antibody_utils.geometry.orientation

Measure the relative orientation of the VH and VL domains with ABangle.

ABangle describes the orientation of an Fv’s VH and VL domains with five angles and a distance. It was introduced by Dunbar J, Fuchs A, Shi J and Deane CM, “ABangle: characterising the VH–VL orientation in antibodies”, Protein Eng Des Sel 26:611–620 (2013). Each domain is given a coordinate frame by superposing a consensus domain on to the CA atoms of a core set of framework positions. A vector C joins the two domains, and each domain has two vectors in a plane fitted to it: H1 and H2 on VH, and L1 and L2 on VL. The measures are:

  • HL: the torsion angle between H1 and L1 about C.

  • HC1 and HC2: the angles between H1 and H2, and C.

  • LC1 and LC2: the angles between L1 and L2, and C.

  • dc: the length of C.

The core sets are defined in Chothia numbering, so the Fv must be numbered in the Chothia or IMGT scheme.

Functions

abangle(fv)

Calculate the ABangle orientation measures of an Fv.

Classes

OrientationAngles(hl, hc1, lc1, hc2, lc2, dc)

The ABangle measures of an Fv.
class antibody_utils.geometry.orientation.OrientationAngles(hl, hc1, lc1, hc2, lc2, dc)[source]

Bases: object

The ABangle measures of an Fv.

hl

The torsion angle HL, in degrees, from -180 to 180.

hc1

The bend angle HC1, in degrees.

lc1

The bend angle LC1, in degrees.

hc2

The twist angle HC2, in degrees.

lc2

The twist angle LC2, in degrees.

dc

The distance dc between the domains, in angstroms.

as_dict()[source]

The measures, keyed by the symbols used in the paper and by legacy ABDB.

Return type:

dict[str, float]

Returns:

The measures, keyed “HL”, “HC1”, “LC1”, “HC2”, “LC2” and “dc”.

>>> OrientationAngles(-60.0, 70.0, 120.0, 110.0, 80.0, 16.0).as_dict()
{'HL': -60.0, 'HC1': 70.0, 'LC1': 120.0, 'HC2': 110.0, 'LC2': 80.0, 'dc': 16.0}
antibody_utils.geometry.orientation.abangle(fv)[source]

Calculate the ABangle orientation measures of an Fv.

Parameters:

fv (Fv) – The Fv, numbered in the Chothia or IMGT scheme.

Return type:

OrientationAngles

Returns:

The angles and distance.

Raises:

ValueError – If the Fv is numbered in another scheme, or either domain has CA atoms at fewer than three core positions.