schrodinger.structutils.interactions.steric

clash_iterator(struc1, atoms1=None, struc2=None, atoms2=None, allowable_overlap=0.4)

Iterate through all steric clashes between two groups of atoms

Parameters:

struc1 (schrodinger.structure.Structure) - The first structure to examine
atoms1 (list) - A list of atom numbers for struc1. If given, only the specified atoms will be examined. If not given, all atoms of struc1 will be used.
struc1 (schrodinger.structure.Structure) - The second structure to examine. If not given struc1 will be used
atoms2 (list) - A list of atom numbers for struc2. If given, only the specified atoms will be examined. If not given, all atoms of struc2 will be used.
allowable_overlap (float) - Steric clashes smaller than this will be ignored. The default (0.4 A) is a reasonable value when examining protein- protein interactions.

Returns: generator

A generator that iterates through steric clashes. Each iteration will yield a tuple of:

An atom from struc1 (schrodinger.structure._StructureAtom object)
An atom from struc2 (schrodinger.structure._StructureAtom object)
The distance between the two specified atoms in Angstroms (float). Note that this is the distance between the nuclear centers, not the size of the overlap.

sphere_overlap_volume(radius1, radius2, dist)

Calculate the volume of the overlap between two spheres

Parameters:

radius1 (float) - The radius of the first sphere
radius2 (float) - The radius of the second sphere
dist (float) - The distance between the centers of the two spheres

Returns: float

The overlap volume

Note: The equation implemented here is taken from http://mathworld.wolfram.com/Sphere-SphereIntersection.html, equation 16

clash_volume(struc1, atoms1=None, struc2=None, atoms2=None)

Calculate the volume of the steric overlap between two structures

Parameters:

struc1 (schrodinger.structure.Structure) - The first structure to examine
atoms1 (list) - A list of atom numbers for struc1. If given, only the specified atoms will be examined. If not given, all atoms of struc1 will be used.
struc1 (schrodinger.structure.Structure) - The second structure to examine. If not given struc1 will be used
atoms2 (list) - A list of atom numbers for struc2. If given, only the specified atoms will be examined. If not given, all atoms of struc2 will be used.

Returns: float

The steric overlap volume in cubic Angstroms

Note: The overlap volume is calculated as a sum of pair-wise steric clashes. This may double count overlaps for very severe steric clashes where there are really three spheres overlapping.

DEPRECATION_WARNING

Value:

'Steric clashes should be found with schrodinger.infra.structure.get_c
ontacts()'

Module steric_clash

clash_iterator(struc1, atoms1=None, struc2=None, atoms2=None, allowable_overlap=0.4)

sphere_overlap_volume(radius1, radius2, dist)

clash_volume(struc1, atoms1=None, struc2=None, atoms2=None)

DEPRECATION_WARNING