kyleabeauchamp/pymbar — pull request #1 by Lnaden (2014-09-03 14:38:43+00:00)
Title: Set negative square uncertainty within cutoff to zero. 

Changed the warning messages and updated behavior when square uncertainty is negative. Previously, if a negative square uncertainty was within the tolerance (e.g. -1E-13 with cutoff of 1E-10), a True/False was being passed into d2DeltaF[True/False] which was doing: d2DeltaF[0,:] = 0 or d2DeltaF[1,:] = 0 instead of what I think it was trying to do of d2DeltaF[d2DeltaF < 0.0] = 0.0

If any of the negative values of d2DeltaF are greater in magnitude than the cutoff, a warning is issued saying how many entries violate the cutoff and no entries are set to 0.0. This results in NaN's for dDeltaF_ij, but such behavior should be left to the user to figure out why they are getting them.