model_occupancy.cpp File Reference

Library routines to count components in maps. More...

#include "model_occupancy.h"
#include "binomial.h"
#include "ps_plot.h"
#include "img_combine.h"
#include "model_extract_build.h"
#include "model_compare.h"
#include "model_util.h"
#include "math_util.h"
#include "utilities.h"
#include "linked_list.h"

Functions
double	component_coverage (Bimage *p, int img_num, Bcomponent *comp, double threshold)
int	model_occupancy (Bmodel *model, Bimage *pmask, double mol_weight, double rho, double cutoff, int invert_flag)
	Calculates the occupancy of components in a map. More...
vector< double >	model_occupancy_distribution (Bmodel *model, double cutoff, int nfit, long &ncomp, vector< double > &prob, double &R)
	Calculates the occupancy distribution of models. More...
int	model_refine_comp_for_occupancy (Bmodel *model, Bimage *pmask2, Bimage *ptemp, Bimage *pmask, double hires, double lores, double max_shift)
	Refines component views and positions by cross-correlation. More...

Variables
int	verbose

Detailed Description

Library routines to count components in maps.

Author

Daniel Nemecek and Bernard Heymann

Date

Created: 20091202

Modified: 20151110

Function Documentation

component_coverage()

double component_coverage	(	Bimage *	p,
		int	img_num,
		Bcomponent *	comp,
		double	threshold
	)

model_occupancy()

int model_occupancy	(	Bmodel *	model,
		Bimage *	pmask,
		double	mol_weight,
		double	rho,
		double	cutoff,
		int	invert_flag
	)

Calculates the occupancy of components in a map.

Author

Daniel Nemecek and Bernard Heymann

Parameters

*model	model structure to be modified.
*pmask
mol_weight	molecular weight to determine threshold.
rho	protein density in Da/A3.
cutoff	coverage cutoff to use for assigning occupancy.
invert_flag	flag to invert map density.

Returns

int 0.

The map must have positive density (higher values are considered density).
The coverage for a component is defined as the fraction of voxels within
a sphere around the component location that is above the threshold.
The threshold can be derived from the molecular weight or is taken as
the sum of the map average and standard deviation.
The radius of the sphere is taken from the component radius.

model_occupancy_distribution()

vector< double > model_occupancy_distribution	(	Bmodel *	model,
		double	cutoff,
		int	nfit,
		long &	ncomp,
		vector< double > &	prob,
		double &	R
	)

Calculates the occupancy distribution of models.

Author

Daniel Nemecek and Bernard Heymann

Parameters

*model	model structure to be modified.
cutoff	coverage cutoff to determine occupancy.
nfit	number of binomial curves to fit.
&ncomp	maximum number of components in a model.
*prob	weight and probability array (2*nfit).
&R	pointer to fit residual.

Returns

vector<double>& occupancy distribution histogram and fits.

The component coverage must already be calculated and stored in the
FOM property of each component. A component is considered occupied
if its coverage exceeds the given cutoff value.
The distribution, error and fit array is set up with 3+nfit columns:
    Column1:    Distribution histogram
    Column2:    Standard deviations
    Column3:    Overall binomial fit curve (sum of remaining columns)
    Column4+:   nfit individual binomial curves

model_refine_comp_for_occupancy()

int model_refine_comp_for_occupancy	(	Bmodel *	model,
		Bimage *	pmask2,
		Bimage *	ptemp,
		Bimage *	pmask,
		double	hires,
		double	lores,
		double	max_shift
	)

Refines component views and positions by cross-correlation.

Author

Daniel Nemecek and Bernard Heymann

Parameters

*model	model.
*pmask2	mask for the input image.
*ptemp	density template.
*pmask	cross-correlation mask.
hires	high resolution limit for cross-correlation.
lores	low resolution limit for cross-correlation.
max_shift	maximum shift in coordinates (angstrom).

Returns

int 0.

The density origin is positioned on the component.
The component views must already be set.
The density and search radii are derived from the radius of each component.
When a shift is out-of-range, returns to the initial position.
The size of the template determines the search area.

Variable Documentation

verbose

int verbose

extern