Rosetta Protocols  2014.35
Classes | Public Types | Public Member Functions | Static Public Member Functions | Private Types | Private Member Functions | Static Private Member Functions | Private Attributes | List of all members
protocols::forge::remodel::RemodelMover Class Reference

#include <RemodelMover.hh>

Classes

struct  instruction_flags
 

Public Types

typedef std::string String
 
typedef core::Real Real
 
typedef core::Size Size
 
typedef
core::pack::task::TaskFactoryOP 
TaskFactoryOP
 
typedef core::pose::Pose Pose
 
typedef
core::scoring::ScoreFunction 
ScoreFunction
 
typedef
core::scoring::ScoreFunctionOP 
ScoreFunctionOP
 
typedef
protocols::forge::build::BuildInstructionOP 
BuildInstructionOP
 
typedef
protocols::forge::build::BuildManager 
BuildManager
 
typedef
protocols::forge::build::BuildManager::Original2Modified 
Original2Modified
 
typedef
protocols::forge::build::Interval 
Interval
 
typedef protocols::moves::MoverOP MoverOP
 
typedef
protocols::forge::components::VarLengthBuildOP 
VarLengthBuildOP
 
typedef
protocols::forge::components::VarLengthBuild 
VarLengthBuild
 
typedef
protocols::forge::remodel::RemodelData 
RemodelData
 
typedef
protocols::forge::remodel::RemodelWorkingSet 
RemodelWorkingSet
 
typedef std::pair< Interval,
String
OriginalInterval2DesignString
 A pair storing a instruction's original interval and a string denoting the sequence during design. More...
 
typedef utility::vector1
< OriginalInterval2DesignString
DesignInfo
 
typedef utility::tag::TagCOP TagCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef basic::datacache::DataMap DataMap
 
typedef
protocols::moves::Movers_map 
Movers_map
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 

Public Member Functions

 RemodelMover ()
 default constructor More...
 
 RemodelMover (RemodelMover const &rval)
 copy constructor More...
 
virtual ~RemodelMover ()
 default destructor More...
 
virtual MoverOP clone () const
 clone this object, for parser More...
 
virtual MoverOP fresh_instance () const
 create this type of object, for parser More...
 
virtual MoverOP clone ()
 clone this object More...
 
virtual MoverOP fresh_instance ()
 create this type of object More...
 
ScoreFunction const & centroid_scorefunction () const
 the centroid level score function, default "remodel_cen" More...
 
ScoreFunction const & fullatom_scorefunction () const
 the full-atom level score function More...
 
void max_linear_chainbreak (Real const threshold)
 add instruction to the manager of this RemodelMover (no copy) More...
 
void centroid_loop_mover_str (String const &loop_mover_str)
 the loop mover string to use during centroid build More...
 
void redesign_loop_neighborhood (bool const flag)
 redesign the neighborhood around the loop? if false, then just repacks during the design phase More...
 
void dr_cycles (Size const cycles)
 set the number of design-refine cycles to perform More...
 
void centroid_scorefunction (ScoreFunction const &sfx)
 set the centroid level score function More...
 
void centroid_scorefunction (ScoreFunctionOP const &sfx)
 set the centroid level score function More...
 
void fullatom_scorefunction (ScoreFunction const &sfx)
 set the full-atom level score function More...
 
void fullatom_scorefunction (ScoreFunctionOP const &sfx)
 set the full-atom level score function More...
 
virtual void apply (Pose &pose)
 apply defined moves to given Pose More...
 
virtual std::string get_name () const
 get_name function for JobDistributor More...
 
bool confirm_sequence (core::pose::Pose &pose)
 As best as I can tell, does some loop closure and calculates RMSD to native. Returns true. NOTE: CURRENTLY ALWAYS RETURNS TRUE regardless of rmsd value, because this stage is not being used as a filter Checks the value of -remodelswap_refine_confirm_protocols. More...
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &, Movers_map const &, Pose const &)
 parse xml More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
void set_type (std::string const &setting)
 
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
 
void set_current_tag (std::string const &new_tag)
 
virtual void set_input_pose (PoseCOP pose)
 setter for poses contained for rms More...
 
virtual void set_native_pose (PoseCOP pose)
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
 
PoseCOP get_input_pose () const
 
PoseCOP get_native_pose () const
 
virtual void test_move (Pose &pose)
 : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
 
void type (const std::string &type_in)
 
std::string get_type () const
 
MoverStatus get_last_move_status () const
 end parser interface, start Job Distributor interface///////////// More...
 
void reset_status ()
 resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
 
virtual core::pose::PoseOP get_additional_output ()
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
 
virtual void clear_info ()
 Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
 
virtual Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool reinitialize_for_each_job () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
 
virtual bool reinitialize_for_new_input () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 

Static Public Member Functions

static String neighborhood_calc_name ()
 the name for the loops' neighborhood calculator More...
 
static String loops_buns_polar_calc_name ()
 the name for the loops' buried unsatisfied polars calculator More...
 
static String neighborhood_buns_polar_calc_name ()
 the name for the loops' neighborhood buried unsatisfied polars calculator More...
 
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
 
static void register_options ()
 Overload this static method if you access options within the mover. More...
 

Private Types

typedef protocols::moves::Mover Super
 

Private Member Functions

RemodelMoveroperator= (RemodelMover const &rval)
 copy assignment More...
 
bool SamePose (Pose const &pose1, Pose const &pose2)
 Apply method for Mover. Checks the values of the following options -remodelcheckpoint -remodel::domainFusion::insert_segment_from_pdb -remodelbypass_fragments, -remodelnum_trajectory, -remodelrepeat_structure -remodelbuild_disulf -remodelquick_and_dirty -remodeluse_pose_relax -remodelrun_confirmation -enzdescstfile -symmetrysymmetry_definition -runshow_simulation_in_pymol. More...
 
void register_user_options ()
 Checks for presence of any score term weight override options and calls set_weight on the centroid scorefunction. Note: options only get applied to centroid scorefunction - fullatom scorefunction left as is. More...
 
bool centroid_build (Pose &pose, protocols::forge::build::BuildManager &manager)
 Does the same as function below, but takes in a BuildManager object. Also checks the value of the option -remodelbypass_fragments. More...
 
bool centroid_build (Pose &pose)
 run the centroid level build stage More...
 
bool design_refine_seq_relax (Pose &pose, RemodelDesignMover &designMover)
 Sets up constraints and a modified scorefunction and run design/relax cycles. Checks the value of -remodel:repeat_structure. More...
 
bool design_refine_cart_relax (Pose &pose, RemodelDesignMover &designMover)
 
bool design_refine (Pose &pose, RemodelDesignMover &designMover)
 run the design-refine stage More...
 
TaskFactoryOP generic_taskfactory ()
 return a TaskFactory useable as a starting point for either design or refinement More...
 
void process_continuous_design_string (Interval const &original_interval, String const &design_str, Original2Modified const &original2modified_interval_endpoints, TaskFactoryOP design_tf)
 process a continuous design string, adding appropriate operations to the TaskFactory More...
 
void process_insert_design_string (Interval const &original_interval, String const &design_str, Original2Modified const &original2modified_interval_endpoints, TaskFactoryOP design_tf)
 process a design string containing an insert, adding appropriate operations to the TaskFactory More...
 
void set_param_from_options ()
 

Static Private Member Functions

static utility::vector1< bool >
const & 
allowed_surface_aa ()
 return a boolean vector specifying allowed a.a. when designing on the surface More...
 

Private Attributes

BuildManager manager_
 the BuildManager More...
 
Pose native_pose_
 
RemodelData remodel_data_
 holds all the blueprint info, contains build manager More...
 
RemodelWorkingSet working_model_
 working set holds all the modified index that is required for the remodeling task More...
 
DesignInfo design_info_
 Stores instructions' original interval and a string denoting the sequence during design. More...
 
Real max_linear_chainbreak_
 use sequence biased fragments when building the loop? (default false) bool use_sequence_bias_; More...
 
String centroid_loop_mover_str_
 the loop mover string to use during centroid build (default "RemodelLoopMover") More...
 
bool redesign_loop_neighborhood_
 redesign the neighborhood around the loop? if false, then just repacks during the design phase (default true) More...
 
Size dr_cycles_
 name of the resfile to use during design-refine; empty string implies no resfile String resfile_; More...
 
ScoreFunctionOP centroid_sfx_
 the centroid scorefunction to use, default "remodel_cen" More...
 
ScoreFunctionOP fullatom_sfx_
 the full-atom scorefunction to use More...
 
String blueprint_
 
bool rosetta_scripts_quick_and_dirty_
 
bool rosetta_scripts_build_disulfide_
 
bool rosetta_scripts_fast_disulfide_
 
bool rosetta_scripts_bypass_fragments_
 
core::Real rosetta_scripts_match_rt_limit_
 
Size rosetta_scripts_min_disulfides_
 
Size rosetta_scripts_max_disulfides_
 
bool rosetta_scripts_include_current_ds_
 
bool rosetta_scripts_keep_current_ds_
 
Size rosetta_scripts_min_loop_
 
bool rosetta_scripts_
 
core::pose::PoseOP last_input_pose_
 
forge::remodel::RemodelAccumulator accumulator_
 
VarLengthBuildOP vlb_
 VLB for centroid_build. More...
 

Additional Inherited Members

- Protected Member Functions inherited from protocols::moves::Mover
void set_last_move_status (MoverStatus status)
 nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...
 

Member Typedef Documentation

A pair storing a instruction's original interval and a string denoting the sequence during design.

Remarks
This is only for instructions such as SegmentRebuild or SegmentInsert. Non-applicable instructions will not have any data stored here.

Constructor & Destructor Documentation

protocols::forge::remodel::RemodelMover::RemodelMover ( )
protocols::forge::remodel::RemodelMover::RemodelMover ( RemodelMover const &  rval)

copy constructor

Copy constructor.

RemodelMover::RemodelMover( RemodelMover )

References clone(), utility::pointer::owning_ptr< T >::get(), and vlb_.

protocols::forge::remodel::RemodelMover::~RemodelMover ( )
virtual

default destructor

Default destructor. Does this need to free the VarLengthBuild memory?

RemodelMover::~RemodelMover

Member Function Documentation

utility::vector1< bool > const & protocols::forge::remodel::RemodelMover::allowed_surface_aa ( )
staticprivate

return a boolean vector specifying allowed a.a. when designing on the surface

RemodelMover::process_insert_design_string

References core::chemical::aa_from_oneletter_code(), and aa_from_oneletter_code().

Referenced by process_continuous_design_string(), and process_insert_design_string().

void protocols::forge::remodel::RemodelMover::apply ( Pose pose)
virtual

apply defined moves to given Pose

Implements protocols::moves::Mover.

References accumulator_, protocols::viewer::add_conformation_viewer(), protocols::simple_moves::symmetry::SetupNCSMover::add_group(), add_lower_terminus_type_to_pose_residue(), protocols::moves::AddPyMolObserver(), protocols::forge::remodel::RemodelGlobalFrame::align_segment(), protocols::simple_filters::ScoreTypeFilter::apply(), protocols::simple_moves::symmetry::SetupForSymmetryMover::apply(), protocols::forge::remodel::RemodelAccumulator::apply(), protocols::simple_moves::symmetry::SetupNCSMover::apply(), protocols::forge::remodel::RemodelGlobalFrame::apply(), protocols::forge::remodel::RemodelDesignMover::apply(), protocols::simple_moves::MinMover::apply(), core::scoring::atom_pair_constraint, atom_pair_constraint, protocols::forge::remodel::RemodelData::blueprint, blueprint_, core::scoring::cart_bonded_angle, core::scoring::cart_bonded_length, core::scoring::cart_bonded_torsion, core::scoring::cen_hb, core::chemical::CENTROID, centroid_build(), centroid_sfx_, chemical, protocols::forge::remodel::RemodelAccumulator::clear(), protocols::forge::remodel::RemodelAccumulator::cluster_switch(), protocols::forge::remodel::RemodelAccumulator::clustered_best_poses(), protocols::forge::remodel::RemodelData::collectInsertionPose(), protocols::simple_filters::ScoreTypeFilter::compute(), confirm_sequence(), core::pose::Pose::conformation(), protocols::forge::remodel::RemodelAccumulator::contents_in_pose_store(), core::scoring::coordinate_constraint, core::conformation::ResidueFactory::create_residue(), core::id::D, core::conformation::Conformation::delete_residue_slow(), design_refine(), design_refine_cart_relax(), design_refine_seq_relax(), core::scoring::dihedral_constraint, protocols::simple_filters::dssp(), core::scoring::dssp::Dssp::dssp_reduced(), protocols::forge::build::BuildManager::dummy_modify(), end, protocols::moves::FAIL_DO_NOT_RETRY, protocols::moves::FAIL_RETRY, protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), core::pose::Pose::fold_tree(), fullatom_sfx_, core::kinematics::MoveMap::get_bb(), protocols::toolbox::match_enzdes_util::get_enzdes_observer(), protocols::forge::remodel::RemodelData::getLoopsToBuildFromBlueprint(), protocols::forge::remodel::RemodelData::getLoopsToBuildFromFile(), core::scoring::hbond_lr_bb, core::scoring::hbond_sr_bb, core::kinematics::MoveMap::import(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), core::scoring::dssp::Dssp::insert_ss_into_pose(), last_input_pose_, loops_buns_polar_calc_name(), protocols::forge::remodel::RemodelDesignMover::make_disulfide(), protocols::forge::remodel::RemodelDesignMover::make_disulfide_fast(), protocols::forge::remodel::RemodelWorkingSet::manager, manager_, match_rt_limit, core::pose::Pose::metric(), protocols::forge::build::BuildManager::modify(), protocols::forge::build::BuildManager::movemap(), protocols::moves::MS_SUCCESS, core::pose::Pose::n_residue(), core::chemical::ResidueTypeSet::name_map(), native_pose_, protocols::forge::remodel::RemodelData::natro_movemap_, neighborhood_buns_polar_calc_name(), neighborhood_calc_name(), core::conformation::Residue::nheavyatoms(), num_traj, core::pose::Pose::observer_cache(), core::pose::Pose::omega(), core::scoring::omega, option, core::pose::Pose::pdb_info(), core::pose::Pose::phi(), protocols::forge::remodel::RemodelAccumulator::pop(), prefix, core::pose::Pose::psi(), protocols::forge::remodel::RemodelAccumulator::recover_checkpoint(), protocols::forge::remodel::recursive_multiple_disulfide_former(), remodel_data_, core::pose::Pose::remove_constraints(), core::pose::renumber_pdbinfo_based_on_conf_chains(), core::kinematics::FoldTree::reorder(), replace_pose_residue_copying_existing_coordinates(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::conformation::Residue::residue_type_set(), rosetta_scripts_, rosetta_scripts_build_disulfide_, rosetta_scripts_bypass_fragments_, rosetta_scripts_fast_disulfide_, rosetta_scripts_include_current_ds_, rosetta_scripts_keep_current_ds_, rosetta_scripts_match_rt_limit_, rosetta_scripts_max_disulfides_, rosetta_scripts_min_disulfides_, rosetta_scripts_min_loop_, rosetta_scripts_quick_and_dirty_, protocols::forge::remodel::RemodelWorkingSet::safe_root_, core::conformation::Conformation::safely_append_polymer_residue_after_seqpos(), SamePose(), score, protocols::forge::remodel::RemodelDesignMover::scorefunction(), core::pose::Pose::secstruct(), protocols::forge::remodel::RemodelData::sequence, core::pose::datacache::ObserverCache::set(), core::kinematics::MoveMap::set(), protocols::moves::Mover::set_last_move_status(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_secstruct(), protocols::forge::remodel::RemodelDesignMover::set_state(), protocols::forge::remodel::RemodelAccumulator::size(), protocols::forge::build::BuildManager::size(), core::util::switch_to_residue_type_set(), core::id::THETA, core::pose::Pose::total_residue(), total_score, protocols::forge::remodel::TR, protocols::forge::build::BuildManager::union_of_intervals_containing_undefined_positions(), protocols::forge::remodel::RemodelData::updateWithDsspAssignment(), user, working_model_, protocols::forge::remodel::RemodelWorkingSet::workingSetGen(), and protocols::forge::remodel::RemodelAccumulator::write_checkpoint().

bool protocols::forge::remodel::RemodelMover::centroid_build ( Pose pose,
protocols::forge::build::BuildManager manager 
)
private

Does the same as function below, but takes in a BuildManager object. Also checks the value of the option -remodelbypass_fragments.

RemodelMover::centroid_build

References manager_, option, rosetta_scripts_bypass_fragments_, rosetta_scripts_fast_disulfide_, and protocols::forge::remodel::TR.

Referenced by apply().

bool protocols::forge::remodel::RemodelMover::centroid_build ( Pose pose)
private
void protocols::forge::remodel::RemodelMover::centroid_loop_mover_str ( String const &  loop_mover_str)
inline

the loop mover string to use during centroid build

Remarks
set to either a string the create_loop_mover() LoopMoverFactory recognizes or the "RemodelLoopMover"

References centroid_loop_mover_str_.

ScoreFunction const & protocols::forge::remodel::RemodelMover::centroid_scorefunction ( ) const

the centroid level score function, default "remodel_cen"

References centroid_sfx_.

void protocols::forge::remodel::RemodelMover::centroid_scorefunction ( ScoreFunction const &  sfx)

set the centroid level score function

References centroid_sfx_, and core::scoring::ScoreFunction::clone().

void protocols::forge::remodel::RemodelMover::centroid_scorefunction ( ScoreFunctionOP const &  sfx)

set the centroid level score function

References centroid_sfx_, and core::scoring::ScoreFunction::clone().

RemodelMover::MoverOP protocols::forge::remodel::RemodelMover::clone ( ) const
virtual

clone this object, for parser

clone for parser

Reimplemented from protocols::moves::Mover.

References RemodelMover().

RemodelMover::MoverOP protocols::forge::remodel::RemodelMover::clone ( )
virtual

clone this object

References RemodelMover().

bool protocols::forge::remodel::RemodelMover::confirm_sequence ( core::pose::Pose pose)

As best as I can tell, does some loop closure and calculates RMSD to native. Returns true. NOTE: CURRENTLY ALWAYS RETURNS TRUE regardless of rmsd value, because this stage is not being used as a filter Checks the value of -remodelswap_refine_confirm_protocols.

RemodelMover::confirm_sequence

References protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), end, protocols::loops::loop_mover::LoopMover::false_movemap(), core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), fullatom_sfx_, generic_taskfactory(), core::kinematics::MoveMap::import(), protocols::forge::build::BuildManager::intervals_containing_undefined_positions(), protocols::forge::methods::intervals_to_confirmation_loops(), core::conformation::Residue::is_DNA(), protocols::loops::loop_mover::KIC(), manager_, protocols::forge::build::BuildManager::movemap(), native_pose_, protocols::forge::remodel::RemodelData::natro_movemap_, neighborhood_calc_name(), option, core::pose::Pose::pdb_info(), core::pack::task::TaskFactory::push_back(), refine, remodel_data_, core::pose::Pose::residue(), rmsd, core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_task_factory(), utility::to_string(), core::pose::Pose::total_residue(), protocols::forge::remodel::TR, user, core::pose::RemarkInfo::value, and core::conformation::Residue::xyz().

Referenced by apply().

bool protocols::forge::remodel::RemodelMover::design_refine ( Pose pose,
RemodelDesignMover designMover 
)
private

run the design-refine stage

Run the design-refine stage. Checks the value of -remodel:repeat_structure and -remodel:swap_refine_confirm_protocols NOTE: CURRENTLY ALWAYS RETURNS TRUE regardless of if chain breaks test passes or fails.

Returns
currently always true

RemodelMover::design_refine

References protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::forge::remodel::RemodelDesignMover::apply(), core::scoring::atom_pair_constraint, c, core::scoring::Energies::clear(), core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, dr_cycles_, core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), protocols::loops::loop_mover::LoopMover::false_movemap(), core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), generic_taskfactory(), core::kinematics::MoveMap::get_chi(), core::scoring::get_score_function(), core::kinematics::MoveMap::import(), protocols::forge::build::BuildManager::intervals_containing_undefined_positions(), protocols::forge::methods::intervals_to_loops(), core::conformation::Residue::is_DNA(), protocols::loops::loop_mover::KIC(), l, protocols::forge::methods::linear_chainbreak(), loops, manager_, max_linear_chainbreak_, protocols::forge::build::BuildManager::movemap(), protocols::forge::remodel::RemodelData::natro_movemap_, neighborhood_calc_name(), option, protocols::forge::build::BuildManager::original2modified_interval_endpoints(), refine, remodel_data_, protocols::loops::remove_cutpoint_variants(), core::pose::Pose::residue(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), protocols::forge::remodel::RemodelDesignMover::set_state(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_task_factory(), core::pose::Pose::total_residue(), protocols::forge::remodel::TR, and user.

Referenced by apply().

bool protocols::forge::remodel::RemodelMover::design_refine_cart_relax ( Pose pose,
RemodelDesignMover designMover 
)
private
bool protocols::forge::remodel::RemodelMover::design_refine_seq_relax ( Pose pose,
RemodelDesignMover designMover 
)
private
void protocols::forge::remodel::RemodelMover::dr_cycles ( Size const  cycles)
inline

set the number of design-refine cycles to perform

Remarks
set this to 0 to skip design-refine

References dr_cycles_.

RemodelMover::MoverOP protocols::forge::remodel::RemodelMover::fresh_instance ( ) const
virtual

create this type of object, for parser

fresh instance for parser

Reimplemented from protocols::moves::Mover.

References RemodelMover().

RemodelMover::MoverOP protocols::forge::remodel::RemodelMover::fresh_instance ( )
virtual

create this type of object

References RemodelMover().

ScoreFunction const & protocols::forge::remodel::RemodelMover::fullatom_scorefunction ( ) const

the full-atom level score function

References fullatom_sfx_.

void protocols::forge::remodel::RemodelMover::fullatom_scorefunction ( ScoreFunction const &  sfx)

set the full-atom level score function

References core::scoring::ScoreFunction::clone(), and fullatom_sfx_.

void protocols::forge::remodel::RemodelMover::fullatom_scorefunction ( ScoreFunctionOP const &  sfx)

set the full-atom level score function

References core::scoring::ScoreFunction::clone(), and fullatom_sfx_.

RemodelMover::TaskFactoryOP protocols::forge::remodel::RemodelMover::generic_taskfactory ( )
private

return a TaskFactory useable as a starting point for either design or refinement

Returns a TaskFactory useable as a starting point for either design or refinement. Only adds the NoRepackDisulfides, IncludeCurrent, and Init from command line ops. ReadResfile is not included.

RemodelMover::generic_taskfactory

References option, and user.

Referenced by confirm_sequence(), and design_refine().

std::string protocols::forge::remodel::RemodelMover::get_name ( ) const
virtual

get_name function for JobDistributor

Implements protocols::moves::Mover.

static String protocols::forge::remodel::RemodelMover::loops_buns_polar_calc_name ( )
inlinestatic

the name for the loops' buried unsatisfied polars calculator

Referenced by apply().

void protocols::forge::remodel::RemodelMover::max_linear_chainbreak ( Real const  threshold)
inline

add instruction to the manager of this RemodelMover (no copy)

Parameters
[in]biBuildInstruction
[in]aa_during_design_refineThe allowed amino acid sequence during design. Only applicable to BuildInstructions like SegmentRebuild and SegmentInsert. Make sure the length of this string matches up properly, and remember to use any special characters, e.g. the insertion character for SegmentInsert the maximum allowed linear chainbreak

References max_linear_chainbreak_.

static String protocols::forge::remodel::RemodelMover::neighborhood_buns_polar_calc_name ( )
inlinestatic

the name for the loops' neighborhood buried unsatisfied polars calculator

Referenced by apply().

static String protocols::forge::remodel::RemodelMover::neighborhood_calc_name ( )
inlinestatic

the name for the loops' neighborhood calculator

Referenced by apply(), confirm_sequence(), and design_refine().

RemodelMover& protocols::forge::remodel::RemodelMover::operator= ( RemodelMover const &  rval)
private

copy assignment

Remarks
Mover base class prevents this from working properly...
void protocols::forge::remodel::RemodelMover::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap data,
Filters_map const &  ,
Movers_map const &  ,
Pose const &   
)
virtual
void protocols::forge::remodel::RemodelMover::process_continuous_design_string ( Interval const &  original_interval,
String const &  design_str,
Original2Modified const &  original2modified_interval_endpoints,
TaskFactoryOP  design_tf 
)
private

process a continuous design string, adding appropriate operations to the TaskFactory

RemodelMover::process_continuous_design_string

References allowed_surface_aa(), protocols::forge::build::Interval::left, and core::pack::task::TaskFactory::push_back().

void protocols::forge::remodel::RemodelMover::process_insert_design_string ( Interval const &  original_interval,
String const &  design_str,
Original2Modified const &  original2modified_interval_endpoints,
TaskFactoryOP  design_tf 
)
private
void protocols::forge::remodel::RemodelMover::redesign_loop_neighborhood ( bool const  flag)
inline

redesign the neighborhood around the loop? if false, then just repacks during the design phase

References redesign_loop_neighborhood_.

void protocols::forge::remodel::RemodelMover::register_user_options ( )
private

Checks for presence of any score term weight override options and calls set_weight on the centroid scorefunction. Note: options only get applied to centroid scorefunction - fullatom scorefunction left as is.

RemodelMover::register_user_options

References cbeta, cenpack, centroid_sfx_, hbond_lr_bb, hbond_sr_bb, option, rama, protocols::simple_moves::rg, rg_local, rsigma, ss_pair, protocols::forge::remodel::TR, user, and vdw.

Referenced by RemodelMover().

bool protocols::forge::remodel::RemodelMover::SamePose ( Pose const &  pose1,
Pose const &  pose2 
)
private

Apply method for Mover. Checks the values of the following options -remodelcheckpoint -remodel::domainFusion::insert_segment_from_pdb -remodelbypass_fragments, -remodelnum_trajectory, -remodelrepeat_structure -remodelbuild_disulf -remodelquick_and_dirty -remodeluse_pose_relax -remodelrun_confirmation -enzdescstfile -symmetrysymmetry_definition -runshow_simulation_in_pymol.

RemodelMover::apply

References core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), and core::pose::Pose::total_residue().

Referenced by apply().

void protocols::forge::remodel::RemodelMover::set_param_from_options ( )
private

Member Data Documentation

forge::remodel::RemodelAccumulator protocols::forge::remodel::RemodelMover::accumulator_
private

Referenced by apply().

String protocols::forge::remodel::RemodelMover::blueprint_
private

Referenced by apply(), parse_my_tag(), and RemodelMover().

String protocols::forge::remodel::RemodelMover::centroid_loop_mover_str_
private

the loop mover string to use during centroid build (default "RemodelLoopMover")

Remarks
set to either a string the create_loop_mover() LoopMoverFactory recognizes or the "RemodelLoopMover"

Referenced by centroid_build(), centroid_loop_mover_str(), and RemodelMover().

ScoreFunctionOP protocols::forge::remodel::RemodelMover::centroid_sfx_
private

the centroid scorefunction to use, default "remodel_cen"

Referenced by apply(), centroid_build(), centroid_scorefunction(), register_user_options(), and RemodelMover().

DesignInfo protocols::forge::remodel::RemodelMover::design_info_
private

Stores instructions' original interval and a string denoting the sequence during design.

Remarks
This is only for instructions such as SegmentRebuild or SegmentInsert. Non-applicable instructions will not have any data stored here.
Size protocols::forge::remodel::RemodelMover::dr_cycles_
private

name of the resfile to use during design-refine; empty string implies no resfile String resfile_;

the number of design-refine cycles to perform, default 3

Referenced by design_refine(), design_refine_cart_relax(), design_refine_seq_relax(), dr_cycles(), and RemodelMover().

ScoreFunctionOP protocols::forge::remodel::RemodelMover::fullatom_sfx_
private

the full-atom scorefunction to use

Referenced by apply(), confirm_sequence(), fullatom_scorefunction(), and RemodelMover().

core::pose::PoseOP protocols::forge::remodel::RemodelMover::last_input_pose_
private

Referenced by apply(), and RemodelMover().

BuildManager protocols::forge::remodel::RemodelMover::manager_
private
Real protocols::forge::remodel::RemodelMover::max_linear_chainbreak_
private

use sequence biased fragments when building the loop? (default false) bool use_sequence_bias_;

the maximum allowed linear chainbreak (default 0.07)

Referenced by centroid_build(), design_refine(), max_linear_chainbreak(), and RemodelMover().

Pose protocols::forge::remodel::RemodelMover::native_pose_
private

Referenced by apply(), and confirm_sequence().

bool protocols::forge::remodel::RemodelMover::redesign_loop_neighborhood_
private

redesign the neighborhood around the loop? if false, then just repacks during the design phase (default true)

Referenced by redesign_loop_neighborhood(), and RemodelMover().

RemodelData protocols::forge::remodel::RemodelMover::remodel_data_
private

holds all the blueprint info, contains build manager

Referenced by apply(), centroid_build(), confirm_sequence(), design_refine(), and design_refine_cart_relax().

bool protocols::forge::remodel::RemodelMover::rosetta_scripts_
private

Referenced by apply(), parse_my_tag(), and RemodelMover().

bool protocols::forge::remodel::RemodelMover::rosetta_scripts_build_disulfide_
private

Referenced by apply(), parse_my_tag(), and RemodelMover().

bool protocols::forge::remodel::RemodelMover::rosetta_scripts_bypass_fragments_
private
bool protocols::forge::remodel::RemodelMover::rosetta_scripts_fast_disulfide_
private
bool protocols::forge::remodel::RemodelMover::rosetta_scripts_include_current_ds_
private

Referenced by apply(), parse_my_tag(), and RemodelMover().

bool protocols::forge::remodel::RemodelMover::rosetta_scripts_keep_current_ds_
private

Referenced by apply(), parse_my_tag(), and RemodelMover().

core::Real protocols::forge::remodel::RemodelMover::rosetta_scripts_match_rt_limit_
private

Referenced by apply(), parse_my_tag(), and RemodelMover().

Size protocols::forge::remodel::RemodelMover::rosetta_scripts_max_disulfides_
private

Referenced by apply(), parse_my_tag(), and RemodelMover().

Size protocols::forge::remodel::RemodelMover::rosetta_scripts_min_disulfides_
private

Referenced by apply(), parse_my_tag(), and RemodelMover().

Size protocols::forge::remodel::RemodelMover::rosetta_scripts_min_loop_
private

Referenced by apply(), parse_my_tag(), and RemodelMover().

bool protocols::forge::remodel::RemodelMover::rosetta_scripts_quick_and_dirty_
private

Referenced by apply(), parse_my_tag(), and RemodelMover().

VarLengthBuildOP protocols::forge::remodel::RemodelMover::vlb_
private

VLB for centroid_build.

Remarks
Store it here instead of re-instantiation each centroid_build() call so fragment caching works.
Warning
Remember to set this to null if the BuildManager changes.

Referenced by centroid_build(), and RemodelMover().

RemodelWorkingSet protocols::forge::remodel::RemodelMover::working_model_
private

working set holds all the modified index that is required for the remodeling task

Referenced by apply(), and centroid_build().


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