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 |
 Public Types inherited from protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber | |
| typedef KinematicPerturber | parent |
Public Member Functions | |
| NeighborDependentTabooSamplingKinematicPerturber (KinematicMoverCAP kinmover_in) | |
| ~NeighborDependentTabooSamplingKinematicPerturber () override | |
| std::string | perturber_type () const override |
| Public Member Functions inherited from protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber | |
| BaseTabooPerturber (KinematicMoverCAP kinmover_in) | |
| ~BaseTabooPerturber () override | |
| void | perturb_chain (core::pose::Pose const &pose, utility::vector1< core::Real > &torsions, utility::vector1< core::Real > &bond_ang, utility::vector1< core::Real > &) override |
| 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 More... | |
| void | set_pose_after_closure (core::pose::Pose &pose, utility::vector1< core::Real > const &torsions, utility::vector1< core::Real > const &bond_ang, utility::vector1< core::Real > const &bond_len, bool closure_successful) const override |
| 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 More... | |
| void | set_vary_ca_bond_angles (bool vary_ca_bond_angles) |
| void | clear_torsion_string_stack () |
| core::Size | num_strings () const |
| core::conformation::torsion_bin_string | next_torsion_string () |
| Public Member Functions inherited from protocols::loops::loop_closure::kinematic_closure::KinematicPerturber | |
| KinematicPerturber () | |
| ~KinematicPerturber () override | |
| void | set_kinmover (KinematicMoverCAP kinmover) |
| void | set_movemap (core::kinematics::MoveMapCOP mm) |
| core::kinematics::MoveMapCOP | get_movemap () const |
| virtual bool | perturber_exhausted () const |
| void | set_max_sample_iterations (core::Size sample_its) |
| core::Size | max_sample_iterations () const |
| void | clear_torsion_string_stack () |
| KinematicMoverCAP | kinmover () const |
Private Member Functions | |
| void | get_random_phi_psi_for_residue (core::pose::Pose const &pose, core::Size resid, core::conformation::ppo_torsion_bin torbin, core::Real &phi, core::Real &psi) const override |
| std::map< core::conformation::ppo_torsion_bin, core::Size > | get_entries_per_torsion_bin (utility::vector1< core::chemical::AA > loop_seq, core::Size resid) const override |
| This function is implemented by the derived classes and is used to interface with the particular Ramachandran library that the derived classs relies upon it is invoked inside of refill_torsion_string_vector. More... | |
Private Attributes | |
| core::scoring::Ramachandran2B const & | rama_ |
Detailed Description
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)
- Date
- Mon May 21 11:39:26 PDT 2012
Member Typedef Documentation
◆ parent
| typedef KinematicPerturber protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::parent |
Constructor & Destructor Documentation
◆ NeighborDependentTabooSamplingKinematicPerturber()
| protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::NeighborDependentTabooSamplingKinematicPerturber | ( | KinematicMoverCAP | kinmover_in | ) |
◆ ~NeighborDependentTabooSamplingKinematicPerturber()
|
overridedefault |
Member Function Documentation
◆ get_entries_per_torsion_bin()
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overrideprivatevirtual |
This function is implemented by the derived classes and is used to interface with the particular Ramachandran library that the derived classs relies upon it is invoked inside of refill_torsion_string_vector.
Implements protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber.
References core::scoring::Ramachandran2B::get_entries_per_torsion_bin_left(), core::scoring::Ramachandran2B::get_entries_per_torsion_bin_right(), protocols::mean_field::min(), and rama_.
◆ get_random_phi_psi_for_residue()
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overrideprivatevirtual |
Implements protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber.
References core::pose::Pose::aa(), core::conformation::Residue::has_property(), protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::kinmover(), rama_, core::scoring::Ramachandran2B::random_phipsi_from_rama_by_torsion_bin_left(), core::scoring::Ramachandran2B::random_phipsi_from_rama_by_torsion_bin_right(), core::conformation::remap_cis_omega_torsion_bins_to_trans(), core::pose::Pose::residue(), and core::scoring::rg.
◆ perturber_type()
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inlineoverridevirtual |
Member Data Documentation
◆ rama_
|
private |
Referenced by get_entries_per_torsion_bin(), and get_random_phi_psi_for_residue().
The documentation for this class was generated from the following files:
- src/protocols/loops/loop_closure/kinematic_closure/KinematicPerturber.hh
- src/protocols/loops/loop_closure/kinematic_closure/KinematicPerturber.cc
