New adaptive dihedral restraints #1
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added 8 commits
December 16, 2019 14:48
A torsion-space analogue of the AdaptiveDistanceRestraint class. OpenMM CustomTorsionForce is implemented, as are ChimeraX-side C++ classes and Python manager class. More work still needed to plug it together.
Not yet connected to simulations, but display and management of parameter values is working.
Now just need to add command-line control.
New commands "isolde restrain torsions", "isolde adjust torsions" and "isolde release torsions".
If kappa gets very close to but not exactly zero, numerical instability develops (division of a very large number by a very small number). Values less than 1e-3 are now set to zero, which triggers the special case of E = -k cos (delta theta)
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For torsion-space reference model restraints. Available via ChimeraX command-line commands "isolde restrain torsions", "isolde adjust torsions" and "isolde release torsions".