Rosetta
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#include <ConstraintSetMover.hh>
Public Types | |
typedef core::scoring::constraints::ConstraintSet | ConstraintSet |
typedef core::scoring::constraints::ConstraintSetOP | ConstraintSetOP |
typedef core::scoring::constraints::ConstraintSetCOP | ConstraintSetCOP |
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typedef utility::tag::TagCOP | TagCOP |
typedef core::pose::Pose | Pose |
typedef core::pose::PoseCOP | PoseCOP |
typedef std::list< std::string > | Strings |
Public Member Functions | |
ConstraintSetMover () | |
~ConstraintSetMover () override | |
ConstraintSetMover (std::string const &) | |
Options constructor that sets the mover name. More... | |
void | read_options () |
void | constraint_file (std::string const &) |
void | constraint_set (ConstraintSetCOP) |
ConstraintSetOP | constraint_set () |
ConstraintSetCOP | constraint_set () const |
void | apply (Pose &) override |
Main Method. 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... | |
void | parse_my_tag (TagCOP, basic::datacache::DataMap &) override |
Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
void | add_constraints (bool const a) |
bool | add_constraints () const |
void | set_cst_file (std::string const &file_name) |
Set the (centroid) constraint file name. More... | |
void | set_cst_fa_file (std::string const &file_name) |
Set the (full-atom) constraint file name. More... | |
void | set_cst_map_file (std::string const &file_name) |
Set the constraint map file name. More... | |
void | set_cst_map_file_contents (std::string const &file_contents) |
Set the constraint map file from previously loaded file contents in memory. 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 void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More... | |
Static Public Member Functions | |
static void | register_options () |
Associates relevant options with the ConstraintSetMover class. More... | |
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 Attributes | |
ConstraintSetOP | constraint_set_low_res_ |
ConstraintSetOP | constraint_set_high_res_ |
std::string | cst_file_ |
std::string | cst_fa_file_ |
bool | add_constraints_ |
std::unordered_map< std::string, std::string > | file_to_input_map_ |
std::string | current_input_name_ |
Additional Inherited Members | |
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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... | |
typedef core::scoring::constraints::ConstraintSet protocols::constraint_movers::ConstraintSetMover::ConstraintSet |
typedef core::scoring::constraints::ConstraintSetCOP protocols::constraint_movers::ConstraintSetMover::ConstraintSetCOP |
typedef core::scoring::constraints::ConstraintSetOP protocols::constraint_movers::ConstraintSetMover::ConstraintSetOP |
protocols::constraint_movers::ConstraintSetMover::ConstraintSetMover | ( | ) |
References read_options().
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overridedefault |
protocols::constraint_movers::ConstraintSetMover::ConstraintSetMover | ( | std::string const & | type | ) |
Options constructor that sets the mover name.
References read_options().
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inline |
References add_constraints_.
Referenced by apply(), and parse_my_tag().
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inline |
References core::pose::motif::a(), and add_constraints_.
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overridevirtual |
Main Method.
Implements protocols::moves::Mover.
References add_constraints(), core::pose::Pose::add_constraints(), core::pose::Pose::constraint_set(), constraint_set_high_res_, constraint_set_low_res_, cst_fa_file_, cst_file_, current_input_name_, file_to_input_map_, core::pose::Pose::is_fullatom(), and protocols::TR().
Referenced by protocols::symmetric_docking::SymDockProtocol::apply().
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overridevirtual |
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::constraint_movers::ConstraintSetMover::constraint_file | ( | std::string const & | cst_file | ) |
References cst_fa_file_, and cst_file_.
Referenced by protocols::glycan_docking::GlycanDockProtocol::setup_scorefxn().
ConstraintSetOP protocols::constraint_movers::ConstraintSetMover::constraint_set | ( | ) |
References constraint_set_low_res_.
ConstraintSetCOP protocols::constraint_movers::ConstraintSetMover::constraint_set | ( | ) | const |
References constraint_set_low_res_.
void protocols::constraint_movers::ConstraintSetMover::constraint_set | ( | ConstraintSetCOP | cst_set | ) |
References constraint_set_high_res_, and constraint_set_low_res_.
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overridevirtual |
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.
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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 |
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_constraints(), cst_fa_file_, cst_file_, current_input_name_, set_cst_fa_file(), set_cst_file(), set_cst_map_file(), and protocols::TR().
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static |
void protocols::constraint_movers::ConstraintSetMover::read_options | ( | ) |
References add_constraints_, cst_fa_file_, and cst_file_.
Referenced by ConstraintSetMover().
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static |
Associates relevant options with the ConstraintSetMover class.
Referenced by protocols::docking::DockingProtocol::register_options(), and protocols::glycan_docking::GlycanDockProtocol::register_options().
void protocols::constraint_movers::ConstraintSetMover::set_cst_fa_file | ( | std::string const & | file_name | ) |
void protocols::constraint_movers::ConstraintSetMover::set_cst_file | ( | std::string const & | file_name | ) |
void protocols::constraint_movers::ConstraintSetMover::set_cst_map_file | ( | std::string const & | file_name | ) |
Set the constraint map file name.
References set_cst_map_file_contents().
Referenced by parse_my_tag().
void protocols::constraint_movers::ConstraintSetMover::set_cst_map_file_contents | ( | std::string const & | file_contents | ) |
Set the constraint map file from previously loaded file contents in memory.
References file_to_input_map_, and protocols::sparta::split().
Referenced by set_cst_map_file().
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private |
Referenced by add_constraints(), and read_options().
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private |
Referenced by apply(), and constraint_set().
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private |
Referenced by apply(), and constraint_set().
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private |
Referenced by apply(), constraint_file(), parse_my_tag(), read_options(), and set_cst_fa_file().
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private |
Referenced by apply(), constraint_file(), parse_my_tag(), read_options(), and set_cst_file().
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private |
Referenced by apply(), and parse_my_tag().
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private |
Referenced by apply(), and set_cst_map_file_contents().