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salilab / pmi

Python Modeling Interface
https://integrativemodeling.org/nightly/doc/ref/namespaceIMP_1_1pmi.html
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Crosslinking restraint outputs take -log of score #236

Closed sethaxen closed 3 years ago

sethaxen commented 7 years ago

Several of the cross-linking restraints add -log of score to outputs. Not only does this seem weird, but since the score can be negative, in some cases this will raise an error. Examples are here and here.

Is this simply an oversight or was this done for a reason?

Pellarin commented 7 years ago

The reason is the following: the CrossLinkMSRestartaint returns the probability and not the score, which is always less than one. All restrants are wrapped in the LogWrapperRestraint to finally return the total score.

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On Aug 2, 2017, at 3:04 AM, Seth Axen notifications@github.com wrote:

Several of the cross-linking restraints add -log of score to outputs. Not only does this seem weird, but since the score can be negative, in some cases this will raise an error. Examples are here and here.

Is this simply an oversight or was this done for a reason?

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benmwebb commented 3 years ago

Closing, not a bug.