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protocols::loophash::LoopHashMoverWrapper Class Reference

Use LoopHash to sample new high-resolution conformations for the given pose. More...

#include <LoopHashMoverWrapper.hh>

Inheritance diagram for protocols::loophash::LoopHashMoverWrapper:
Inheritance graph
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Public Member Functions

 LoopHashMoverWrapper ()
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
core::pose::PoseOP get_additional_output () override
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
 ~LoopHashMoverWrapper () override
 
core::Real min_bbrms () const
 
void min_bbrms (core::Real const min_bbrms)
 
core::Real max_bbrms () const
 
void max_bbrms (core::Real const max_bbrms)
 
core::Real min_rms () const
 
void min_rms (core::Real const min_rms)
 
core::Real max_rms () const
 
void max_rms (core::Real const max_rms)
 
core::Size max_nstruct () const
 
void max_nstruct (core::Size const max_nstruct)
 
utility::vector1< core::Sizeloop_sizes () const
 
void add_loop_size (core::Size const loop_size)
 
void cenfilter (protocols::filters::FilterOP cenfilter)
 
void fafilter (protocols::filters::FilterOP fafilter)
 
void ranking_fafilter (protocols::filters::FilterOP ranking_fafilter)
 
void ranking_cenfilter (protocols::filters::FilterOP filter)
 
protocols::filters::FilterOP ranking_cenfilter () const
 
void relax_mover (protocols::relax::FastRelaxOP relax_mover)
 
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...
 
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 Attributes

utility::vector1< core::Sizeloop_sizes_
 
LoopHashLibraryOP library_
 
protocols::relax::FastRelaxOP fastrelax_
 
core::Real min_bbrms_
 
core::Real max_bbrms_
 
core::Real min_rms_
 
core::Real max_rms_
 
std::string start_res_
 
std::string stop_res_
 
core::Size max_struct_
 
core::Size max_radius_
 
core::Size max_struct_per_radius_
 
core::Size max_nstruct_
 
core::Size ncentroid_
 
core::Size nfullatom_
 
core::Size batch_size_
 
protocols::filters::FilterOP cenfilter_
 
protocols::filters::FilterOP ranking_cenfilter_
 
protocols::filters::FilterOP fafilter_
 
protocols::filters::FilterOP ranking_fafilter_
 
core::Size nprefilter_
 
core::scoring::ScoreFunctionOP prefilter_scorefxn_
 
bool ideal_
 
bool filter_by_phipsi_
 
std::vector< std::pair
< core::Real,
core::io::silent::SilentStructOP > > 
all_structs_
 
core::Real sample_weight_const_
 

Additional Inherited Members

- 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
 
- 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...
 

Detailed Description

Use LoopHash to sample new high-resolution conformations for the given pose.

The algorithm in pseudo-code:

Constructor & Destructor Documentation

protocols::loophash::LoopHashMoverWrapper::LoopHashMoverWrapper ( )

References loop_sizes_.

protocols::loophash::LoopHashMoverWrapper::~LoopHashMoverWrapper ( )
overridedefault

Member Function Documentation

void protocols::loophash::LoopHashMoverWrapper::add_loop_size ( core::Size const  loop_size)

References loop_sizes_.

Referenced by parse_my_tag().

void protocols::loophash::LoopHashMoverWrapper::apply ( core::pose::Pose )
overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_vrt, core::pose::add_comment(), all_structs_, core::pose::Pose::batch_set_xyz(), batch_size_, protocols::loophash::LoopHashSampler::build_structures(), cenfilter_, core::chemical::CENTROID_t, core::pose::symmetry::extract_asymmetric_unit(), fafilter_, protocols::moves::FAIL_RETRY, fastrelax_, filter_by_phipsi_, core::chemical::FULL_ATOM_t, ideal_, core::pose::symmetry::is_symmetric(), library_, max_bbrms(), max_nstruct(), max_radius_, max_rms(), max_struct_, max_struct_per_radius_, min_bbrms(), min_rms(), core::chemical::ResidueType::natoms(), ncentroid_, nfullatom_, nprefilter_, core::pose::parse_resnum(), prefilter_scorefxn_, ranking_cenfilter(), ranking_fafilter_, core::pose::Pose::residue_type(), core::scoring::rg, sample_weight_const_, protocols::loophash::LoopHashSampler::set_filter_by_phipsi(), protocols::moves::Mover::set_last_move_status(), protocols::loophash::LoopHashSampler::set_max_bbrms(), protocols::loophash::LoopHashSampler::set_max_nstruct(), protocols::loophash::LoopHashSampler::set_max_radius(), protocols::loophash::LoopHashSampler::set_max_rms(), protocols::loophash::LoopHashSampler::set_max_struct(), protocols::loophash::LoopHashSampler::set_max_struct_per_radius(), protocols::loophash::LoopHashSampler::set_min_bbrms(), protocols::loophash::LoopHashSampler::set_min_rms(), protocols::loophash::LoopHashSampler::set_nonideal(), core::pose::set_ss_from_phipsi(), protocols::loophash::LoopHashSampler::set_start_res(), protocols::loophash::LoopHashSampler::set_stop_res(), core::pose::Pose::size(), start_res_, stop_res_, core::util::switch_to_residue_type_set(), core::id::to_string(), protocols::loophash::TR(), protocols::loophash::LoopHashSampler::use_prefiltering(), and core::pose::Pose::xyz().

void protocols::loophash::LoopHashMoverWrapper::cenfilter ( protocols::filters::FilterOP  cenfilter)

References cenfilter_.

Referenced by parse_my_tag().

protocols::moves::MoverOP protocols::loophash::LoopHashMoverWrapper::clone ( ) const
inlineoverridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

void protocols::loophash::LoopHashMoverWrapper::fafilter ( protocols::filters::FilterOP  fafilter)

References fafilter_.

Referenced by parse_my_tag().

protocols::moves::MoverOP protocols::loophash::LoopHashMoverWrapper::fresh_instance ( ) const
inlineoverridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

core::pose::PoseOP protocols::loophash::LoopHashMoverWrapper::get_additional_output ( )
overridevirtual

Mechanism by which a mover may return multiple output poses from a single input pose.

fpd

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

Mechanism by which a mover may return multiple output poses from a single input pose. After apply is called, calling this function will return subsequent output poses. NULL is returned if the mover has no more output poses remaining. The base class implementation returns NULL always; multi-output movers must override this. RosettaScripts uses this interface to produce a 'branched' protocol.

Reimplemented from protocols::moves::Mover.

References all_structs_, and protocols::loophash::TR().

std::string protocols::loophash::LoopHashMoverWrapper::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

utility::vector1< core::Size > protocols::loophash::LoopHashMoverWrapper::loop_sizes ( ) const

References loop_sizes_.

Referenced by parse_my_tag().

Real protocols::loophash::LoopHashMoverWrapper::max_bbrms ( ) const

References max_bbrms_.

Referenced by apply(), and max_bbrms().

void protocols::loophash::LoopHashMoverWrapper::max_bbrms ( core::Real const  max_bbrms)

References max_bbrms(), and max_bbrms_.

Size protocols::loophash::LoopHashMoverWrapper::max_nstruct ( ) const

References max_nstruct_.

Referenced by apply(), and max_nstruct().

void protocols::loophash::LoopHashMoverWrapper::max_nstruct ( core::Size const  max_nstruct)

References max_nstruct(), and max_nstruct_.

Real protocols::loophash::LoopHashMoverWrapper::max_rms ( ) const

References max_rms_.

Referenced by apply(), and max_rms().

void protocols::loophash::LoopHashMoverWrapper::max_rms ( core::Real const  max_rms)

References max_rms(), and max_rms_.

Real protocols::loophash::LoopHashMoverWrapper::min_bbrms ( ) const

References min_bbrms_.

Referenced by apply(), and min_bbrms().

void protocols::loophash::LoopHashMoverWrapper::min_bbrms ( core::Real const  min_bbrms)

References min_bbrms(), and min_bbrms_.

Real protocols::loophash::LoopHashMoverWrapper::min_rms ( ) const

References min_rms_.

Referenced by apply(), and min_rms().

void protocols::loophash::LoopHashMoverWrapper::min_rms ( core::Real const  min_rms)

References min_rms(), and min_rms_.

std::string protocols::loophash::LoopHashMoverWrapper::mover_name ( )
static
void protocols::loophash::LoopHashMoverWrapper::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References add_loop_size(), batch_size_, cenfilter(), fafilter(), fastrelax_, filter_by_phipsi_, core::pose::get_resnum_string(), ideal_, library_, loop_sizes(), max_bbrms_, max_nstruct_, max_radius_, max_rms_, max_struct_, max_struct_per_radius_, min_bbrms_, min_rms_, ncentroid_, nfullatom_, nprefilter_, protocols::rosetta_scripts::parse_filter(), protocols::rosetta_scripts::parse_filter_or_null(), protocols::rosetta_scripts::parse_mover_or_null(), prefilter_scorefxn_, ranking_cenfilter(), ranking_fafilter(), relax_mover(), sample_weight_const_, start_res_, stop_res_, and protocols::loophash::TR().

void protocols::loophash::LoopHashMoverWrapper::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::loophash::LoopHashMoverWrapper::ranking_cenfilter ( protocols::filters::FilterOP  filter)
inline

References ranking_cenfilter_.

protocols::filters::FilterOP protocols::loophash::LoopHashMoverWrapper::ranking_cenfilter ( ) const
inline

References ranking_cenfilter_.

Referenced by apply(), and parse_my_tag().

void protocols::loophash::LoopHashMoverWrapper::ranking_fafilter ( protocols::filters::FilterOP  ranking_fafilter)

References ranking_fafilter_.

Referenced by parse_my_tag().

void protocols::loophash::LoopHashMoverWrapper::relax_mover ( protocols::relax::FastRelaxOP  relax_mover)

References fastrelax_.

Referenced by parse_my_tag().

Member Data Documentation

std::vector< std::pair< core::Real, core::io::silent::SilentStructOP > > protocols::loophash::LoopHashMoverWrapper::all_structs_
private

Referenced by apply(), and get_additional_output().

core::Size protocols::loophash::LoopHashMoverWrapper::batch_size_
private

Referenced by apply(), and parse_my_tag().

protocols::filters::FilterOP protocols::loophash::LoopHashMoverWrapper::cenfilter_
private

Referenced by apply(), and cenfilter().

protocols::filters::FilterOP protocols::loophash::LoopHashMoverWrapper::fafilter_
private

Referenced by apply(), and fafilter().

protocols::relax::FastRelaxOP protocols::loophash::LoopHashMoverWrapper::fastrelax_
private

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

bool protocols::loophash::LoopHashMoverWrapper::filter_by_phipsi_
private

Referenced by apply(), and parse_my_tag().

bool protocols::loophash::LoopHashMoverWrapper::ideal_
private

Referenced by apply(), and parse_my_tag().

LoopHashLibraryOP protocols::loophash::LoopHashMoverWrapper::library_
private

Referenced by apply(), and parse_my_tag().

utility::vector1< core::Size > protocols::loophash::LoopHashMoverWrapper::loop_sizes_
private
core::Real protocols::loophash::LoopHashMoverWrapper::max_bbrms_
private

Referenced by max_bbrms(), and parse_my_tag().

core::Size protocols::loophash::LoopHashMoverWrapper::max_nstruct_
private

Referenced by max_nstruct(), and parse_my_tag().

core::Size protocols::loophash::LoopHashMoverWrapper::max_radius_
private

Referenced by apply(), and parse_my_tag().

core::Real protocols::loophash::LoopHashMoverWrapper::max_rms_
private

Referenced by max_rms(), and parse_my_tag().

core::Size protocols::loophash::LoopHashMoverWrapper::max_struct_
private

Referenced by apply(), and parse_my_tag().

core::Size protocols::loophash::LoopHashMoverWrapper::max_struct_per_radius_
private

Referenced by apply(), and parse_my_tag().

core::Real protocols::loophash::LoopHashMoverWrapper::min_bbrms_
private

Referenced by min_bbrms(), and parse_my_tag().

core::Real protocols::loophash::LoopHashMoverWrapper::min_rms_
private

Referenced by min_rms(), and parse_my_tag().

core::Size protocols::loophash::LoopHashMoverWrapper::ncentroid_
private

Referenced by apply(), and parse_my_tag().

core::Size protocols::loophash::LoopHashMoverWrapper::nfullatom_
private

Referenced by apply(), and parse_my_tag().

core::Size protocols::loophash::LoopHashMoverWrapper::nprefilter_
private

Referenced by apply(), and parse_my_tag().

core::scoring::ScoreFunctionOP protocols::loophash::LoopHashMoverWrapper::prefilter_scorefxn_
private

Referenced by apply(), and parse_my_tag().

protocols::filters::FilterOP protocols::loophash::LoopHashMoverWrapper::ranking_cenfilter_
private

Referenced by ranking_cenfilter().

protocols::filters::FilterOP protocols::loophash::LoopHashMoverWrapper::ranking_fafilter_
private

Referenced by apply(), and ranking_fafilter().

core::Real protocols::loophash::LoopHashMoverWrapper::sample_weight_const_
private

Referenced by apply(), and parse_my_tag().

std::string protocols::loophash::LoopHashMoverWrapper::start_res_
private

Referenced by apply(), and parse_my_tag().

std::string protocols::loophash::LoopHashMoverWrapper::stop_res_
private

Referenced by apply(), and parse_my_tag().


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