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protocols::fldsgn::BluePrintBDR Class Reference

#include <BluePrintBDR.hh>

Inheritance diagram for protocols::fldsgn::BluePrintBDR:
Inheritance graph
[legend]

Public Types

typedef std::string String
 
typedef core::Real Real
 
typedef core::Size Size
 
typedef core::scoring::dssp::Dssp Dssp
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseOP PoseOP
 
typedef
core::scoring::ScoreFunction 
ScoreFunction
 
typedef
core::scoring::ScoreFunctionOP 
ScoreFunctionOP
 
typedef
protocols::parser::BluePrint 
BluePrint
 
typedef
protocols::parser::BluePrintOP 
BluePrintOP
 
typedef
protocols::forge::build::BuildInstructionOP 
BuildInstructionOP
 
typedef
protocols::forge::build::BuildManager 
BuildManager
 
typedef
protocols::forge::build::Interval 
Interval
 
typedef
protocols::forge::components::VarLengthBuild 
VarLengthBuild
 
typedef
protocols::forge::components::VarLengthBuildOP 
VarLengthBuildOP
 
typedef protocols::moves::MoverOP MoverOP
 
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

 BluePrintBDR ()
 default constructor More...
 
 BluePrintBDR (String const &filename, bool const ss_from_blueprint=true)
 value constructor More...
 
 BluePrintBDR (BluePrintOP blueprintOP, bool const ss_from_blueprint=true)
 moves the BluePrintOP More...
 
 BluePrintBDR (BluePrintBDR const &rval)
 copy constructor More...
 
 ~BluePrintBDR () override
 default destructor More...
 
MoverOP clone () const override
 clone this object More...
 
MoverOP fresh_instance () const override
 create this type of object More...
 
ScoreFunction const & scorefunction () const
 the centroid level score function, default "fldsgn_cen" More...
 
core::Size instruction_size () const
 
String const & loop_mover_str () const
 the loop mover string to use during centroid build (default "RemodelLoopMover") More...
 
bool use_fullmer () const
 use full-mer fragments when building the loop? (default false) More...
 
core::Size num_fragpick () const
 the number of fragments to pick at each position More...
 
bool use_sequence_bias () const
 use sequence biased fragments when building the loop? (default false) More...
 
bool use_abego_bias () const
 use abego biased fragments when building the loop? (default false) More...
 
Real max_linear_chainbreak () const
 the maximum allowed linear chainbreak (default 0.07) More...
 
bool is_initialized () const
 define secondary structrue by blueprint More...
 
void add_instruction (BuildInstructionOP bi)
 add instruction to the manager of this BluePrintBDR (no copy) More...
 
void create_directed_dependency (BuildInstructionOP u, BuildInstructionOP v)
 create directed dependency between two instructions More...
 
void use_fullmer (bool const flag)
 use full-mer fragments when building the loop? More...
 
void use_sequence_bias (bool const flag)
 use sequence biased fragments when building the loop? (default false) More...
 
void use_abego_bias (bool const flag)
 use abego biased fragments when building the loop? (default false) More...
 
void max_linear_chainbreak (Real const threshold)
 the maximum allowed linear chainbreak More...
 
void loop_mover_str (String const &loop_mover_str)
 the loop mover string to use during centroid build More...
 
void num_fragpick (core::Size const num)
 the number of fragments to pick at each position More...
 
void ss_from_blueprint (bool const flag)
 define secondary structrue by blueprint More...
 
void scorefunction (ScoreFunction const &sfx)
 set the centroid level score function More...
 
void scorefunction (ScoreFunctionOP sfx)
 set the centroid level score function More...
 
void set_blueprint (String const &filename)
 set blueprint file by filename More...
 
void set_blueprint (BluePrintOP const &blp)
 set blueprint file More...
 
void set_constraints_NtoC (Real const &weight)
 set constraints between N- and C- Ca atoms More...
 
void set_constraint_file (String const &constraint_file)
 set constraint file More...
 
void dump_pdb_when_fail (String const &dump_pdb_when_fail)
 dump pdb when this protocol failed More...
 
void set_rcgs (utility::vector1< protocols::forge::remodel::RemodelConstraintGeneratorOP > const &rcgs)
 set list of remodel constraint generators More...
 
void apply (Pose &pose) override
 apply defined moves to given Pose More...
 
void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
 parse xml file 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 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 Types

typedef protocols::moves::Mover Super
 

Private Member Functions

BluePrintBDRoperator= (BluePrintBDR const &rval)
 copy assignment More...
 
bool centroid_build (Pose &pose)
 run the centroid level build stage More...
 
bool set_instruction_blueprint (Pose const &pose)
 set instruction by blueprint More...
 
void setup_invrot_tree_in_vlb (VarLengthBuild &vlb, Pose &pose) const
 set up folding aroung theozyme in a vlb More...
 

Private Attributes

BluePrintOP blueprint_
 bluerprint file for setting build instruction More...
 
BuildManager manager_
 the BuildManager More...
 
ScoreFunctionOP sfx_
 the centroid scorefunction to use, default "remodel_cen" More...
 
String loop_mover_str_
 the loop mover string to use during centroid build (default "RemodelLoopMover") More...
 
bool use_fullmer_
 use full-mer fragments when building the loop? (default false) More...
 
core::Size num_fragpick_
 the number of fragments to pick at each position More...
 
bool use_sequence_bias_
 use sequence biased fragments when building the loop? (default false) More...
 
bool use_abego_bias_
 use abego biased fragments when building the loop? (default false) More...
 
Real max_linear_chainbreak_
 the maximum allowed linear chainbreak (default 0.07) More...
 
bool initialized_
 vlb_ is intialized or not More...
 
bool ss_from_blueprint_
 define secondary structure by blueprint More...
 
Real constraints_NtoC_
 add constraints between N- and C- terminal Ca atoms More...
 
Real constraints_sheet_
 add constraints betwee Ca atoms in sheet More...
 
String constraint_file_
 constraint file More...
 
String dump_pdb_when_fail_
 dump pdb when this protocol failed More...
 
String loop_mover_
 loop mover for loop building, default RemodelLoopMover More...
 
core::Size rmdl_attempts_
 number of allowed_closure_attempts_ of RemodelLoopMover More...
 
bool use_poly_val_
 Entire sequence except for rebuilding regions become poly Val. More...
 
bool tell_vlb_to_not_touch_fold_tree_
 if we a fold tree has already been set up prior More...
 
protocols::toolbox::match_enzdes_util::InvrotTreeOP invrot_tree_
 in case we're folding up around a ligand More...
 
toolbox::match_enzdes_util::EnzConstraintIOCOP enzcst_io_
 
utility::vector1
< protocols::forge::remodel::RemodelConstraintGeneratorOP
rcgs_
 User-specified constraint generators which will be called from the VarLengthBuild. More...
 
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

typedef basic::datacache::DataMap protocols::fldsgn::BluePrintBDR::DataMap
typedef utility::tag::TagCOP protocols::fldsgn::BluePrintBDR::TagCOP

Constructor & Destructor Documentation

protocols::fldsgn::BluePrintBDR::BluePrintBDR ( )

default constructor

References rcgs_.

protocols::fldsgn::BluePrintBDR::BluePrintBDR ( String const &  filename,
bool const  ss_from_blueprint = true 
)

value constructor

References rcgs_, and set_blueprint().

protocols::fldsgn::BluePrintBDR::BluePrintBDR ( BluePrintOP  blueprintOP,
bool const  ss_from_blueprint = true 
)

moves the BluePrintOP

value constructor

References rcgs_.

protocols::fldsgn::BluePrintBDR::BluePrintBDR ( BluePrintBDR const &  rval)

copy constructor

copy constructor

References vlb_.

protocols::fldsgn::BluePrintBDR::~BluePrintBDR ( )
overridedefault

default destructor

Member Function Documentation

void protocols::fldsgn::BluePrintBDR::add_instruction ( BuildInstructionOP  bi)

add instruction to the manager of this BluePrintBDR (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
[in]biBuildInstruction

References protocols::forge::build::BuildManager::add(), manager_, and vlb_.

Referenced by set_instruction_blueprint().

void protocols::fldsgn::BluePrintBDR::apply ( Pose pose)
overridevirtual
bool protocols::fldsgn::BluePrintBDR::centroid_build ( Pose pose)
private
BluePrintBDR::MoverOP protocols::fldsgn::BluePrintBDR::clone ( ) const
overridevirtual

clone this object

Reimplemented from protocols::moves::Mover.

void protocols::fldsgn::BluePrintBDR::create_directed_dependency ( BuildInstructionOP  u,
BuildInstructionOP  v 
)

create directed dependency between two instructions

References protocols::forge::build::BuildManager::create_directed_dependency(), and manager_.

void protocols::fldsgn::BluePrintBDR::dump_pdb_when_fail ( String const &  dump_pdb_when_fail)

dump pdb when this protocol failed

References dump_pdb_when_fail_.

BluePrintBDR::MoverOP protocols::fldsgn::BluePrintBDR::fresh_instance ( ) const
overridevirtual

create this type of object

Reimplemented from protocols::moves::Mover.

std::string protocols::fldsgn::BluePrintBDR::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

core::Size protocols::fldsgn::BluePrintBDR::instruction_size ( ) const
inline
bool protocols::fldsgn::BluePrintBDR::is_initialized ( ) const
inline

define secondary structrue by blueprint

References initialized_.

String const& protocols::fldsgn::BluePrintBDR::loop_mover_str ( ) const
inline

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"

References loop_mover_str_.

void protocols::fldsgn::BluePrintBDR::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 loop_mover_str(), and loop_mover_str_.

Referenced by loop_mover_str().

Real protocols::fldsgn::BluePrintBDR::max_linear_chainbreak ( ) const
inline

the maximum allowed linear chainbreak (default 0.07)

References max_linear_chainbreak_.

void protocols::fldsgn::BluePrintBDR::max_linear_chainbreak ( Real const  threshold)
inline

the maximum allowed linear chainbreak

References max_linear_chainbreak_.

std::string protocols::fldsgn::BluePrintBDR::mover_name ( )
static
core::Size protocols::fldsgn::BluePrintBDR::num_fragpick ( ) const
inline

the number of fragments to pick at each position

References num_fragpick_.

void protocols::fldsgn::BluePrintBDR::num_fragpick ( core::Size const  num)
inline

the number of fragments to pick at each position

References num_fragpick_.

BluePrintBDR& protocols::fldsgn::BluePrintBDR::operator= ( BluePrintBDR const &  rval)
private

copy assignment

Remarks
Mover base class prevents this from working properly...
void protocols::fldsgn::BluePrintBDR::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::fldsgn::BluePrintBDR::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
BluePrintBDR::ScoreFunction const & protocols::fldsgn::BluePrintBDR::scorefunction ( ) const

the centroid level score function, default "fldsgn_cen"

the centroid level score function, default "remodel_cen"

References sfx_.

void protocols::fldsgn::BluePrintBDR::scorefunction ( ScoreFunction const &  sfx)

set the centroid level score function

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

void protocols::fldsgn::BluePrintBDR::scorefunction ( ScoreFunctionOP  sfx)

set the centroid level score function

References sfx_.

void protocols::fldsgn::BluePrintBDR::set_blueprint ( String const &  filename)

set blueprint file by filename

use blueprint

References blueprint_, and protocols::abinitio::filename().

Referenced by BluePrintBDR(), and parse_my_tag().

void protocols::fldsgn::BluePrintBDR::set_blueprint ( BluePrintOP const &  blp)

set blueprint file

use blueprint

References blueprint_.

void protocols::fldsgn::BluePrintBDR::set_constraint_file ( String const &  constraint_file)

set constraint file

References constraint_file_.

void protocols::fldsgn::BluePrintBDR::set_constraints_NtoC ( Real const &  weight)

set constraints between N- and C- Ca atoms

set constraint between N- and C- terminal residues, need to set the weight

References constraints_NtoC_.

bool protocols::fldsgn::BluePrintBDR::set_instruction_blueprint ( Pose const &  pose)
private
void protocols::fldsgn::BluePrintBDR::set_rcgs ( utility::vector1< protocols::forge::remodel::RemodelConstraintGeneratorOP > const &  rcgs)

set list of remodel constraint generators

References rcgs_.

void protocols::fldsgn::BluePrintBDR::setup_invrot_tree_in_vlb ( VarLengthBuild vlb,
Pose pose 
) const
private
void protocols::fldsgn::BluePrintBDR::ss_from_blueprint ( bool const  flag)
inline

define secondary structrue by blueprint

References ss_from_blueprint_.

bool protocols::fldsgn::BluePrintBDR::use_abego_bias ( ) const
inline

use abego biased fragments when building the loop? (default false)

References use_abego_bias_.

void protocols::fldsgn::BluePrintBDR::use_abego_bias ( bool const  flag)
inline

use abego biased fragments when building the loop? (default false)

References use_abego_bias_.

bool protocols::fldsgn::BluePrintBDR::use_fullmer ( ) const
inline

use full-mer fragments when building the loop? (default false)

References use_fullmer_.

void protocols::fldsgn::BluePrintBDR::use_fullmer ( bool const  flag)
inline

use full-mer fragments when building the loop?

References use_fullmer_.

bool protocols::fldsgn::BluePrintBDR::use_sequence_bias ( ) const
inline

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

References use_sequence_bias_.

void protocols::fldsgn::BluePrintBDR::use_sequence_bias ( bool const  flag)
inline

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

References use_sequence_bias_.

Member Data Documentation

BluePrintOP protocols::fldsgn::BluePrintBDR::blueprint_
private

bluerprint file for setting build instruction

Referenced by apply(), centroid_build(), set_blueprint(), set_instruction_blueprint(), and setup_invrot_tree_in_vlb().

String protocols::fldsgn::BluePrintBDR::constraint_file_
private

constraint file

Referenced by centroid_build(), parse_my_tag(), and set_constraint_file().

Real protocols::fldsgn::BluePrintBDR::constraints_NtoC_
private

add constraints between N- and C- terminal Ca atoms

Referenced by centroid_build(), parse_my_tag(), and set_constraints_NtoC().

Real protocols::fldsgn::BluePrintBDR::constraints_sheet_
private

add constraints betwee Ca atoms in sheet

Referenced by centroid_build(), and parse_my_tag().

String protocols::fldsgn::BluePrintBDR::dump_pdb_when_fail_
private

dump pdb when this protocol failed

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

toolbox::match_enzdes_util::EnzConstraintIOCOP protocols::fldsgn::BluePrintBDR::enzcst_io_
private
bool protocols::fldsgn::BluePrintBDR::initialized_
private

vlb_ is intialized or not

Referenced by apply(), and is_initialized().

protocols::toolbox::match_enzdes_util::InvrotTreeOP protocols::fldsgn::BluePrintBDR::invrot_tree_
private

in case we're folding up around a ligand

Referenced by centroid_build(), parse_my_tag(), and setup_invrot_tree_in_vlb().

String protocols::fldsgn::BluePrintBDR::loop_mover_
private

loop mover for loop building, default RemodelLoopMover

String protocols::fldsgn::BluePrintBDR::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(), loop_mover_str(), and parse_my_tag().

BuildManager protocols::fldsgn::BluePrintBDR::manager_
private
Real protocols::fldsgn::BluePrintBDR::max_linear_chainbreak_
private

the maximum allowed linear chainbreak (default 0.07)

Referenced by centroid_build(), and max_linear_chainbreak().

core::Size protocols::fldsgn::BluePrintBDR::num_fragpick_
private

the number of fragments to pick at each position

Referenced by centroid_build(), and num_fragpick().

utility::vector1< protocols::forge::remodel::RemodelConstraintGeneratorOP > protocols::fldsgn::BluePrintBDR::rcgs_
private

User-specified constraint generators which will be called from the VarLengthBuild.

Referenced by BluePrintBDR(), centroid_build(), parse_my_tag(), and set_rcgs().

core::Size protocols::fldsgn::BluePrintBDR::rmdl_attempts_
private

number of allowed_closure_attempts_ of RemodelLoopMover

Referenced by parse_my_tag().

ScoreFunctionOP protocols::fldsgn::BluePrintBDR::sfx_
private

the centroid scorefunction to use, default "remodel_cen"

Referenced by centroid_build(), parse_my_tag(), and scorefunction().

bool protocols::fldsgn::BluePrintBDR::ss_from_blueprint_
private

define secondary structure by blueprint

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

bool protocols::fldsgn::BluePrintBDR::tell_vlb_to_not_touch_fold_tree_
private

if we a fold tree has already been set up prior

Referenced by centroid_build(), and parse_my_tag().

bool protocols::fldsgn::BluePrintBDR::use_abego_bias_
private

use abego biased fragments when building the loop? (default false)

Referenced by centroid_build(), parse_my_tag(), setup_invrot_tree_in_vlb(), and use_abego_bias().

bool protocols::fldsgn::BluePrintBDR::use_fullmer_
private

use full-mer fragments when building the loop? (default false)

Referenced by centroid_build(), and use_fullmer().

bool protocols::fldsgn::BluePrintBDR::use_poly_val_
private

Entire sequence except for rebuilding regions become poly Val.

Referenced by centroid_build(), and parse_my_tag().

bool protocols::fldsgn::BluePrintBDR::use_sequence_bias_
private

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

Referenced by centroid_build(), parse_my_tag(), and use_sequence_bias().

VarLengthBuildOP protocols::fldsgn::BluePrintBDR::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 add_instruction(), BluePrintBDR(), centroid_build(), and setup_invrot_tree_in_vlb().


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