Rosetta 3.4
Public Types | Public Member Functions
protocols::protein_interface_design::movers::PlaceStubMover Class Reference

choose a stub based on mc sampling, and place it on the pose. Iterates over stubs until one matches criteria. More...

#include <PlaceStubMover.hh>

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List of all members.

Public Types

typedef std::pair
< simple_moves::DesignRepackMoverOP,
bool
DesignMoverFoldTreePair
typedef std::pair
< simple_moves::DesignRepackMoverOP,
core::Real
DesignMoverRealPair

Public Member Functions

 PlaceStubMover ()
 PlaceStubMover (protocols::hotspot_hashing::HotspotStubSetOP stub_set, core::Real score_threshold, core::Size const host_chain, protocols::filters::FilterOP final_filter, bool const hurry=false, bool const triage_positions=true, core::Real stub_energy_threshold=1.0)
virtual ~PlaceStubMover ()
protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected.
protocols::moves::MoverOP fresh_instance () const
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function _should_ be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).
void stub_minimize_movers (utility::vector1< DesignMoverRealPair > const &dmrp)
utility::vector1
< DesignMoverRealPair > const & 
stub_minimize_movers () const
virtual void apply (core::pose::Pose &pose)
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
virtual void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Detailed Description

choose a stub based on mc sampling, and place it on the pose. Iterates over stubs until one matches criteria.


Member Typedef Documentation


Constructor & Destructor Documentation

protocols::protein_interface_design::movers::PlaceStubMover::PlaceStubMover ( )

Referenced by clone().

protocols::protein_interface_design::movers::PlaceStubMover::PlaceStubMover ( protocols::hotspot_hashing::HotspotStubSetOP  stub_set,
core::Real  score_threshold,
core::Size const  host_chain,
protocols::filters::FilterOP  final_filter,
bool const  hurry = false,
bool const  triage_positions = true,
core::Real  stub_energy_threshold = 1.0 
)
protocols::protein_interface_design::movers::PlaceStubMover::~PlaceStubMover ( ) [virtual]

Member Function Documentation

void protocols::protein_interface_design::movers::PlaceStubMover::apply ( core::pose::Pose pose) [virtual]

Placing a stub in the context of a complex by putting a stub on top of the scaffold. The following steps are taken: 0. minimization of rb dofs in a bb_stub_constraint-dominated force field. Only the constraints implied by the stubset associated with this placestub mover will be applied. 1. stub selection, by iterating over a randomly shuffled stubset. 2. finding a residue on the host chain where the stub may be placed (distance cutoff). 3. testing the stub's repulsive energy on that residue in the context of a poly-alanine host chain. 4. repack/minimize the rb orientation of the pose (plus a little bb minimization around the stub, but no repacking of host_chain_). 5. testing the stub's total_score in the context of the full pose. 6. a vector of user-defined movers derived from DesignRepackMover. These may include further placestub movers. If this is the case, these movers can be constrained with coordinate constraints that are placed on the functional groups of the stub sidechain. These movers can also define the force constant of these harmonic constraints. Notice that this design should in principle be fully extensible to as many stub placement and design movers as the user chooses. If any of the user defined design movers (including subsequent stub placement) fail, another stub placement is attempted and the user defined movers are called again. 7. user_defined final_filter_ is called. If the pose does not pass this, place stub return to iterate over another stub. If all stubs fail, the mover signals failure and exits.

Reimplemented from protocols::simple_moves::DesignRepackMover.

References core::chemical::aa_ala, core::chemical::aa_gly, core::chemical::aa_pro, protocols::protein_interface_design::movers::BuildAlaPose::apply(), core::scoring::backbone_stub_constraint, make_table_of_pilot_apps::begin, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::scoring::ScoreFunctionFactory::create_score_function(), core::kinematics::distance(), core::sequence::end, core::scoring::fa_rep, protocols::moves::FAIL_RETRY, core::pose::Pose::fold_tree(), core::pack::task::operation::PreventRepacking::include_residue(), protocols::moves::modify_ResId_based_object(), protocols::moves::MS_SUCCESS, core::conformation::Residue::name3(), protocols::simple_moves::DesignRepackMover::prevent_repacking(), protocols::simple_moves::DesignRepackMover::prevent_repacking_, protocols::hotspot_hashing::remove_hotspot_constraints_from_pose(), core::pose::Pose::residue(), core::scoring::SCORE12_PATCH, protocols::moves::Mover::set_last_move_status(), core::scoring::SOFT_REP_DESIGN_WTS, core::scoring::STANDARD_WTS, stats_TR(), protocols::protein_interface_design::movers::test_res_res_aln(), core::scoring::total_score, protocols::protein_interface_design::movers::TR(), TR_debug(), and core::conformation::Residue::xyz().

protocols::moves::MoverOP protocols::protein_interface_design::movers::PlaceStubMover::clone ( ) const [virtual]

clone has to be overridden only if clone invocation is expected.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Implements protocols::simple_moves::DesignRepackMover.

References PlaceStubMover().

protocols::moves::MoverOP protocols::protein_interface_design::movers::PlaceStubMover::fresh_instance ( ) const [inline, virtual]

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function _should_ be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Implements protocols::simple_moves::DesignRepackMover.

std::string protocols::protein_interface_design::movers::PlaceStubMover::get_name ( ) const [virtual]

Each derived class must specify its name. The class name.

Reimplemented from protocols::simple_moves::DesignRepackMover.

References protocols::protein_interface_design::movers::PlaceStubMoverCreator::mover_name().

void protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &  pose 
) [virtual]
void protocols::protein_interface_design::movers::PlaceStubMover::stub_minimize_movers ( utility::vector1< DesignMoverRealPair > const &  dmrp) [inline]
utility::vector1< DesignMoverRealPair > const& protocols::protein_interface_design::movers::PlaceStubMover::stub_minimize_movers ( ) const [inline]

The documentation for this class was generated from the following files:
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