Rosetta 3.5
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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) More...
#include <KinematicPerturber.hh>
Public Types | |
typedef KinematicPerturber | parent |
Protected Member Functions | |
void | refill_torsion_string_vector () |
std::string | next_torsion_string () |
Private Attributes | |
bool | vary_ca_bond_angles_ |
bool | sample_omega_for_pre_prolines_ |
core::Size | num_strings_ |
utility::vector1< std::string > | random_torsion_strings_ |
core::scoring::Ramachandran2B const & | rama_ |
Additional Inherited Members | |
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KinematicMoverCAP | kinmover_ |
core::Size | max_sample_iterations_ |
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)
typedef KinematicPerturber protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::parent |
protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::NeighborDependentTabooSamplingKinematicPerturber | ( | KinematicMoverCAP | kinmover_in) |
protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::~NeighborDependentTabooSamplingKinematicPerturber | ( | ) |
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References random_torsion_strings_.
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function that perturbs the chain, i.e. sets new values
for the torsions, bond angles and bond lengths note: the torsions/angles/lengths that are input to this function will be identical to the ones in the pose, i.e. only the dof values that are explicitly set by this function plus the pivots will have changed after loop closure
Implements protocols::loops::loop_closure::kinematic_closure::KinematicPerturber.
References core::pose::Pose::aa(), core::chemical::aa_pro, protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::get_movemap(), protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::kinmover_, next_torsion_string(), rama_, core::scoring::Ramachandran2B::random_phipsi_from_rama_by_torsion_bin_left(), core::scoring::Ramachandran2B::random_phipsi_from_rama_by_torsion_bin_right(), protocols::loops::loop_closure::kinematic_closure::RG(), sample_omega_for_pre_prolines_, and vary_ca_bond_angles_.
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References core::scoring::Ramachandran2B::get_entries_per_torsion_bin_left(), core::scoring::Ramachandran2B::get_entries_per_torsion_bin_right(), protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::kinmover_, num_strings_, rama_, random_torsion_strings_, and RG().
Referenced by next_torsion_string().
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after the kinmover has closed the loop, the perturber needs
to put the solutions into the pose note: the base class version of this function sets the torsions, so any KinematicPerturber that only changes the torsions will not have to implement this function
Reimplemented from protocols::loops::loop_closure::kinematic_closure::KinematicPerturber.
References core::pose::Pose::atom_tree(), core::kinematics::AtomTree::bond_angle_dof_id(), protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::kinmover_, core::pose::Pose::set_dof(), protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::set_pose_after_closure(), and vary_ca_bond_angles_.
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References vary_ca_bond_angles_.
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Referenced by refill_torsion_string_vector().
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Referenced by perturb_chain(), and refill_torsion_string_vector().
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Referenced by clear_torsion_string_stack(), next_torsion_string(), and refill_torsion_string_vector().
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Referenced by perturb_chain().
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Referenced by perturb_chain(), set_pose_after_closure(), and set_vary_ca_bond_angles().