OrientedSDF (Module)

Calculate a three-dimensional spatial distribution function, restricted by axis angles

Overview

The OrientedSDF module calculates a three-dimensional spatial density / distribution function between two sites A and B in a manner analogous to the SDF module, but restricting the selected sites of B based on an angle range between two site axis vectors. Thus, the generated function represents a spatial density of B sites with a particular orientation relative to A. As such, both the central site A and target site B must be oriented sites with full axis definitions.

Options

Targets

Keyword Arguments Default Description
Configuration Configuration

Required

Specifies the configuration on which to operate.

Sites

Keyword Arguments Default Description
SiteA Site ... Specify site(s) which represent the central site ‘A’. All specified sites must be oriented.
AxisA SiteAxis XAxis Axis representing the vector on site A to use in forming the angle.
SiteB Site ... Specify site(s) which represent the surrounding site ‘B’. All specified sites must be oriented.
AxisB SiteAxis XAxis Axis representing the vector on site B to use in forming the angle.

Ranges

Keyword Arguments Default Description
AngleRange double
double
-15.0
15.0
Axis angle range to accept when binning site B
RangeX double
double
double
-10.0
10.0
0.5
Range (min, max, bin width) of volume over which to bin along X.
RangeY double
double
double
-10.0
10.0
0.5
Range (min, max, bin width) of volume over which to bin along Y.
RangeZ double
double
double
-10.0
10.0
0.5
Range (min, max, bin width) of volume over which to bin along Z.

Exclusions & Restrictions

Keyword Arguments Default Description
ExcludeSameMolecule bool false Whether to exclude correlations between A and B sites on the same molecule.
Symmetric bool false Whether to consider the angle as symmetric about 90, mapping all angles to the 0-90 range. For instance, if the target axes are perpendicular to a mirror plane in the molecule, this should be set to true.

Export

Keyword Arguments Default Description
ExportSDF Data3DFileAndFormat File format and file name under which to save calculated SDF data.