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Rosetta
2020.11
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A mover to set mainchain torsions by bin transition probabilities. More...
#include <InitializeByBins.hh>
Public Member Functions | |
InitializeByBins () | |
Default constructor. More... | |
InitializeByBins (InitializeByBins const &src) | |
Copy constructor. More... | |
~InitializeByBins () override | |
Destructor. More... | |
protocols::moves::MoverOP | clone () const override |
Clone – i.e. create a new object copying this one and return an owning pointer to the copy. More... | |
protocols::moves::MoverOP | fresh_instance () const override |
Get a new instance of this mover (NOT copying). More... | |
void | apply (core::pose::Pose &pose) override |
Apply the mover to a pose. More... | |
void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &) override |
Parse XML for RosettaScripts. More... | |
void | set_binfile_and_load (std::string const &name) |
Set the bin transition probability file. More... | |
void | set_residue_range (core::Size const start, core::Size const end) |
Set the residue ranges. If set to (0,0), the start and end of the pose are used as the range bounds. More... | |
std::string | get_name () const override |
Each derived class must specify its name. The class name. More... | |
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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 Strings & | info () |
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) |
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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 | moverclass |
Private Attributes | |
core::Size | start_res_ |
Start of residue range. More... | |
core::Size | end_res_ |
End of residue range. More... | |
std::string | binfile_ |
Bin transition probability data file. More... | |
bool | binfile_loaded_ |
Has the bin transition probability file been loaded already? More... | |
core::scoring::bin_transitions::BinTransitionCalculatorOP | bin_transition_calculator_ |
Owning pointer to the BinTransitionCalculator object used by this mover. More... | |
Additional Inherited Members | |
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typedef utility::tag::TagCOP | TagCOP |
typedef core::pose::Pose | Pose |
typedef core::pose::PoseCOP | PoseCOP |
typedef protocols::filters::Filters_map | Filters_map |
typedef std::list< std::string > | Strings |
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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... | |
A mover to set mainchain torsions by bin transition probabilities.
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private |
protocols::simple_moves::bin_transitions::InitializeByBins::InitializeByBins | ( | ) |
Default constructor.
protocols::simple_moves::bin_transitions::InitializeByBins::InitializeByBins | ( | InitializeByBins const & | src | ) |
Copy constructor.
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overridedefault |
Destructor.
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overridevirtual |
Apply the mover to a pose.
Implements protocols::moves::Mover.
References core::id::BB, bin_transition_calculator_, core::pose::Pose::conformation(), end_res_, core::conformation::Residue::mainchain_torsions(), core::pose::Pose::residue(), core::pose::Pose::set_torsion(), core::pose::Pose::size(), start_res_, and core::pose::Pose::update_residue_neighbors().
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inlineoverridevirtual |
Clone – i.e. create a new object copying this one and return an owning pointer to the copy.
Reimplemented from protocols::moves::Mover.
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inlineoverridevirtual |
Get a new instance of this mover (NOT copying).
Reimplemented from protocols::moves::Mover.
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overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References mover_name().
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static |
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overridevirtual |
Parse XML for RosettaScripts.
Reimplemented from protocols::moves::Mover.
References set_binfile_and_load(), and set_residue_range().
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static |
void protocols::simple_moves::bin_transitions::InitializeByBins::set_binfile_and_load | ( | std::string const & | name | ) |
Set the bin transition probability file.
Also, loads the object.
References bin_transition_calculator_, binfile_, binfile_loaded_, and protocols::moves::Mover::name().
Referenced by parse_my_tag().
void protocols::simple_moves::bin_transitions::InitializeByBins::set_residue_range | ( | core::Size const | start, |
core::Size const | end | ||
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Set the residue ranges. If set to (0,0), the start and end of the pose are used as the range bounds.
References core::sequence::end, end_res_, protocols::loops::start, and start_res_.
Referenced by parse_my_tag().
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private |
Owning pointer to the BinTransitionCalculator object used by this mover.
Object created when the InitializeByBins mover is created.
Referenced by apply(), and set_binfile_and_load().
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private |
Bin transition probability data file.
Referenced by set_binfile_and_load().
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private |
Has the bin transition probability file been loaded already?
This mover is not made to be re-used. Probability file should only be loaded once.
Referenced by set_binfile_and_load().
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private |
End of residue range.
Referenced by apply(), and set_residue_range().
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private |
Start of residue range.
Referenced by apply(), and set_residue_range().