9. Scoring Functions

class ScoringFunctions.ScoringFunctions

A class containing variouse Scoring Function for density fitting. Vasishtan and Topf (2011) Scoring functions for cryoEM density fitting. J Struct Biol 174:333-343.

CCF(map1, map2)

Calculate cross-correlation between two Map instances.

Arguments:

map1, map2

EMMap instances to compare.

LSF(map1, map2)

Calculate least-squares between two Map instances.

Arguments:

map1, map2

EMMap instances to compare.

MI(map1, map2, layers=20)

Calculate the Mutual information Score between two Map instances.

Arguments:

map1, map2

EMMap instances to compare.

layers

value for which to bin the map into a limited number of values. Default is 20 as in Shatsky et al., 2008.

SCCC(map1, resolution_densMap, sigma_map, struct, rb, single_segment=False)

Calculate Segment baed cross-correlation from Pandurangan et al. 2013,J Struct Biol. 2013 Dec 12 Based on the Local CCF (Roseman, 2000). It is a local CCF around a selection of atoms.

Arguments:

map1

Target Map Instance.

resolution_densMap

Parameter need for Structure Blurrer. Resolution of the target map.

sigma_map

Parameter need for Structure Blurrer. The sigma value (multiplied by the resolution) that controls the width of the Gaussian. Default values is 0.356.

Other values used :

0.187R corresponding with the Gaussian width of the Fourier transform falling to half the maximum at 1/resolution, as used in Situs (Wriggers et al, 1999);

0.356R corresponding to the Gaussian width at 1/e maximum height equaling the resolution, the default in Chimera (Petterson et al, 2004);

0.425R the fullwidth half maximum being equal to the resolution, as used by FlexEM (Topf et al, 2008);

0.5R the distance between the two inflection points being the same length as the resolution, an option in Chimera (Petterson et al, 2004);

1R where the sigma value simply equal to the resolution, as used by NMFF (Tama et al, 2004).

struct

Structure Instance to compare

ssefile_name

Rigid-body in which the selection is specified.It can be a list as the one use in break_into_segments or FlexEM input file. See overview for more information.

single_segment

Default False.True return score per element if more then one is specify.

chamfer_distance(map1, map2, min_threshold, max_threshold, kdtree=None)

Calculate the Chamfer Distance Score between two Map instances. NOT RACCOMANDED.

Arguments:

map1, map2

EMMap instances to compare.

min_threshold, max_threshold

need to run get_min_threshold and get_max_threshold for map2

kdtree

If set True It is possible to choose between two option of kdtree in numpy the one that is py-based is a better choice.

envelope_score(map, cutoff, structure, norm=False)

Calculate the Envelope Score between a target Map and a Structure Instances.

Arguments:

map

Target Map Instance.

cutoff

Calculated with min_threshold for map.

structure

Structure Instance to compare.

get_partial_DLSF(x, map1, map2)

Calculate the DLSF score between two Map instances.

Arguments:

map1, map2

EMMap instances to compare.

x

number of significant points.

laplace_CCF(map1, map2, prefil=(False, False))

Calculate Laplacian cross-correlation between two Map instances. Based on (Chacon and Wriggers, 2002).

Arguments:

map1, map2

EMMap instances to compare.

prefil

Tuple of boolean values, one for each map respectively. True if Map instance is already Laplacian-filtered. False otherwise.

mapComparison(map1, map2)

Compare the sampling rate, box size and origin of two maps.

Returns True if they are the same, False otherwise.

Arguments:

map1, map2

EMMap instances to compare.

normal_vector_score(map1, map2, min_threshold, max_threshold)

Calculate the Normal Vector Score between two Map instances. Based on 3SOM algorithm (Ceulemans and Russell, 2004)

Arguments:

map1, map2

EMMap instances to compare.

min_threshold, max_threshold

need to run get_min_threshold and get_max_threshold