On May 29, 2012, at 11:23 AM, JP wrote:
> This value of 1A in the steric filter is not available from the command line,
> correct?
No, there isn't (yet) a way to set that. The current SVN trunk now has an
improved filter. It considers hydrogens, and will also filter based on VdW
radii for each element.
I'm considering adding a "slop," since a near-clash might be less important
after an energy minimization. Consider also that some conformer might suddenly
place a hydrogen bond… So I think I might want something like:
// check distance
if (distanceSquared < m_cutoff // defaults to 1.0A -- filter bad clashes
|| distanceSquared < vdwCutoff - 0.1A // OK if atoms are *just*
touching
What do you think?
Cheers,
-Geoff
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