Rosetta 3.4
Public Types | Public Member Functions | Static Public Member Functions
protocols::flxbb::FlxbbDesign Class Reference

#include <FlxbbDesign.hh>

Inheritance diagram for protocols::flxbb::FlxbbDesign:
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Collaboration diagram for protocols::flxbb::FlxbbDesign:
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List of all members.

Public Types

typedef protocols::moves::Mover Super
typedef std::string String
typedef core::Size Size
typedef core::Real Real
typedef core::kinematics::MoveMapOP MoveMapOP
typedef core::pose::Pose Pose
typedef
core::scoring::ScoreFunction 
ScoreFunction
typedef
core::scoring::ScoreFunctionOP 
ScoreFunctionOP
typedef
core::pack::task::operation::TaskOperation 
TaskOperation
typedef
core::pack::task::operation::TaskOperationOP 
TaskOperationOP
typedef protocols::moves::MoverOP MoverOP
typedef
protocols::jd2::parser::BluePrint 
BluePrint
typedef
protocols::jd2::parser::BluePrintOP 
BluePrintOP
typedef
protocols::flxbb::DesignTaskOP 
DesignTaskOP
typedef
protocols::flxbb::DesignTaskSet 
DesignTaskSet
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

 FlxbbDesign ()
 default constructor
 FlxbbDesign (ScoreFunctionOP const sfxnd, ScoreFunctionOP const sfxnr, Size const ncycle=3, String const layer_mode="", bool const use_origseq_for_not_dsgned_layer=true, bool const no_relax=false)
 value constructor
 FlxbbDesign (FlxbbDesign const &rval)
 copy constructor
virtual ~FlxbbDesign ()
 destructor
virtual MoverOP clone () const
 clone this object
virtual MoverOP fresh_instance () const
 create this type of object
void read_options ()
 read parameters
void initialize_filter (Size const filter_trial, String const &filter_type)
 initialize filter parameters
virtual void apply (Pose &pose)
 mover apply
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
void set_scorefxn_design (ScoreFunctionOP const scorefxn)
 set the score function for fixbb design
void set_scorefxn_relax (ScoreFunctionOP const scorefxn)
 set the score function for relax
void set_ncycles (Size const ncycles)
 the number of cycles of fixbb and relax
void set_layer_mode (String const &layer_mode)
 set layer mode
void use_origseq_for_not_dsgned_layer (bool const use)
 use original sequence for not designed region in layer_mode, otherwise the residues of the region turned into Ala ( default true )
void no_relax (bool const no_relax)
 relax is not performed after design (default false)
void no_design (bool const no_design)
 design protocol will not be performed (default false)
void set_blueprint (BluePrintOP const blueprint)
 set BluePrintOP
void set_weight_constraints_sheet (Real const value)
 set weight of constraints_sheet which constrains between Ca atoms in beta-sheets if this weight > 0.0, the constraints is applied ( default = -1.0 )
void set_weight_constraints_NtoC (Real const value)
 set weight of constraints_NtoC which constrain between Ca atoms of C- and N-terminal if this weight > 0.0, the constraints is applied ( default = -1.0 )
void movemap_from_blueprint (bool const value)
 set movemap for relax
void set_movemap (MoveMapOP const movemap)
 set movemap for relax
void set_design_taskset (DesignTaskSet const &design_taskset)
 set DesignTaskSet Once you set DesignTaskSet, this controls almost every setups of this class
void add_design_task (DesignTaskOP const design_task)
 add the design task which cotrols the iteration of fixbb design and relax
void set_filter_during_design (FilterStructsOP const filter_during_design)
 filtering during design
void clear_design_taskset ()
 clear DesignTaskSet
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 void register_options ()
 register options

Member Typedef Documentation

Reimplemented from protocols::moves::Mover.

Reimplemented from protocols::moves::Mover.

typedef utility::tag::TagPtr protocols::flxbb::FlxbbDesign::TagPtr

Reimplemented from protocols::moves::Mover.


Constructor & Destructor Documentation

protocols::flxbb::FlxbbDesign::FlxbbDesign ( )

default constructor

References read_options().

Referenced by clone(), and fresh_instance().

protocols::flxbb::FlxbbDesign::FlxbbDesign ( ScoreFunctionOP const  sfxnd,
ScoreFunctionOP const  sfxnr,
Size const  ncycle = 3,
String const  layer_mode = "",
bool const  use_origseq_for_not_dsgned_layer = true,
bool const  no_relax = false 
)

value constructor

References read_options().

protocols::flxbb::FlxbbDesign::FlxbbDesign ( FlxbbDesign const &  rval)

copy constructor

protocols::flxbb::FlxbbDesign::~FlxbbDesign ( ) [virtual]

destructor


Member Function Documentation

void protocols::flxbb::FlxbbDesign::add_design_task ( DesignTaskOP const  design_task)

add the design task which cotrols the iteration of fixbb design and relax

set DesignTask

void protocols::flxbb::FlxbbDesign::apply ( pose::Pose pose) [virtual]
void protocols::flxbb::FlxbbDesign::clear_design_taskset ( )

clear DesignTaskSet

FlxbbDesign::MoverOP protocols::flxbb::FlxbbDesign::clone ( ) const [virtual]

clone this object

Reimplemented from protocols::moves::Mover.

References FlxbbDesign().

FlxbbDesign::MoverOP protocols::flxbb::FlxbbDesign::fresh_instance ( ) const [virtual]

create this type of object

Reimplemented from protocols::moves::Mover.

References FlxbbDesign().

std::string protocols::flxbb::FlxbbDesign::get_name ( ) const [virtual]

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

Implements protocols::moves::Mover.

References protocols::flxbb::FlxbbDesignCreator::mover_name().

void protocols::flxbb::FlxbbDesign::initialize_filter ( Size const  filter_trial,
String const &  filter_type 
)

initialize filter parameters

References protocols::TR().

Referenced by parse_my_tag(), and read_options().

void protocols::flxbb::FlxbbDesign::movemap_from_blueprint ( bool const  value)

set movemap for relax

void protocols::flxbb::FlxbbDesign::no_design ( bool const  no_design)

design protocol will not be performed (default false)

void protocols::flxbb::FlxbbDesign::no_relax ( bool const  no_relax)

relax is not performed after design (default false)

void protocols::flxbb::FlxbbDesign::parse_my_tag ( TagPtr const  tag,
DataMap data,
Filters_map const &  ,
Movers_map const &  ,
Pose const &  pose 
) [virtual]
void protocols::flxbb::FlxbbDesign::read_options ( )
void protocols::flxbb::FlxbbDesign::register_options ( ) [static]

register options

registering of options that are relevant for FlxbbDesign

Reimplemented from protocols::moves::Mover.

References protocols::flxbb::constraints_NtoC(), and protocols::flxbb::constraints_sheet().

void protocols::flxbb::FlxbbDesign::set_blueprint ( BluePrintOP const  blueprint)

set BluePrintOP

set BlueprintOP

void protocols::flxbb::FlxbbDesign::set_design_taskset ( DesignTaskSet const &  design_taskset)

set DesignTaskSet Once you set DesignTaskSet, this controls almost every setups of this class

clear DesignTaskSet

void protocols::flxbb::FlxbbDesign::set_filter_during_design ( FilterStructsOP const  filter_during_design)

filtering during design

void protocols::flxbb::FlxbbDesign::set_layer_mode ( String const &  layer_mode)

set layer mode

void protocols::flxbb::FlxbbDesign::set_movemap ( MoveMapOP const  movemap)

set movemap for relax

void protocols::flxbb::FlxbbDesign::set_ncycles ( Size const  ncycles)

the number of cycles of fixbb and relax

void protocols::flxbb::FlxbbDesign::set_scorefxn_design ( ScoreFunctionOP const  scorefxn)

set the score function for fixbb design

set scorefxn for fixbb design

void protocols::flxbb::FlxbbDesign::set_scorefxn_relax ( ScoreFunctionOP const  scorefxn)

set the score function for relax

set scorefxn for relax

void protocols::flxbb::FlxbbDesign::set_weight_constraints_NtoC ( Real const  value)

set weight of constraints_NtoC which constrain between Ca atoms of C- and N-terminal if this weight > 0.0, the constraints is applied ( default = -1.0 )

void protocols::flxbb::FlxbbDesign::set_weight_constraints_sheet ( Real const  value)

set weight of constraints_sheet which constrains between Ca atoms in beta-sheets if this weight > 0.0, the constraints is applied ( default = -1.0 )

void protocols::flxbb::FlxbbDesign::use_origseq_for_not_dsgned_layer ( bool const  use)

use original sequence for not designed region in layer_mode, otherwise the residues of the region turned into Ala ( default true )


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