Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Types | Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::flxbb::FlxbbDesign Class Reference

#include <FlxbbDesign.hh>

Inheritance diagram for protocols::flxbb::FlxbbDesign:
Inheritance graph
[legend]

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::parser::BluePrint 
BluePrint
 
typedef
protocols::parser::BluePrintOP 
BluePrintOP
 
typedef
protocols::flxbb::DesignTaskOP 
DesignTaskOP
 
typedef
protocols::flxbb::DesignTaskSet 
DesignTaskSet
 
typedef utility::tag::TagCOP TagCOP
 
typedef basic::datacache::DataMap DataMap
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef std::list< std::string > Strings
 

Public Member Functions

 FlxbbDesign ()
 default constructor More...
 
 FlxbbDesign (ScoreFunctionOP const sfxnd, ScoreFunctionOP const sfxnr, core::Size const ncycle=3, String const &layer_mode="", bool const use_origseq_for_not_dsgned_layer=true, bool const no_relax=false)
 value constructor More...
 
 FlxbbDesign (FlxbbDesign const &rval)
 copy constructor More...
 
 ~FlxbbDesign () override
 destructor More...
 
MoverOP clone () const override
 clone this object More...
 
MoverOP fresh_instance () const override
 create this type of object More...
 
void read_options ()
 read parameters More...
 
void initialize_filter (core::Size const filter_trial, String const &filter_type)
 initialize filter parameters More...
 
void apply (Pose &pose) override
 mover apply More...
 
void set_scorefxn_design (ScoreFunctionOP const scorefxn)
 set the score function for fixbb design More...
 
void set_scorefxn_relax (ScoreFunctionOP const scorefxn)
 set the score function for relax More...
 
void set_ncycles (core::Size const ncycles)
 the number of cycles of fixbb and relax More...
 
void set_layer_mode (String const &layer_mode)
 set layer mode More...
 
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 ) More...
 
void no_relax (bool const no_relax)
 relax is not performed after design (default false) More...
 
void no_design (bool const no_design)
 design protocol will not be performed (default false) More...
 
void set_blueprint (BluePrintOP const blueprint)
 set BluePrintOP More...
 
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 ) More...
 
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 ) More...
 
void movemap_from_blueprint (bool const value)
 set movemap for relax More...
 
void set_movemap_factory (core::select::movemap::MoveMapFactoryCOP movemap_factory)
 set movemapi_factory for relax More...
 
void set_movemap (MoveMapOP const movemap)
 set movemap for relax More...
 
void set_design_taskset (DesignTaskSet const &design_taskset)
 set DesignTaskSet Once you set DesignTaskSet, this controls almost every setups of this class More...
 
void add_design_task (DesignTaskOP const design_task)
 add the design task which cotrols the iteration of fixbb design and relax More...
 
void set_filter_during_design (FilterStructsOP const filter_during_design)
 filtering during design More...
 
void clear_design_taskset ()
 clear DesignTaskSet More...
 
void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
 parse xml More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
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...
 
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...
 
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...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
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
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
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...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
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 mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static void register_options ()
 register options More...
 
static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- 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 Member Functions

DesignTaskSet build_design_taskset (Pose const &pose)
 build design_task_set More...
 
MoveMapOP get_movemap_from_blueprint (Pose const &pose, BluePrintOP const blueprint)
 make movemap from blueprint for relax More...
 

Private Attributes

ScoreFunctionOP scorefxn_design_
 score function for design More...
 
ScoreFunctionOP scorefxn_relax_
 score function for relax More...
 
core::Size nflxbb_cycles_
 the number of cycles of fixbb and relax More...
 
String layer_mode_
 perform fixbb in layer mode More...
 
bool use_origseq_for_not_dsgned_layer_
 use original sequence for not designed region in layer_mode, otherwise the residues of the region turned into Ala More...
 
bool no_relax_
 relax is not performed after design (default false) More...
 
bool no_design_
 design protocol will not be performed (default false) More...
 
DesignTaskSet design_taskset_
 control the method of design with filter and relax More...
 
FilterStructsOP filter_during_design_
 filter during design More...
 
BluePrintOP blueprint_
 blueprint for setting up constraints of beta sheet More...
 
String resfile_
 resfile More...
 
Real constraints_sheet_
 weight of constraints_sheet which constrains between Ca atoms in beta-sheets if this weight > 0.0, the constraints is applied ( default = -1.0 ) More...
 
Real constraints_NtoC_
 weight of constraints_NtoC which constrains between Ca atoms of C- and N-terminal if this weight > 0.0, the constraints is applied ( default = -1.0 ) More...
 
bool movemap_from_blueprint_
 set movemap from blueprint ( default false ) More...
 
core::select::movemap::MoveMapFactoryCOP movemap_factory_
 movemap Factory for relax ( default NULL ) More...
 
MoveMapOP movemap_
 movemap for relax ( default NULL ) More...
 
utility::vector1< TaskOperationOPtask_operations_
 task operations More...
 
bool use_fast_relax_
 use fast relax or not More...
 
bool clear_all_residues_
 clear all residues before design More...
 
bool relax_constraint_to_design_
 
bool limit_aroma_chi2_
 

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

typedef basic::datacache::DataMap protocols::flxbb::FlxbbDesign::DataMap
typedef utility::tag::TagCOP protocols::flxbb::FlxbbDesign::TagCOP

Constructor & Destructor Documentation

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

default constructor

References design_taskset_, read_options(), and task_operations_.

protocols::flxbb::FlxbbDesign::FlxbbDesign ( ScoreFunctionOP const  sfxnd,
ScoreFunctionOP const  sfxnr,
core::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 design_taskset_, read_options(), and task_operations_.

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

copy constructor

protocols::flxbb::FlxbbDesign::~FlxbbDesign ( )
overridedefault

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

References design_taskset_.

void protocols::flxbb::FlxbbDesign::apply ( pose::Pose pose)
overridevirtual
DesignTaskSet protocols::flxbb::FlxbbDesign::build_design_taskset ( Pose const &  pose)
private
void protocols::flxbb::FlxbbDesign::clear_design_taskset ( )

clear DesignTaskSet

References design_taskset_.

FlxbbDesign::MoverOP protocols::flxbb::FlxbbDesign::clone ( ) const
overridevirtual

clone this object

Reimplemented from protocols::moves::Mover.

FlxbbDesign::MoverOP protocols::flxbb::FlxbbDesign::fresh_instance ( ) const
overridevirtual

create this type of object

Reimplemented from protocols::moves::Mover.

MoveMapOP protocols::flxbb::FlxbbDesign::get_movemap_from_blueprint ( Pose const &  pose,
BluePrintOP const  blueprint 
)
private

make movemap from blueprint for relax

std::string protocols::flxbb::FlxbbDesign::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

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

initialize filter parameters

References filter_during_design_, and protocols::TR().

Referenced by parse_my_tag(), and read_options().

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

set movemap for relax

References movemap_from_blueprint_.

std::string protocols::flxbb::FlxbbDesign::mover_name ( )
static
void protocols::flxbb::FlxbbDesign::no_design ( bool const  no_design)

design protocol will not be performed (default false)

References no_design_.

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

relax is not performed after design (default false)

References no_relax_.

void protocols::flxbb::FlxbbDesign::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::flxbb::FlxbbDesign::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::flxbb::FlxbbDesign::read_options ( )
void protocols::flxbb::FlxbbDesign::register_options ( )
static

register options

registering of options that are relevant for FlxbbDesign

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

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

set BluePrintOP

set BlueprintOP

References blueprint_.

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

References design_taskset_.

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

filtering during design

References filter_during_design_.

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

set layer mode

References layer_mode_.

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

set movemap for relax

References movemap_.

void protocols::flxbb::FlxbbDesign::set_movemap_factory ( core::select::movemap::MoveMapFactoryCOP  movemap_factory)

set movemapi_factory for relax

set movemap factory for relax

References movemap_factory_.

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

the number of cycles of fixbb and relax

References nflxbb_cycles_.

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

set the score function for fixbb design

set scorefxn for fixbb design

References scorefxn_design_.

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

set the score function for relax

set scorefxn for relax

References scorefxn_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 )

References constraints_NtoC_.

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 )

References constraints_sheet_.

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 )

References use_origseq_for_not_dsgned_layer_.

Member Data Documentation

BluePrintOP protocols::flxbb::FlxbbDesign::blueprint_
private

blueprint for setting up constraints of beta sheet

Referenced by apply(), parse_my_tag(), read_options(), and set_blueprint().

bool protocols::flxbb::FlxbbDesign::clear_all_residues_
private

clear all residues before design

Referenced by apply(), and parse_my_tag().

Real protocols::flxbb::FlxbbDesign::constraints_NtoC_
private

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

Referenced by apply(), parse_my_tag(), read_options(), and set_weight_constraints_NtoC().

Real protocols::flxbb::FlxbbDesign::constraints_sheet_
private

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

Referenced by apply(), parse_my_tag(), read_options(), and set_weight_constraints_sheet().

DesignTaskSet protocols::flxbb::FlxbbDesign::design_taskset_
private

control the method of design with filter and relax

Referenced by add_design_task(), apply(), clear_design_taskset(), FlxbbDesign(), and set_design_taskset().

FilterStructsOP protocols::flxbb::FlxbbDesign::filter_during_design_
private

filter during design

Referenced by build_design_taskset(), initialize_filter(), and set_filter_during_design().

String protocols::flxbb::FlxbbDesign::layer_mode_
private

perform fixbb in layer mode

Referenced by build_design_taskset(), parse_my_tag(), read_options(), and set_layer_mode().

bool protocols::flxbb::FlxbbDesign::limit_aroma_chi2_
private
MoveMapOP protocols::flxbb::FlxbbDesign::movemap_
private

movemap for relax ( default NULL )

Referenced by apply(), build_design_taskset(), and set_movemap().

core::select::movemap::MoveMapFactoryCOP protocols::flxbb::FlxbbDesign::movemap_factory_
private

movemap Factory for relax ( default NULL )

Referenced by apply(), build_design_taskset(), parse_my_tag(), and set_movemap_factory().

bool protocols::flxbb::FlxbbDesign::movemap_from_blueprint_
private

set movemap from blueprint ( default false )

Referenced by apply(), movemap_from_blueprint(), parse_my_tag(), and read_options().

core::Size protocols::flxbb::FlxbbDesign::nflxbb_cycles_
private

the number of cycles of fixbb and relax

Referenced by build_design_taskset(), parse_my_tag(), read_options(), and set_ncycles().

bool protocols::flxbb::FlxbbDesign::no_design_
private

design protocol will not be performed (default false)

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

bool protocols::flxbb::FlxbbDesign::no_relax_
private

relax is not performed after design (default false)

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

bool protocols::flxbb::FlxbbDesign::relax_constraint_to_design_
private
String protocols::flxbb::FlxbbDesign::resfile_
private

resfile

Referenced by build_design_taskset(), and parse_my_tag().

ScoreFunctionOP protocols::flxbb::FlxbbDesign::scorefxn_design_
private

score function for design

Referenced by apply(), build_design_taskset(), parse_my_tag(), and set_scorefxn_design().

ScoreFunctionOP protocols::flxbb::FlxbbDesign::scorefxn_relax_
private

score function for relax

Referenced by apply(), build_design_taskset(), parse_my_tag(), and set_scorefxn_relax().

utility::vector1< TaskOperationOP > protocols::flxbb::FlxbbDesign::task_operations_
private

task operations

Referenced by build_design_taskset(), FlxbbDesign(), and parse_my_tag().

bool protocols::flxbb::FlxbbDesign::use_fast_relax_
private

use fast relax or not

Referenced by build_design_taskset(), and parse_my_tag().

bool protocols::flxbb::FlxbbDesign::use_origseq_for_not_dsgned_layer_
private

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

Referenced by build_design_taskset(), parse_my_tag(), and use_origseq_for_not_dsgned_layer().


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