Paper feedback | JW – L238 (conformer generation) - Mention that we use RDKit with some settings? Minimum inter-conformer RMSD? (per this line, it must be > 0.5 A) GAFF2.X? Do we know which minor version we’re using? TFD - L356 - More description of how TFD is calculated (or a link to its definition)? DD – Is there a closed-form equation for this? Or is it just an implementation? JW – The code here shows that it’s an RDKit implementation, based on a 2012 publication by Rarey LD – We do cite that paper JW – Ok, no action needed on this then
L362 - broken figure reference Fig 5 - Instead of dE_SAGE in header, how about dE_OFF-2.0.0. That’s more in line with how we refer to it elsewhere Fig 6, t69 vs. t59, how could N have two single bonds? openff-2.0.0 openff-1.3.0 t59 = [*:1]-[#6X4:2]-[#7X3$(*~[#6X3,#6X2]):3]~[*:4] t69 = [*:1]~[#7X3,#7X2-1:2]-!@[#6X3:3]~[*:4]
LD – The Any in the chemdraw figure refers to bond order, that makes t59 work t69 depiction should have a red line to a * and a black line to a * from the N. In general, we should put * anywhere that it doesn’t have to be carbon
LD – I’ll update the torsion IDs in Fig 6 to correspond to sage parameter IDs (right now they refer to openff-1.3.0 parameter IDs)
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