.
IMP::kernel::FloatKey
Key< 0, true > FloatKey
The type used to identify float attributes in the Particles.
Definition: kernel/base_types.h:32
rigid_fitting.h
preforms rigid fitting between a set of particles and a density map