Fit a molecule inside its density by local or global FFT.

#include <IMP/multifit/fft_based_rigid_fitting.h>

Inheritance diagram for IMP::multifit::FFTFitting:

Public Member Functions
FFTFittingOutput *	do_global_fitting (em::DensityMap *dmap, double density_threshold, atom::Hierarchy mol2fit, double angle_sampling_interval_rad, int num_fits_to_report, double max_clustering_translation, double max_clustering_angle, bool cluster_fits=true, int num_angle_per_voxel=1, const std::string &angles_filename="")
	Fit a molecule inside its density. More...

FFTFittingOutput *	do_local_fitting (em::DensityMap *dmap, double density_threshold, atom::Hierarchy mol2fit, double angle_sampling_interval_rad, double max_angle_sampling_rad, double max_translation, int num_fits_to_report, bool cluster_fits, int num_angle_per_voxel, double max_clustering_translation, double max_clustering_rotation, const std::string &angles_filename="")
	Locally fit a molecule inside its density. More...

virtual std::string	get_type_name () const

virtual ::IMP::base::VersionInfo	get_version_info () const
	Get information about the module and version of the object.

Public Member Functions inherited from IMP::base::Object
virtual void	clear_caches ()

virtual void	do_destroy ()

CheckLevel	get_check_level () const

LogLevel	get_log_level () const

void	set_check_level (CheckLevel l)

void	set_log_level (LogLevel l)
	Set the logging level used in this object. More...

void	set_was_used (bool tf) const

void	show (std::ostream &out=std::cout) const

const std::string &	get_name () const

void	set_name (std::string name)

Protected Member Functions
void	copy_density_data (em::DensityMap dmap, double data_array)

em::DensityMap *	crop_margin (em::DensityMap *in_map)

FittingSolutionRecords	detect_top_fits (const internal::RotScoresVec &rot_scores, bool cluster_fits, double max_translation, double max_clustering_trans, double max_clustering_rotation)
	Detect the top fits.

void	fftw_translational_search (const multifit::internal::EulerAngles &rot, int i)

void	get_unwrapped_index (int wx, int wy, int wz, int &ix, int &iy, int &iz)

void	pad_resolution_map ()

void	prepare_kernels ()

void	prepare_lowres_map (em::DensityMap *dmap)

void	prepare_poslist (em::DensityMap *dmap)

void	prepare_poslist_flipped (em::DensityMap *dmap)

void	prepare_probe (atom::Hierarchy mol2fit)

Protected Member Functions inherited from IMP::base::Object
	Object (std::string name)
	Construct an object with the given name. More...

	Object ()

Protected Attributes
double	asmb_norm_

multifit::FittingSolutionRecords	best_fits_

FittingSolutionRecords	best_trans_per_rot_log_

algebra::Transformation3D	cen_trans_

atom::Hierarchy	copy_mol_

int	corr_mode_

internal::FFTScores	fft_scores_

internal::FFTScores	fft_scores_flipped_

internal::FFTWGrid< fftw_complex >	fftw_grid_hi_

internal::FFTWGrid< fftw_complex >	fftw_grid_lo_

unsigned long	fftw_nvox_c2r_

unsigned long	fftw_nvox_r2c_

double	fftw_pad_factor_

internal::FFTWPlan	fftw_plan_forward_hi_

internal::FFTWPlan	fftw_plan_forward_lo_

internal::FFTWPlan	fftw_plan_reverse_hi_

internal::FFTWGrid< double >	fftw_r_grid_mol_

double	fftw_scale_

unsigned int	fftw_zero_padding_extent_ [3]

boost::scoped_array< double >	filtered_kernel_

unsigned	filtered_kernel_ext_

internal::RotScoresVec	fits_hash_

boost::scoped_array< double >	gauss_kernel_

unsigned int	gauss_kernel_ext_

unsigned long	gauss_kernel_nvox_

atom::Hierarchy	high_mol_

unsigned int	inside_num_

unsigned int	inside_num_flipped_

boost::scoped_array< double >	kernel_filter_

unsigned int	kernel_filter_ext_

double	low_cutoff_

base::Pointer< em::DensityMap >	low_map_

internal::FFTWGrid< double >	low_map_data_

algebra::Vector3D	map_cen_

unsigned	margin_ignored_in_conv_ [3]

int	num_angle_per_voxel_

int	num_fits_reported_

unsigned long	nvox_

unsigned int	nx_

unsigned int	nx_half_

unsigned int	ny_

unsigned int	ny_half_

unsigned int	nz_

unsigned int	nz_half_

algebra::Vector3D	orig_cen_

atom::Hierarchy	orig_mol_

atom::Hierarchy	orig_mol_copy_

core::RigidBody	orig_rb_

double	origx_

double	origy_

double	origz_

double	resolution_

internal::FFTWGrid< double >	reversed_fftw_data_

multifit::internal::EulerAnglesList	rots_

base::Pointer < em::SampledDensityMap >	sampled_map_

internal::FFTWGrid< double >	sampled_map_data_

double	sampled_norm_

double	spacing_

Detailed Description

Definition at line 43 of file fft_based_rigid_fitting.h.

Member Function Documentation

FFTFittingOutput* IMP::multifit::FFTFitting::do_global_fitting	(	em::DensityMap *	dmap,
		double	density_threshold,
		atom::Hierarchy	mol2fit,
		double	angle_sampling_interval_rad,
		int	num_fits_to_report,
		double	max_clustering_translation,
		double	max_clustering_angle,
		bool	cluster_fits = `true`,
		int	num_angle_per_voxel = `1`,
		const std::string &	angles_filename = `""`
	)

Parameters

[in]	dmap	the density map to fit into
[in]	density_threshold	voxels below this value will be treated as 0
[in]	mol2fit	the molecule to fit. The molecule has to be a rigid body
[in]	angle_sampling_interval_rad	Sample every internal angles
[in]	num_fits_to_report	number of top fits to report
[in]	cluster_fits	if true the fits are clustered. Not recommended for refinement mode
[in]	num_angle_per_voxel	number of rotations to save per voxel
[in]	max_clustering_translation	cluster transformations whose translational distance is lower than the parameter
[in]	max_clustering_angle	cluster transformations whose rotational distance is lower than the parameter
[in]	angles_filename	a file containing angles to sample. if not specified, all angles are sampled

FFTFittingOutput* IMP::multifit::FFTFitting::do_local_fitting	(	em::DensityMap *	dmap,
		double	density_threshold,
		atom::Hierarchy	mol2fit,
		double	angle_sampling_interval_rad,
		double	max_angle_sampling_rad,
		double	max_translation,
		int	num_fits_to_report,
		bool	cluster_fits,
		int	num_angle_per_voxel,
		double	max_clustering_translation,
		double	max_clustering_rotation,
		const std::string &	angles_filename = `""`
	)

Parameters

[in]	dmap	the density map to fit into
[in]	density_threshold	voxels below this value will be treated as 0
[in]	mol2fit	the molecule to fit. The molecule has to be a rigid body
[in]	angle_sampling_interval_rad	sample the mol within the range of +- this angle
[in]	max_angle_sampling_rad
[in]	max_translation	sample the mol within +- this translation is all directions
[in]	num_fits_to_report
[in]	cluster_fits	if true the fits are clustered. Not recommended for refinement mode
[in]	num_angle_per_voxel	number of rotations to save per voxel
[in]	max_clustering_translation	cluster transformations whose translational distance is lower than the parameter
[in]	max_clustering_rotation	cluster transformations whose rotational distance is lower than the parameter
[in]	angles_filename	a file containing angles to sample. if not specified, all angles are sampled

The documentation for this class was generated from the following file:

fft_based_rigid_fitting.h

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Function Documentation