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Add generic restraints #90

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aozalevsky opened this issue Sep 7, 2023 · 0 comments
Open

Add generic restraints #90

aozalevsky opened this issue Sep 7, 2023 · 0 comments

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@aozalevsky
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aozalevsky commented Sep 7, 2023

There are multiple types of restraints that are usually applied during modeling (like forcefields, excluded volume, or connectivity) that we do not record right now. In previous discussions, we considered them as "implementation details" and thus decided to ignore them. However, I think they are essential for the understanding of the modeling process. And since the supplementary table and validation report provide a list of restraints, those additional restraints can be easily missed/overlooked, because this information is typically buried in the methods/supplementary methods.

What do you think about adding _ihm.generic_restraint table? Something like:

_ihm.generic_restraint.id
_ihm.generic_restraint.name
_ihm.generic_restraint.description
1 Forcefield 'Amber99sb-ildn molecular mechanics forcefield'
2 'Excluded volume' 'Excluded volume restraint as implemented in IMP'
3 'Connectivity restraint' 'Sequential pairwise harmonic restraints were applied to mimic Ca-Ca distance of 3.8A'
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