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

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

#include <PlaceSimultaneouslyMover.hh>

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List of all members.

Public Types

typedef std::pair
< protocols::hotspot_hashing::HotspotStubSetOP,
std::pair
< protocols::hotspot_hashing::HotspotStubOP,
core::Size > > 
StubSetStubPos
typedef std::pair
< protocols::simple_moves::DesignRepackMoverOP,
core::Real
MoverRealPair
typedef std::pair
< simple_moves::DesignRepackMoverOP,
bool
DesignMoverFoldTreePair
typedef std::pair
< simple_moves::DesignRepackMoverOP,
core::Real
DesignMoverRealPair
typedef std::pair
< protocols::hotspot_hashing::HotspotStubSetOP,
protocols::hotspot_hashing::HotspotStubOP
StubsetStubPair
 ResidueAuction is keyed by energy => we select the residue,stub,stubset combination with the best energy for each stubset,stub combination.
typedef std::pair< core::Real,
std::pair< core::Size,
StubsetStubPair > > 
ResidueAuctionItem
typedef std::multimap
< core::Real, std::pair
< core::Size, StubsetStubPair > > 
ResidueAuction

Public Member Functions

 PlaceSimultaneouslyMover ()
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).
virtual void apply (core::pose::Pose &pose)
 a dummy apply so that instantiation of this baseclass would be possible.
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
bool minimize_no_bb (core::pose::Pose &pose) const
 minimize towards clouds of stubs made up of all the stub sets
void minimize_all (core::pose::Pose &pose, core::Size const minimization_steps) const
 minimize simultaneously towards the placed stubs from each of the stub sets returns false if one of the filters fails
bool pair_sets_with_positions (core::pose::Pose &pose)
 pair each stub set with a position on the scaffold
void design (core::pose::Pose &pose)
 conducts user-specified design movers. Returns true if the energy per residue filter passes for each of the placed hotspots
bool place_stubs (core::pose::Pose &pose) const
 will be removed
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.
void final_cleanup (core::pose::Pose &pose)
void refresh_coordinate_constraints (core::pose::Pose &pose, core::Real const coord_sdev)
 removes and reinstates coordinate constraints for all placed hotspots according to coord_sdev
core::pack::task::PackerTaskOP create_task_for_hotspot_packing (core::pose::Pose const &)
void stub_sets (utility::vector1< StubSetStubPos > const sets)
void host_chain (core::Size const host_chain)
virtual ~PlaceSimultaneouslyMover ()

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

ResidueAuction is keyed by energy => we select the residue,stub,stubset combination with the best energy for each stubset,stub combination.


Constructor & Destructor Documentation

protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::PlaceSimultaneouslyMover ( )
protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::~PlaceSimultaneouslyMover ( ) [virtual]

Member Function Documentation

void protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::apply ( core::pose::Pose ) [virtual]
protocols::moves::MoverOP protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::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.

core::pack::task::PackerTaskOP protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::create_task_for_hotspot_packing ( core::pose::Pose const &  pose)

setup the residue level tasks for each of the paired positions in stub_sets_. This sets the explosion level as well as the allowed identities at each position Note that two things happen in this function: 1) the task is modified to reflect the rotamer explosion operations. 2) residue_level_tasks_for_placed_hotspots_ is updated with these operations

References core::pack::task::EX_THREE_THIRD_STEP_STDDEVS, and core::chemical::num_canonical_aas.

void protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::design ( core::pose::Pose pose)

conducts user-specified design movers. Returns true if the energy per residue filter passes for each of the placed hotspots

wraps around the user-defined design movers. Applies coordinate constraints as specified by the user. Prevents repacking of placed hotspots

References core::pose::Pose::add_constraints(), protocols::protein_interface_design::movers::BuildAlaPose::apply(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, protocols::simple_moves::DesignRepackMover::prevent_repacking(), protocols::protein_interface_design::remove_coordinate_constraints_from_pose(), protocols::simple_moves::DesignRepackMover::task_factory(), and core::scoring::TR().

void protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::final_cleanup ( core::pose::Pose pose)

This should be called before failing placesimultaneously.

References core::pose::Pose::clear(), and core::scoring::TR().

protocols::moves::MoverOP protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::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::PlaceSimultaneouslyMover::get_name ( ) const [virtual]

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

Reimplemented from protocols::simple_moves::DesignRepackMover.

void protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::host_chain ( core::Size const  host_chain) [inline]

References host_chain().

Referenced by host_chain().

void protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_all ( core::pose::Pose pose,
core::Size const  minimization_steps 
) const
bool protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_no_bb ( core::pose::Pose pose) const

minimize towards clouds of stubs made up of all the stub sets

if bb_cst score is 0 return false, o/w true

preliminary rb minimization step in the presence of strong hotspot constraints. Reports failure if pre-minimization bb_cst score is 0. Note that setting up constraints should be done outside

References core::scoring::backbone_stub_constraint, protocols::simple_filters::ScoreTypeFilter::compute(), protocols::protein_interface_design::movers::make_stub_scorefxn(), MinimizeInterface(), core::pose::Pose::total_residue(), and core::scoring::TR().

bool protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions ( core::pose::Pose pose)

pair each stub set with a position on the scaffold

if no mutually exclusive matches are found for all sets, return false

positions on the scaffold are auctioned to hotspot stub sets. The stubset that has a stub with the lowest constraint energy with respect to that position wins the auction. If the number of positions that are paired is less than the number of hotspot families, then failure is reported. If pairing succeeds, each of the paired positions is allowed to adopt an identity from its parent stubset that has below 0 constraint energy. Following which pack_rotamers is called with ex1, ex2, and rotamer explosion if directed by the user. Finally, each placed hotspot is tested for its total energy and for a user-defined filter. If one of these filters fails, failure is reported. Note that residues other than the lowest constraint energy identities might emerge from this process.

References protocols::simple_filters::EnergyPerResidueFilter::apply(), core::scoring::ScoreFunctionFactory::create_score_function(), core::kinematics::distance(), core::conformation::Residue::is_protein(), protocols::protein_interface_design::movers::make_stub_scorefxn(), MinimizeInterface(), protocols::moves::modify_ResId_based_object(), protocols::moves::MS_SUCCESS, core::pack::pack_rotamers(), core::pose::Pose::residue(), core::scoring::SCORE12_PATCH, core::scoring::STANDARD_WTS, core::pose::Pose::total_residue(), core::scoring::total_score, core::scoring::TR(), and core::conformation::Residue::xyz().

void protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::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]
bool protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::place_stubs ( core::pose::Pose pose) const
void protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::refresh_coordinate_constraints ( core::pose::Pose pose,
core::Real const  coord_sdev 
)

removes and reinstates coordinate constraints for all placed hotspots according to coord_sdev

removes the coordinate constraints from the pose and reapplies them individually.

References core::pose::Pose::add_constraints(), core::scoring::constraints::add_coordinate_constraints(), protocols::protein_interface_design::remove_coordinate_constraints_from_pose(), and core::scoring::TR().

void protocols::protein_interface_design::filters::StubScoreFilter::stub_sets ( utility::vector1< StubSetStubPos > const  sets) [inline]

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