model_extract_build.cpp File Reference

Functions to extract subvolumes and build new maps. More...

#include "Bimage.h"
#include "model_extract_build.h"
#include "model_util.h"
#include "file_util.h"
#include "linked_list.h"
#include "random_numbers.h"
#include "utilities.h"

Functions
Matrix3	get_link_matrix (Blink *link)
Vector3< double >	component_find_shift (Bcomponent *comp, Bimage *p, Bimage *ptemp, Bimage *pmask, Bimage *pfsmask, View2< float > view, double hires, double lores, double shift_limit, int shift_flag, fft_plan planf, fft_plan planb)
Vector3< double >	component_find_shift2 (Bcomponent *comp, Bimage *p, Bimage *ptemp, Bimage *pmask, Bimage *pfsmask, View2< float > view, double hires, double lores, double shift_limit, int shift_flag, fft_plan planf, fft_plan planb)
int	component_refine_random (Bcomponent *comp, Bimage *p, Bimage *ptemp, Bimage *pmask, Bimage *pfsmask, int max_iter, double hires, double lores, double max_shift, double max_view_angle, double max_rot_angle, int shift_flag, fft_plan planf, fft_plan planb)
int	component_refine (Bcomponent *comp, Bimage *p, Bimage *ptemp, Bimage *pmask, Bimage *pfsmask, double viewmax, double rotmax, double viewstep, double rotstep, double hires, double lores, double accuracy, double max_shift, int shift_flag, fft_plan planf, fft_plan planb)
int	model_refine_components (Bmodel *model, Bstring *ct_names, Bimage *ptemp, Bimage *pmask, Bimage *pfsmask, int max_iter, double viewstep, double rotstep, double hires, double lores, double accuracy, double max_shift, double max_view_angle, double max_rot_angle, int shift_flag)
	Refines component views and positions by cross-correlation. More...
int	model_refine_link_positions (Bmodel *model, Bimage *ptemp, Bimage *pmask, Bimage *pfsmask, double hires, double lores, double max_shift, int shift_flag, double bias)
	Refines link positions by cross-correlation. More...
Bimage *	model_average_component_density (Bmodel *model, Vector3< long > size, Vector3< double > origin, int npt)
	Averages the density associated with each component type in a model. More...
Bimage *	model_extract_component_densities (Bmodel *model, Vector3< long > size, Vector3< double > origin)
	Extracts all densities associated with components in a model. More...
Bimage *	model_average_link_density (Bmodel *model, Vector3< long > size, Vector3< double > origin)
	Extracts a density associated with each link in a model. More...
Bimage *	model_build_from_component_density (Bmodel *model, Vector3< long > size, Vector3< double > origin, int flags)
	Builds a new map from a densities of components in a model. More...
Bimage *	model_build_from_link_density (Bmodel *model, Bstring &linkmap, Vector3< long > size, Vector3< double > origin, int link_select, int flags)
	Builds a new map from a density of a link in a model. More...

Variables
int	verbose

Detailed Description

Functions to extract subvolumes and build new maps.

Author

Bernard Heymann

Date

Created: 20060411

Modified: 20150915

Function Documentation

component_find_shift()

Vector3< double > component_find_shift	(	Bcomponent *	comp,
		Bimage *	p,
		Bimage *	ptemp,
		Bimage *	pmask,
		Bimage *	pfsmask,
		View2< float >	view,
		double	hires,
		double	lores,
		double	shift_limit,
		int	shift_flag,
		fft_plan	planf,
		fft_plan	planb
	)

component_find_shift2()

Vector3< double > component_find_shift2	(	Bcomponent *	comp,
		Bimage *	p,
		Bimage *	ptemp,
		Bimage *	pmask,
		Bimage *	pfsmask,
		View2< float >	view,
		double	hires,
		double	lores,
		double	shift_limit,
		int	shift_flag,
		fft_plan	planf,
		fft_plan	planb
	)

component_refine()

int component_refine	(	Bcomponent *	comp,
		Bimage *	p,
		Bimage *	ptemp,
		Bimage *	pmask,
		Bimage *	pfsmask,
		double	viewmax,
		double	rotmax,
		double	viewstep,
		double	rotstep,
		double	hires,
		double	lores,
		double	accuracy,
		double	max_shift,
		int	shift_flag,
		fft_plan	planf,
		fft_plan	planb
	)

component_refine_random()

int component_refine_random	(	Bcomponent *	comp,
		Bimage *	p,
		Bimage *	ptemp,
		Bimage *	pmask,
		Bimage *	pfsmask,
		int	max_iter,
		double	hires,
		double	lores,
		double	max_shift,
		double	max_view_angle,
		double	max_rot_angle,
		int	shift_flag,
		fft_plan	planf,
		fft_plan	planb
	)

get_link_matrix()

Matrix3 get_link_matrix

(

Blink *

link

)

model_average_component_density()

Bimage * model_average_component_density	(	Bmodel *	model,
		Vector3< long >	size,
		Vector3< double >	origin,
		int	npt
	)

Averages the density associated with each component type in a model.

Parameters

*model	model.
size	size of component density to extract.
origin	origin of new component density image.
npt	number per type.

Returns

Bimage* average density around a component.

The densities associated with each vertex type is extracted and averaged.
The extracted density origin is placed on the component coordinates.
The component views must already be set.
Only the first model in the list is processed.
The map file for the model must exist.

model_average_link_density()

Bimage * model_average_link_density	(	Bmodel *	model,
		Vector3< long >	size,
		Vector3< double >	origin
	)

Extracts a density associated with each link in a model.

Parameters

*model	model.
size	size of link density to extract.
origin	origin of new link density image.

Returns

Bimage* new image with the density around the link.

The link density origin is positioned on the center of the link.
The component views must already be set.

model_build_from_component_density()

Bimage * model_build_from_component_density	(	Bmodel *	model,
		Vector3< long >	size,
		Vector3< double >	origin,
		int	flags
	)

Builds a new map from a densities of components in a model.

Parameters

*model	model.
size	size of new map.
origin	origin of new map with respect to the model.
flags	flags to weigh by contributions (1) and build separate maps (2).

Returns

Bimage* new map.

The number of new maps depends on the number of selected component types
and access to their density maps.
The component views must already be set.
The sampling must be the same for all component type maps.

model_build_from_link_density()

Bimage * model_build_from_link_density	(	Bmodel *	model,
		Bstring &	linkmap,
		Vector3< long >	size,
		Vector3< double >	origin,
		int	link_select,
		int	flags
	)

Builds a new map from a density of a link in a model.

Parameters

*model	model.
&linkmap	link map filename.
size	size of new map.
origin	origin of new map with respect to the model.
link_select	link selection number to build (first = 1).
flags	flags to weigh by contributions (1) and build separate maps (2).

Returns

Bimage* new map.

The component views must already be set.

model_extract_component_densities()

Bimage * model_extract_component_densities	(	Bmodel *	model,
		Vector3< long >	size,
		Vector3< double >	origin
	)

Extracts all densities associated with components in a model.

Parameters

*model	model.
size	size of component density to extract.
origin	origin of new component density image.

Returns

Bimage* all densities around components.

The densities associated with each component is extracted.
The extracted density origin is placed on the component coordinates.
The component views must already be set.
Only the first model in the list is processed.
The map file for the model must exist.

model_refine_components()

int model_refine_components	(	Bmodel *	model,
		Bstring *	ct_names,
		Bimage *	ptemp,
		Bimage *	pmask,
		Bimage *	pfsmask,
		int	max_iter,
		double	viewstep,
		double	rotstep,
		double	hires,
		double	lores,
		double	accuracy,
		double	max_shift,
		double	max_view_angle,
		double	max_rot_angle,
		int	shift_flag
	)

Refines component views and positions by cross-correlation.

Parameters

*model	model.
*ct_names	list of names associated with template sub-images.
*ptemp	density template.
*pmask	real space mask.
*pfsmask	cross-correlation mask.
max_iter	maximum number of iterations, 0 means only positional refinement.
viewstep	first view direction angular step size (radians).
rotstep	rotation around view angular step size (radians).
hires	high resolution limit for cross-correlation.
lores	low resolution limit for cross-correlation.
accuracy	angular accuracy (radians).
max_shift	maximum shift in coordinates (angstrom).
max_view_angle	maximum angular change in view vector (radians).
max_rot_angle	maximum angular change in rotation around view vector (radians).
shift_flag	flag to shift only along the normal (1) or perpendicular to it (2).

Returns

int 0, <0 on error.

The density origin is positioned on the component.
The component views must already be set.
The number of component type names should be equal to the number of 
sub-images in the template.

model_refine_link_positions()

int model_refine_link_positions	(	Bmodel *	model,
		Bimage *	ptemp,
		Bimage *	pmask,
		Bimage *	pfsmask,
		double	hires,
		double	lores,
		double	max_shift,
		int	shift_flag,
		double	bias
	)

Refines link positions by cross-correlation.

Parameters

*model	model.
*ptemp	density template.
*pmask	real space mask.
*pfsmask	cross-correlation mask.
hires	high resolution limit for cross-correlation.
lores	low resolution limit for cross-correlation.
max_shift	maximum shift in coordinates (angstrom).
shift_flag	flag to shift only along the normal (1) or perpendicular to it (2).
bias	bias to apply to first correlation coefficient.

Returns

Bimage* density around the component.

The density origin is positioned on the link center.
The component views must already be set.

Variable Documentation

verbose

int verbose

extern