Rosetta 3.4
Public Member Functions | Protected Attributes
protocols::simple_moves::DesignRepackMover Class Reference

a pure virtual base class for movers which redesign and repack the interface More...

#include <DesignRepackMover.hh>

Inheritance diagram for protocols::simple_moves::DesignRepackMover:
Inheritance graph
[legend]
Collaboration diagram for protocols::simple_moves::DesignRepackMover:
Collaboration graph
[legend]

List of all members.

Public Member Functions

 DesignRepackMover ()
 DesignRepackMover (std::string const name)
void setup_packer_and_movemap (core::pose::Pose const &pose)
protocols::moves::MoverOP clone () const =0
 clone has to be overridden only if clone invocation is expected.
protocols::moves::MoverOP fresh_instance () const =0
 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 parse_my_tag (utility::tag::TagPtr const, 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 min_rb (utility::vector1< bool > const min_rb)
void min_rb (bool const min_rb)
 in most cases, there would only be one rb dof making it useful to have a non-vector accessor to min_rb_. However, if the pose has multiple jumps, setting min_rb_ in this way might cause trouble in other parts of the code.
utility::vector1< bool > const & min_rb () const
bool min_rb_set () const
void min_sc (utility::vector1< bool > const &min_sc)
utility::vector1< bool > const & min_sc () const
bool min_sc_set () const
void min_bb (utility::vector1< bool > const &min_bb)
utility::vector1< bool > const & min_bb () const
bool min_bb_set () const
bool optimize_foldtree () const
void optimize_foldtree (bool const opt)
virtual void apply (core::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.
void prevent_repacking (utility::vector1< core::Size > const p)
utility::vector1< core::Size >
const & 
prevent_repacking () const
void restrict_to_repacking (utility::vector1< core::Size > const p)
utility::vector1< core::Size >
const & 
restrict_to_repacking () const
void design (bool const des)
bool design () const
void set_scorefxn_repack (core::scoring::ScoreFunctionCOP scorefxn)
void set_scorefxn_minimize (core::scoring::ScoreFunctionCOP scorefxn)
core::scoring::ScoreFunctionOP scorefxn_repack () const
core::scoring::ScoreFunctionOP scorefxn_minimize () const
core::pack::task::PackerTaskCOP task () const
core::pack::task::PackerTaskOPtask ()
void clear_task ()
 after fiddling with a task from outside this mover, clear it, or else, on the next iteration through the mover the changes will be remembered
void clear_task_factory ()
void use_preset_task (bool const bt)
bool use_preset_task () const
void task_factory (core::pack::task::TaskFactoryOP p)
core::pack::task::TaskFactoryOPtask_factory ()
core::pack::task::TaskFactoryOP task_factory () const
virtual ~DesignRepackMover ()

Protected Attributes

core::scoring::ScoreFunctionOP scorefxn_repack_
core::scoring::ScoreFunctionOP scorefxn_minimize_
bool repack_partner1_
bool repack_partner2_
bool design_partner1_
bool design_partner2_
utility::vector1< boolmin_sc_
utility::vector1< boolcurr_min_sc_
utility::vector1< boolmin_rb_
utility::vector1< boolmin_bb_
utility::vector1< boolcurr_min_bb_
utility::vector1< boolcurr_min_rb_
bool min_rb_set_
bool min_sc_set_
bool min_bb_set_
utility::vector1< core::Sizetarget_residues_
core::Real interface_distance_cutoff_
bool repack_non_ala_
bool optimize_foldtree_
bool automatic_repacking_definition_
core::pack::task::PackerTaskOP task_
bool use_preset_task_
utility::vector1< boolallowed_aas_
utility::vector1< core::Sizeprevent_repacking_
utility::vector1< core::Sizerestrict_to_repacking_
core::pack::task::TaskFactoryOP task_factory_
bool symmetry_

Detailed Description

a pure virtual base class for movers which redesign and repack the interface


Constructor & Destructor Documentation

protocols::simple_moves::DesignRepackMover::DesignRepackMover ( )
protocols::simple_moves::DesignRepackMover::DesignRepackMover ( std::string const  name)
protocols::simple_moves::DesignRepackMover::~DesignRepackMover ( ) [virtual]

Member Function Documentation

virtual void protocols::simple_moves::DesignRepackMover::apply ( core::pose::Pose ) [inline, virtual]
void protocols::simple_moves::DesignRepackMover::clear_task ( )

after fiddling with a task from outside this mover, clear it, or else, on the next iteration through the mover the changes will be remembered

References task_.

void protocols::simple_moves::DesignRepackMover::clear_task_factory ( )

References task_factory_.

protocols::moves::MoverOP protocols::simple_moves::DesignRepackMover::clone ( ) const [pure virtual]
void protocols::simple_moves::DesignRepackMover::design ( bool const  des) [inline]
bool protocols::simple_moves::DesignRepackMover::design ( ) const [inline]
protocols::moves::MoverOP protocols::simple_moves::DesignRepackMover::fresh_instance ( ) const [pure 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.

Reimplemented from protocols::moves::Mover.

Implemented in protocols::protein_interface_design::movers::BackrubDDMover, protocols::protein_interface_design::movers::BuildAlaPose, protocols::protein_interface_design::movers::DesignMinimizeHbonds, protocols::protein_interface_design::movers::DisulfideMover, protocols::protein_interface_design::movers::LoopFinder, protocols::protein_interface_design::movers::LoopMoverFromCommandLine, protocols::protein_interface_design::movers::LoopRemodel, protocols::protein_interface_design::movers::PlacementAuctionMover, protocols::protein_interface_design::movers::PlacementMinimizationMover, protocols::protein_interface_design::movers::PlaceOnLoop, protocols::protein_interface_design::movers::PlaceSimultaneouslyMover, protocols::protein_interface_design::movers::PlaceStubMover, protocols::protein_interface_design::movers::RepackMinimize, protocols::protein_interface_design::movers::SaveAndRetrieveSidechains, and protocols::simple_moves::ddG.

std::string protocols::simple_moves::DesignRepackMover::get_name ( ) const [virtual]
void protocols::simple_moves::DesignRepackMover::min_bb ( utility::vector1< bool > const &  min_bb) [inline]

References min_bb(), min_bb_, and min_bb_set_.

Referenced by min_bb().

utility::vector1< bool > const& protocols::simple_moves::DesignRepackMover::min_bb ( ) const [inline]

References min_bb_, and min_bb_set().

Referenced by parse_my_tag().

bool protocols::simple_moves::DesignRepackMover::min_bb_set ( ) const [inline]

References min_bb_set_.

Referenced by min_bb(), and setup_packer_and_movemap().

void protocols::simple_moves::DesignRepackMover::min_rb ( utility::vector1< bool > const  min_rb) [inline]

References min_rb(), min_rb_, and min_rb_set_.

Referenced by min_rb().

void protocols::simple_moves::DesignRepackMover::min_rb ( bool const  min_rb) [inline]

in most cases, there would only be one rb dof making it useful to have a non-vector accessor to min_rb_. However, if the pose has multiple jumps, setting min_rb_ in this way might cause trouble in other parts of the code.

References min_rb_, and min_rb_set_.

utility::vector1< bool > const& protocols::simple_moves::DesignRepackMover::min_rb ( ) const [inline]
bool protocols::simple_moves::DesignRepackMover::min_rb_set ( ) const [inline]

References min_rb_set_.

Referenced by min_rb(), and setup_packer_and_movemap().

void protocols::simple_moves::DesignRepackMover::min_sc ( utility::vector1< bool > const &  min_sc) [inline]

References min_sc(), min_sc_, and min_sc_set_.

Referenced by min_sc().

utility::vector1< bool > const& protocols::simple_moves::DesignRepackMover::min_sc ( ) const [inline]

References min_sc_, and min_sc_set().

Referenced by parse_my_tag().

bool protocols::simple_moves::DesignRepackMover::min_sc_set ( ) const [inline]

References min_sc_set_.

Referenced by min_sc(), and setup_packer_and_movemap().

void protocols::simple_moves::DesignRepackMover::optimize_foldtree ( bool const  opt) [inline]

References optimize_foldtree_.

bool protocols::simple_moves::DesignRepackMover::optimize_foldtree ( ) const [inline]

References optimize_foldtree_.

void protocols::simple_moves::DesignRepackMover::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]

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::protein_interface_design::movers::BackrubDDMover, protocols::protein_interface_design::movers::BuildAlaPose, protocols::protein_interface_design::movers::DesignMinimizeHbonds, protocols::protein_interface_design::movers::DisulfideMover, protocols::protein_interface_design::movers::LoopFinder, protocols::protein_interface_design::movers::LoopMoverFromCommandLine, protocols::protein_interface_design::movers::LoopRemodel, protocols::protein_interface_design::movers::PlacementAuctionMover, protocols::protein_interface_design::movers::PlacementMinimizationMover, protocols::protein_interface_design::movers::PlaceOnLoop, protocols::protein_interface_design::movers::PlaceSimultaneouslyMover, protocols::protein_interface_design::movers::PlaceStubMover, protocols::protein_interface_design::movers::RepackMinimize, protocols::protein_interface_design::movers::SaveAndRetrieveSidechains, and protocols::simple_moves::ddG.

References automatic_repacking_definition_, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), design(), design_partner1_, design_partner2_, protocols::moves::DataMap::get(), protocols::rosetta_scripts::get_resnum(), interface_distance_cutoff_, min_bb(), min_rb(), min_sc(), optimize_foldtree_, protocols::rosetta_scripts::parse_task_operations(), repack_non_ala_, repack_partner1_, repack_partner2_, scorefxn_minimize(), scorefxn_minimize_, scorefxn_repack(), scorefxn_repack_, symmetry_, target_residues_, task_factory(), core::pose::Pose::total_residue(), and protocols::simple_moves::TR().

void protocols::simple_moves::DesignRepackMover::prevent_repacking ( utility::vector1< core::Size > const  p) [inline]
utility::vector1< core::Size > const& protocols::simple_moves::DesignRepackMover::prevent_repacking ( ) const [inline]
void protocols::simple_moves::DesignRepackMover::restrict_to_repacking ( utility::vector1< core::Size > const  p) [inline]
utility::vector1< core::Size > const& protocols::simple_moves::DesignRepackMover::restrict_to_repacking ( ) const [inline]
core::scoring::ScoreFunctionOP protocols::simple_moves::DesignRepackMover::scorefxn_minimize ( ) const
core::scoring::ScoreFunctionOP protocols::simple_moves::DesignRepackMover::scorefxn_repack ( ) const
void protocols::simple_moves::DesignRepackMover::set_scorefxn_minimize ( core::scoring::ScoreFunctionCOP  scorefxn)

References scorefxn_minimize_.

void protocols::simple_moves::DesignRepackMover::set_scorefxn_repack ( core::scoring::ScoreFunctionCOP  scorefxn)

References scorefxn_repack_.

void protocols::simple_moves::DesignRepackMover::setup_packer_and_movemap ( core::pose::Pose const &  pose)

References core::conformation::Residue::aa(), core::chemical::aa_ala, core::chemical::aa_gly, core::chemical::aa_pro, allowed_aas_, core::pack::task::operation::RestrictAbsentCanonicalAAS::apply(), protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::apply(), automatic_repacking_definition_, protocols::scoring::Interface::calculate(), core::pack::task::TaskFactory::create_packer_task(), curr_min_bb_, curr_min_rb_, curr_min_sc_, protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::design_chain1(), protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::design_chain2(), design_partner1_, design_partner2_, core::kinematics::distance(), protocols::scoring::Interface::distance(), core::pose::Pose::fold_tree(), protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::interface_distance_cutoff(), interface_distance_cutoff_, protocols::scoring::Interface::is_interface(), core::conformation::Residue::is_protein(), core::pack::make_symmetric_PackerTask(), min_bb_, min_bb_set(), min_rb_, min_rb_set(), min_sc_, min_sc_set(), core::chemical::ResidueType::name(), core::pose::Pose::num_jump(), core::pack::task::parse_resfile(), core::kinematics::FoldTree::partition_by_jump(), prevent_repacking_, protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::repack_chain1(), protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::repack_chain2(), repack_non_ala_, repack_partner1_, repack_partner2_, core::pose::Pose::residue(), restrict_to_repacking_, symmetry_, target_residues_, task_, task_factory_, core::pose::Pose::total_residue(), core::conformation::Residue::type(), core::pose::Pose::update_residue_neighbors(), and use_preset_task_.

Referenced by protocols::protein_interface_design::movers::RepackMinimize::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), and protocols::protein_interface_design::movers::BuildAlaPose::apply().

core::pack::task::PackerTaskCOP protocols::simple_moves::DesignRepackMover::task ( ) const
core::pack::task::PackerTaskOP & protocols::simple_moves::DesignRepackMover::task ( )

References task_.

core::pack::task::TaskFactoryOP protocols::simple_moves::DesignRepackMover::task_factory ( ) const

References task_factory_.

core::pack::task::TaskFactoryOP & protocols::simple_moves::DesignRepackMover::task_factory ( )
void protocols::simple_moves::DesignRepackMover::task_factory ( core::pack::task::TaskFactoryOP  p)
void protocols::simple_moves::DesignRepackMover::use_preset_task ( bool const  bt) [inline]

References use_preset_task_.

bool protocols::simple_moves::DesignRepackMover::use_preset_task ( ) const [inline]

References use_preset_task_.


Member Data Documentation

Referenced by min_bb(), and setup_packer_and_movemap().

Referenced by min_rb(), and setup_packer_and_movemap().

Referenced by min_sc(), and setup_packer_and_movemap().


The documentation for this class was generated from the following files:
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines