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

Use LoopHash to generate low-resolution alternate conformations for the given pose. More...

#include <LoopHashDiversifier.hh>

Inheritance diagram for protocols::loophash::LoopHashDiversifier:
Inheritance graph
[legend]

Public Member Functions

 LoopHashDiversifier ()
 
 LoopHashDiversifier (LoopHashLibraryOP library, core::Real min_inter_ss_bbrms, core::Real max_inter_ss_bbrms, core::Real min_intra_ss_bbrms, core::Real max_intra_ss_bbrms, core::Real min_rms, core::Real max_rms, std::string const &start_res, std::string const &stop_res, core::Size window_size, core::Size max_radius, core::Size max_struct, core::Size num_iterations, core::Size num_try_div, bool diversify_loop_only, bool ideal, bool filter_by_phipsi, protocols::filters::FilterOP cenfilter, protocols::filters::FilterOP ranking_cenfilter, core::scoring::ScoreFunctionOP scorefxn_cen_cst, core::scoring::ScoreFunctionOP scorefxn_rama_cst)
 
void apply (core::pose::Pose &pose) override
 Main Method. 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...
 
 ~LoopHashDiversifier () override
 ****Creator Methods****/// More...
 
core::Real min_inter_ss_bbrms () const
 
void min_inter_ss_bbrms (core::Real const min_inter_ss_bbrms)
 
core::Real max_inter_ss_bbrms () const
 
void max_inter_ss_bbrms (core::Real const max_inter_ss_bbrms)
 
core::Real min_intra_ss_bbrms () const
 
void min_intra_ss_bbrms (core::Real const min_intra_ss_bbrms)
 
core::Real max_intra_ss_bbrms () const
 
void max_intra_ss_bbrms (core::Real const max_intra_ss_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 num_iterations () const
 
void num_iterations (core::Size const num_iterations)
 
core::Size num_try_div () const
 
void num_try_div (core::Size const num_try_div)
 
utility::vector1< core::Sizeloop_sizes () const
 
void add_loop_size (core::Size const loop_size)
 
void cenfilter (protocols::filters::FilterOP cenfilter)
 
void ranking_cenfilter (protocols::filters::FilterOP filter)
 
protocols::filters::FilterOP ranking_cenfilter () const
 
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 Attributes

utility::vector1< core::Sizeloop_sizes_
 
LoopHashLibraryOP library_
 
core::Real min_inter_ss_bbrms_
 
core::Real max_inter_ss_bbrms_
 
core::Real min_intra_ss_bbrms_
 
core::Real max_intra_ss_bbrms_
 
core::Real min_rms_
 
core::Real max_rms_
 
std::string start_res_
 
std::string stop_res_
 
core::Size window_size_
 
core::Size max_radius_
 
core::Size max_struct_
 
core::Size num_iterations_
 
core::Size num_try_div_
 
bool diversify_loop_only_
 
bool ideal_
 
bool filter_by_phipsi_
 
protocols::filters::FilterOP cenfilter_
 
protocols::filters::FilterOP ranking_cenfilter_
 
core::scoring::ScoreFunctionOP scorefxn_cen_cst_
 
core::scoring::ScoreFunctionOP scorefxn_rama_cst_
 
std::vector< std::pair
< core::Real,
core::io::silent::SilentStructOP > > 
all_structs_
 

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 generate low-resolution alternate conformations for the given pose.

It's possible to limit the amount of movement based on the secondary structure, such that secondary structure elements either move less than loops or don't move at all. The algorithm in pseudo-code:

Constructor & Destructor Documentation

protocols::loophash::LoopHashDiversifier::LoopHashDiversifier ( )
protocols::loophash::LoopHashDiversifier::LoopHashDiversifier ( LoopHashLibraryOP  library,
core::Real  min_inter_ss_bbrms,
core::Real  max_inter_ss_bbrms,
core::Real  min_intra_ss_bbrms,
core::Real  max_intra_ss_bbrms,
core::Real  min_rms,
core::Real  max_rms,
std::string const &  start_res,
std::string const &  stop_res,
core::Size  window_size,
core::Size  max_radius,
core::Size  max_struct,
core::Size  num_iterations,
core::Size  num_try_div,
bool  diversify_loop_only,
bool  ideal,
bool  filter_by_phipsi,
protocols::filters::FilterOP  cenfilter,
protocols::filters::FilterOP  ranking_cenfilter,
core::scoring::ScoreFunctionOP  scorefxn_cen_cst,
core::scoring::ScoreFunctionOP  scorefxn_rama_cst 
)
protocols::loophash::LoopHashDiversifier::~LoopHashDiversifier ( )
overridedefault

****Creator Methods****///

****End Creator Methods****///

Member Function Documentation

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

References loop_sizes_.

Referenced by parse_my_tag().

void protocols::loophash::LoopHashDiversifier::apply ( core::pose::Pose )
overridevirtual
void protocols::loophash::LoopHashDiversifier::cenfilter ( protocols::filters::FilterOP  cenfilter)

References cenfilter_.

Referenced by parse_my_tag().

protocols::moves::MoverOP protocols::loophash::LoopHashDiversifier::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.

protocols::moves::MoverOP protocols::loophash::LoopHashDiversifier::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.

std::string protocols::loophash::LoopHashDiversifier::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::LoopHashDiversifier::loop_sizes ( ) const

References loop_sizes_.

Referenced by LoopHashDiversifier(), and parse_my_tag().

Real protocols::loophash::LoopHashDiversifier::max_inter_ss_bbrms ( ) const

References max_inter_ss_bbrms_.

Referenced by apply(), and max_inter_ss_bbrms().

void protocols::loophash::LoopHashDiversifier::max_inter_ss_bbrms ( core::Real const  max_inter_ss_bbrms)
Real protocols::loophash::LoopHashDiversifier::max_intra_ss_bbrms ( ) const

References max_intra_ss_bbrms_.

Referenced by apply(), and max_intra_ss_bbrms().

void protocols::loophash::LoopHashDiversifier::max_intra_ss_bbrms ( core::Real const  max_intra_ss_bbrms)
Real protocols::loophash::LoopHashDiversifier::max_rms ( ) const

References max_rms_.

Referenced by apply(), and max_rms().

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

References max_rms(), and max_rms_.

Real protocols::loophash::LoopHashDiversifier::min_inter_ss_bbrms ( ) const

References min_inter_ss_bbrms_.

Referenced by apply(), and min_inter_ss_bbrms().

void protocols::loophash::LoopHashDiversifier::min_inter_ss_bbrms ( core::Real const  min_inter_ss_bbrms)
Real protocols::loophash::LoopHashDiversifier::min_intra_ss_bbrms ( ) const

References min_intra_ss_bbrms_.

Referenced by apply(), and min_intra_ss_bbrms().

void protocols::loophash::LoopHashDiversifier::min_intra_ss_bbrms ( core::Real const  min_intra_ss_bbrms)
Real protocols::loophash::LoopHashDiversifier::min_rms ( ) const

References min_rms_.

Referenced by apply(), and min_rms().

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

References min_rms(), and min_rms_.

std::string protocols::loophash::LoopHashDiversifier::mover_name ( )
static
Size protocols::loophash::LoopHashDiversifier::num_iterations ( ) const

References num_iterations_.

Referenced by num_iterations().

void protocols::loophash::LoopHashDiversifier::num_iterations ( core::Size const  num_iterations)
Size protocols::loophash::LoopHashDiversifier::num_try_div ( ) const

References num_try_div_.

Referenced by num_try_div().

void protocols::loophash::LoopHashDiversifier::num_try_div ( core::Size const  num_try_div)

References num_try_div(), and num_try_div_.

void protocols::loophash::LoopHashDiversifier::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(), cenfilter(), diversify_loop_only_, filter_by_phipsi_, core::pose::get_resnum_string(), ideal_, library_, loop_sizes(), max_inter_ss_bbrms_, max_intra_ss_bbrms_, max_radius_, max_rms_, max_struct_, min_inter_ss_bbrms_, min_intra_ss_bbrms_, min_rms_, num_iterations_, num_try_div_, protocols::rosetta_scripts::parse_filter(), protocols::rosetta_scripts::parse_filter_or_null(), ranking_cenfilter(), scorefxn_cen_cst_, scorefxn_rama_cst_, start_res_, stop_res_, and window_size_.

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

References ranking_cenfilter_.

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

References ranking_cenfilter_.

Referenced by apply(), and parse_my_tag().

Member Data Documentation

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

Referenced by apply().

protocols::filters::FilterOP protocols::loophash::LoopHashDiversifier::cenfilter_
private

Referenced by apply(), and cenfilter().

bool protocols::loophash::LoopHashDiversifier::diversify_loop_only_
private

Referenced by apply(), and parse_my_tag().

bool protocols::loophash::LoopHashDiversifier::filter_by_phipsi_
private

Referenced by apply(), and parse_my_tag().

bool protocols::loophash::LoopHashDiversifier::ideal_
private

Referenced by apply(), and parse_my_tag().

LoopHashLibraryOP protocols::loophash::LoopHashDiversifier::library_
private
utility::vector1< core::Size > protocols::loophash::LoopHashDiversifier::loop_sizes_
private
core::Real protocols::loophash::LoopHashDiversifier::max_inter_ss_bbrms_
private

Referenced by max_inter_ss_bbrms(), and parse_my_tag().

core::Real protocols::loophash::LoopHashDiversifier::max_intra_ss_bbrms_
private

Referenced by max_intra_ss_bbrms(), and parse_my_tag().

core::Size protocols::loophash::LoopHashDiversifier::max_radius_
private

Referenced by apply(), and parse_my_tag().

core::Real protocols::loophash::LoopHashDiversifier::max_rms_
private

Referenced by max_rms(), and parse_my_tag().

core::Size protocols::loophash::LoopHashDiversifier::max_struct_
private

Referenced by apply(), and parse_my_tag().

core::Real protocols::loophash::LoopHashDiversifier::min_inter_ss_bbrms_
private

Referenced by min_inter_ss_bbrms(), and parse_my_tag().

core::Real protocols::loophash::LoopHashDiversifier::min_intra_ss_bbrms_
private

Referenced by min_intra_ss_bbrms(), and parse_my_tag().

core::Real protocols::loophash::LoopHashDiversifier::min_rms_
private

Referenced by min_rms(), and parse_my_tag().

core::Size protocols::loophash::LoopHashDiversifier::num_iterations_
private

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

core::Size protocols::loophash::LoopHashDiversifier::num_try_div_
private

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

protocols::filters::FilterOP protocols::loophash::LoopHashDiversifier::ranking_cenfilter_
private

Referenced by ranking_cenfilter().

core::scoring::ScoreFunctionOP protocols::loophash::LoopHashDiversifier::scorefxn_cen_cst_
private

Referenced by apply(), and parse_my_tag().

core::scoring::ScoreFunctionOP protocols::loophash::LoopHashDiversifier::scorefxn_rama_cst_
private

Referenced by apply(), and parse_my_tag().

std::string protocols::loophash::LoopHashDiversifier::start_res_
private

Referenced by apply(), and parse_my_tag().

std::string protocols::loophash::LoopHashDiversifier::stop_res_
private

Referenced by apply(), and parse_my_tag().

core::Size protocols::loophash::LoopHashDiversifier::window_size_
private

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