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BaseTabooPerturber Taboo-sampling perturber base class, the two variants of which, share much code in common, but interface with separate Ramachandran potentials. |
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| BaseTabooPerturberAP | |||
| BaseTabooPerturberCAP | |||
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KinematicMover A mover class for performing kinematic loop closure on a peptide segment @detail //////////////////////////////////////////////////////////////////////////// |
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| KinematicMoverAP | |||
| KinematicMoverCAP | |||
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KinematicPerturber pure virtual base class for KinematicPerturber. |
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| KinematicPerturberAP | |||
| KinematicPerturberCAP | |||
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KinematicWrapper This class extends KinematicMover by composition (has-a KinematicMover). |
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| KinematicWrapperAP | |||
| KinematicWrapperCAP | |||
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NeighborDependentTabooSamplingKinematicPerturber Neighbor-dependent Taboo-sampling kinematic perturber (still samples randomly, but only within a given torsion bin; the Taboo sampler ensures that this torsion bin is varied in each iteration) that uses neighbor-dependent Ramachandran distributions (rama2b) Amelie Stein |
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| NeighborDependentTabooSamplingKinematicPerturberAP | |||
| NeighborDependentTabooSamplingKinematicPerturberCAP | |||
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NeighborDependentTorsionSamplingKinematicPerturber Amelie Stein neighbor-dependent torsion sampling kinematic perturber -- uses rama2b for phi/psi lookup |
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| NeighborDependentTorsionSamplingKinematicPerturberAP | |||
| NeighborDependentTorsionSamplingKinematicPerturberCAP | |||
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TabooSamplingKinematicPerturber Taboo-sampling kinematic perturber (still samples randomly, but only within a specific torsion bin, and the Taboo sampler ensures that this torsion bin is varied in each iteration) Amelie Stein |
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| TabooSamplingKinematicPerturberAP | |||
| TabooSamplingKinematicPerturberCAP | |||
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TorsionRestrictedKinematicPerturber torsion-restricted kinematic perturber (still samples randomly, but only within a given torsion bin) Amelie Stein |
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| TorsionRestrictedKinematicPerturberAP | |||
| TorsionRestrictedKinematicPerturberCAP | |||
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TorsionSamplingKinematicPerturber torsion sampling kinematic perturber |
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| TorsionSamplingKinematicPerturberAP | |||
| TorsionSamplingKinematicPerturberCAP | |||
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TorsionSweepingKinematicPerturber WARNING WARNING UNTESTED!!!! torsion sweeping kinematic perturber WARNING WARNING UNTESTED!!!! used to work in other implementation probably works now, but to make sure you shoud doublecheck Here's some commentary on why the TorsionSweepingKinematicPerturber is Fun and Awesome to use! Basically, you take the loop as given and search for solutions nearby. |
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| TorsionSweepingKinematicPerturberAP | |||
| TorsionSweepingKinematicPerturberCAP | |||
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VicinitySamplingKinematicPerturber vicinity sampling kinematic perturber Amelie Stein (just the refactoring) |
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| VicinitySamplingKinematicPerturberAP | |||
| VicinitySamplingKinematicPerturberCAP | |||
| __CPP_KinematicMover__ | |||
| __CPP_KinematicPerturber__ | |||
| __CPP_KinematicWrapper__ | |||
| __CPP_NeighborDependentTorsionSamplingKinematicPerturber__ | |||
| __CPP_TorsionRestrictedKinematicPerturber__ | |||
| __CPP_TorsionSamplingKinematicPerturber__ | |||
| __CPP_TorsionSweepingKinematicPerturber__ | |||
| __CPP_VicinitySamplingKinematicPerturber__ | |||
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__package__ = None
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