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ReliaSolve / Molprobity2

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Handle adjustment of NHQ atoms after flips #111

Closed russell-taylor closed 3 years ago

russell-taylor commented 3 years ago

See the 2018 Williams paper describing how these are handled, and the associated code in Reduce.

Reduce does not do this adjustment for the testing, only if the flip is accepted. Doing it before the testing makes the testing less reliable.

Testing involves renaming the atoms (and presumably moving the hydrogens).

russell-taylor commented 3 years ago

From Jane: "Page 5 in the attached paper explains the reasoning and the 3 steps of the NQH approximation for coordinate output. Christopher and the whole group worked out the best protocol we could, he wrote code in Python, and Swati Jain put it into Reduce in C++. You can see her commits in the GitHub history. On the preceding actual determination of flip state, Dave and I know what was done and why, but not exactly how it was accomplished in the code."