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- initializeRadii()
- readXplorRadii(filename)
- vdwViolations(threshold, selection='not PSEUDO', selection2=None, radiusScale=None)
determine nbonded violations:
atoms pairs in selection for which threshold plus the distance
between the atom positions is less than the sums of the appropriate,
scaled vdw radii.
The scale factor is taken from the XPLOR REPEl parameter, if it is used.
Otherwise the variable defaultRadiusScale is used (default value is 0.8).
The XPLOR NBXMod parameter is consulted and the appropriate 1-2,3,4
interactions are excluded. Also, explicitly excluded interactions are
excluded, if NBXMod>0.
If selection2 is specified, only distances between atoms in the two
selections are considered.
Radius scale is normally set from the value of the XPLOR REPEL
parameter. An alternative value can be specified using the radiusScale
argument.
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