Rosetta 3.4
Classes | Public Types | Public Member Functions | Static Public Member Functions
protocols::forge::remodel::RemodelMover Class Reference

#include <RemodelMover.hh>

Inheritance diagram for protocols::forge::remodel::RemodelMover:
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List of all members.

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::WorkingRemodelSet 
RemodelWorkingSet
typedef std::pair< Interval,
String
OriginalInterval2DesignString
 A pair storing a instruction's original interval and a string denoting the sequence during design.
typedef utility::vector1
< OriginalInterval2DesignString
DesignInfo
typedef utility::tag::TagPtr TagPtr
typedef
protocols::filters::Filters_map 
Filters_map
typedef protocols::moves::DataMap DataMap
typedef
protocols::moves::Movers_map 
Movers_map

Public Member Functions

 RemodelMover ()
 default constructor
 RemodelMover (RemodelMover const &rval)
 copy constructor
virtual ~RemodelMover ()
 default destructor
virtual MoverOP clone () const
 clone this object, for parser
virtual MoverOP fresh_instance () const
 create this type of object, for parser
virtual MoverOP clone ()
 clone this object
virtual MoverOP fresh_instance ()
 create this type of object
ScoreFunction const & centroid_scorefunction () const
 the centroid level score function, default "remodel_cen"
ScoreFunction const & fullatom_scorefunction () const
 the full-atom level score function, default score12
void max_linear_chainbreak (Real const threshold)
 add instruction to the manager of this RemodelMover (no copy)
void centroid_loop_mover_str (String const &loop_mover_str)
 the loop mover string to use during centroid build
void redesign_loop_neighborhood (bool const flag)
 redesign the neighborhood around the loop? if false, then just repacks during the design phase
void dr_cycles (Size const cycles)
 set the number of design-refine cycles to perform
void centroid_scorefunction (ScoreFunction const &sfx)
 set the centroid level score function
void centroid_scorefunction (ScoreFunctionOP const &sfx)
 set the centroid level score function
void fullatom_scorefunction (ScoreFunction const &sfx)
 set the full-atom level score function
void fullatom_scorefunction (ScoreFunctionOP const &sfx)
 set the full-atom level score function
virtual void apply (Pose &pose)
 apply defined moves to given Pose
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
bool confirm_sequence (core::pose::Pose &pose)
virtual void parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &, Movers_map const &, Pose const &)
 parse xml

Static Public Member Functions

static String neighborhood_calc_name ()
 the name for the loops' neighborhood calculator
static String loops_buns_polar_calc_name ()
 the name for the loops' buried unsatisfied polars calculator
static String neighborhood_buns_polar_calc_name ()
 the name for the loops' neighborhood buried unsatisfied polars calculator

Member Typedef Documentation

Reimplemented from protocols::moves::Mover.

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.

Reimplemented from protocols::moves::Mover.

Reimplemented from protocols::moves::Mover.


Constructor & Destructor Documentation

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

copy constructor

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

default destructor


Member Function Documentation

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

apply defined moves to given Pose

Implements protocols::moves::Mover.

References protocols::viewer::add_conformation_viewer(), protocols::simple_moves::symmetry::SetupNCSMover::add_group(), protocols::simple_moves::symmetry::SetupNCSMover::apply(), protocols::forge::remodel::RemodelAccumulator::apply(), protocols::simple_filters::ScoreTypeFilter::apply(), protocols::forge::remodel::RemodelDesignMover::apply(), protocols::simple_moves::symmetry::SetupForSymmetryMover::apply(), core::scoring::atom_pair_constraint, core::scoring::cen_hb, core::chemical::CENTROID, protocols::forge::remodel::RemodelAccumulator::cluster_switch(), protocols::forge::remodel::RemodelAccumulator::clustered_best_poses(), protocols::simple_filters::ScoreTypeFilter::compute(), confirm_sequence(), core::pose::Pose::conformation(), protocols::forge::remodel::RemodelAccumulator::contents_in_pose_store(), core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::dihedral_constraint, core::sequence::end, core::pose::datacache::CacheableObserverType::ENZDES_OBSERVER, core::chemical::FA_STANDARD, protocols::moves::FAIL_DO_NOT_RETRY, protocols::moves::FAIL_RETRY, protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), core::pose::Pose::fold_tree(), protocols::toolbox::match_enzdes_util::get_enzdes_observer(), core::scoring::hbond_lr_bb, core::scoring::hbond_sr_bb, loops_buns_polar_calc_name(), protocols::forge::remodel::RemodelDesignMover::make_disulfide(), core::pose::Pose::metric(), protocols::moves::MS_SUCCESS, core::pose::Pose::n_residue(), neighborhood_buns_polar_calc_name(), neighborhood_calc_name(), core::pose::Pose::observer_cache(), core::pose::Pose::omega(), core::pose::Pose::pdb_info(), core::pose::Pose::phi(), core::pose::Pose::psi(), protocols::forge::remodel::RemodelAccumulator::recover_checkpoint(), core::pose::Pose::remove_constraints(), core::pose::renumber_pdbinfo_based_on_conf_chains(), core::scoring::res_type_constraint, core::scoring::res_type_linking_constraint, core::scoring::SCORE12_PATCH, protocols::forge::remodel::RemodelDesignMover::scorefunction(), protocols::moves::Mover::set_last_move_status(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::forge::remodel::RemodelDesignMover::set_state(), core::scoring::STANDARD_WTS, core::util::switch_to_residue_type_set(), core::pose::Pose::total_residue(), core::scoring::total_score, protocols::forge::remodel::TR(), and protocols::forge::remodel::RemodelAccumulator::write_checkpoint().

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

the centroid level score function, default "remodel_cen"

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

set the centroid level score function

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. Default empty string. create directed dependency between two instructions set the centroid level score function

References core::scoring::ScoreFunction::clone().

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

set the centroid level score function

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

create this type of object

References RemodelMover().

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

the full-atom level score function, default score12

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

set the full-atom level score function

References core::scoring::ScoreFunction::clone().

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

set the full-atom level score function

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

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

Implements protocols::moves::Mover.

static String protocols::forge::remodel::RemodelMover::loops_buns_polar_calc_name ( ) [inline, static]

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
static String protocols::forge::remodel::RemodelMover::neighborhood_buns_polar_calc_name ( ) [inline, static]

the name for the loops' neighborhood buried unsatisfied polars calculator

Referenced by apply().

static String protocols::forge::remodel::RemodelMover::neighborhood_calc_name ( ) [inline, static]

the name for the loops' neighborhood calculator

Referenced by apply(), and confirm_sequence().

void protocols::forge::remodel::RemodelMover::parse_my_tag ( TagPtr const  tag,
DataMap data,
Filters_map const &  ,
Movers_map const &  ,
Pose const &  pose 
) [virtual]

parse xml

Reimplemented from protocols::moves::Mover.

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


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