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Rosetta
3.8
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#include <RotamerTrialsMinMover.hh>
Public Types | |
typedef core::scoring::ScoreFunctionOP | ScoreFunctionOP |
typedef core::scoring::ScoreFunctionCOP | ScoreFunctionCOP |
typedef core::pack::task::PackerTask | PackerTask |
typedef core::pack::task::PackerTaskOP | PackerTaskOP |
typedef core::pack::task::PackerTaskCOP | PackerTaskCOP |
typedef core::pack::task::TaskFactoryCOP | TaskFactoryCOP |
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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 |
Public Member Functions | |
RotamerTrialsMinMover () | |
RotamerTrialsMinMover (ScoreFunctionCOP scorefxn_in, PackerTask &task_in) | |
constructor with PackerTask. use a PackerTask ONLY for fixed-sequence work. WARNING TO ANY DESIGNER WHO PASSES IN A TASK: YOUR DESIGN STEPS WILL BE UNDONE AS THIS TASK CONCEIVES OF THE INPUT SEQUENCE THAT CORRESPONDS TO THE ORIGINAL SEQUENCE More... | |
RotamerTrialsMinMover (ScoreFunctionCOP scorefxn_in, TaskFactoryCOP factory_in) | |
constructor with TaskFactory for producing the packer task More... | |
void | init () |
~RotamerTrialsMinMover () override | |
void | apply (core::pose::Pose &pose) override |
Apply Rotamer-Trials with minimization to pose, using the score function and tasks provided by the constructor. More... | |
void | show (std::ostream &output=std::cout) const override |
Outputs details about the Mover, including current settings. More... | |
void | score_function (core::scoring::ScoreFunctionCOP sf) |
void | task_factory (core::pack::task::TaskFactoryCOP tf) |
void | parse_my_tag (TagCOP, basic::datacache::DataMap &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &) override |
Parse XML for RosettaScripts. More... | |
protocols::moves::MoverOP | fresh_instance () const override |
Return a new mover instance (for RosettaScripts) More... | |
protocols::moves::MoverOP | clone () const override |
Return a copy of this mover instance (for RosettaScripts) More... | |
std::string | get_name () const override |
Each derived class must specify its name. The class name. More... | |
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Mover () | |
~Mover () override | |
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 type_name) | |
sets the type for a mover; name_ has been removed (2010/05/14) More... | |
Mover (Mover const &other) | |
Mover & | operator= (Mover const &other) |
assignment operator More... | |
virtual core::Real | last_proposal_density_ratio () |
std::string const & | type () const |
void | set_type (std::string const &setting) |
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 | set_current_tag (std::string const &new_tag) |
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 |
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... | |
void | type (const std::string &type_in) |
std::string | get_type () const |
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... | |
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 | 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... | |
void | set_current_job (protocols::jobdist::BasicJobCOP job) |
jobdist::BasicJobCOP | get_current_job () const |
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... | |
Protected Member Functions | |
ScoreFunctionCOP | scorefxn () const |
read access for derived classes More... | |
PackerTaskOP | task (core::pose::Pose const &pose) const |
read access for derived classes, pose needed to run TaskFactory More... | |
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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... | |
Private Attributes | |
ScoreFunctionCOP | scorefxn_ |
RotamerTrailsMinMover does not have its own score function, rather, it shares one with other classes – CAUTION: the score function is externally modifiable, but this is probably the way users expect this to behave when they use this mover). More... | |
PackerTaskOP | task_ |
use a PackerTask ONLY for fixed-sequence work. WARNING TO ANY DESIGNER WHO PASSES IN A TASK: YOUR DESIGN STEPS WILL BE UNDONE AS THIS TASK CONCEIVES OF THE INPUT SEQUENCE THAT CORRESPONDS TO THE ORIGINAL SEQUENCE If a factory is present it overwrites this task with each call to apply() More... | |
TaskFactoryCOP | factory_ |
TaskFactory allows for nonconstant sequences to be used with RotamerTrialsMover CAUTION: the factory is externally modifiable. More... | |
bool | nonideal_ |
bool | cartesian_ |
typedef core::pack::task::PackerTaskCOP protocols::simple_moves::RotamerTrialsMinMover::PackerTaskCOP |
typedef core::scoring::ScoreFunctionCOP protocols::simple_moves::RotamerTrialsMinMover::ScoreFunctionCOP |
typedef core::scoring::ScoreFunctionOP protocols::simple_moves::RotamerTrialsMinMover::ScoreFunctionOP |
typedef core::pack::task::TaskFactoryCOP protocols::simple_moves::RotamerTrialsMinMover::TaskFactoryCOP |
protocols::simple_moves::RotamerTrialsMinMover::RotamerTrialsMinMover | ( | ) |
References init(), and protocols::moves::Mover::type().
protocols::simple_moves::RotamerTrialsMinMover::RotamerTrialsMinMover | ( | ScoreFunctionCOP | scorefxn_in, |
PackerTask & | task_in | ||
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constructor with PackerTask. use a PackerTask ONLY for fixed-sequence work. WARNING TO ANY DESIGNER WHO PASSES IN A TASK: YOUR DESIGN STEPS WILL BE UNDONE AS THIS TASK CONCEIVES OF THE INPUT SEQUENCE THAT CORRESPONDS TO THE ORIGINAL SEQUENCE
scorefxn_in | The score function used for packing and minimization (which may be modified externally) |
task_in | The task that will pass to the rotamers packer |
References core::pack::task::PackerTask::clone(), init(), task_, and protocols::moves::Mover::type().
protocols::simple_moves::RotamerTrialsMinMover::RotamerTrialsMinMover | ( | ScoreFunctionCOP | scorefxn_in, |
TaskFactoryCOP | factory_in | ||
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constructor with TaskFactory for producing the packer task
scorefxn_in | The score function used for packing and minimization (which may be modified externally) |
factory_in | The task that will pass to the rotamers packer |
References init(), and protocols::moves::Mover::type().
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overridedefault |
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overridevirtual |
Apply Rotamer-Trials with minimization to pose, using the score function and tasks provided by the constructor.
Implements protocols::moves::Mover.
Reimplemented in protocols::simple_moves::EnergyCutRotamerTrialsMinMover.
References cartesian_, nonideal_, scorefxn_, core::pack::RTMin::set_nonideal(), and task().
Referenced by protocols::protein_interface_design::movers::PrepackMover::apply().
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overridevirtual |
Return a copy of this mover instance (for RosettaScripts)
Reimplemented from protocols::moves::Mover.
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overridevirtual |
Return a new mover instance (for RosettaScripts)
Reimplemented from protocols::moves::Mover.
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overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
Reimplemented in protocols::simple_moves::EnergyCutRotamerTrialsMinMover.
References mover_name().
void protocols::simple_moves::RotamerTrialsMinMover::init | ( | void | ) |
References cartesian_, and nonideal_.
Referenced by protocols::simple_moves::EnergyCutRotamerTrialsMinMover::EnergyCutRotamerTrialsMinMover(), and RotamerTrialsMinMover().
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static |
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overridevirtual |
Parse XML for RosettaScripts.
Reimplemented from protocols::moves::Mover.
References cartesian_, core::scoring::get_score_function(), nonideal_, protocols::rosetta_scripts::parse_score_function(), protocols::rosetta_scripts::parse_task_operations(), score_function(), task_factory(), and protocols::simple_moves::TR().
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static |
References protocols::rosetta_scripts::attributes_for_parse_score_function(), protocols::rosetta_scripts::attributes_for_parse_task_operations(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().
Referenced by protocols::simple_moves::RotamerTrialsMinMoverCreator::provide_xml_schema().
void protocols::simple_moves::RotamerTrialsMinMover::score_function | ( | core::scoring::ScoreFunctionCOP | sf | ) |
References scorefxn_.
Referenced by parse_my_tag().
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protected |
read access for derived classes
References scorefxn_.
Referenced by protocols::simple_moves::EnergyCutRotamerTrialsMinMover::apply(), and show().
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overridevirtual |
Outputs details about the Mover, including current settings.
Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.
Reimplemented from protocols::moves::Mover.
References scorefxn(), and protocols::moves::Mover::show().
Referenced by protocols::simple_moves::operator<<().
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protected |
read access for derived classes, pose needed to run TaskFactory
read access for derived classes
References factory_, and task_.
Referenced by apply(), and protocols::simple_moves::EnergyCutRotamerTrialsMinMover::apply().
void protocols::simple_moves::RotamerTrialsMinMover::task_factory | ( | core::pack::task::TaskFactoryCOP | tf | ) |
References factory_.
Referenced by parse_my_tag().
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private |
Referenced by apply(), init(), and parse_my_tag().
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private |
TaskFactory allows for nonconstant sequences to be used with RotamerTrialsMover CAUTION: the factory is externally modifiable.
Referenced by task(), and task_factory().
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private |
Referenced by apply(), init(), and parse_my_tag().
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private |
RotamerTrailsMinMover does not have its own score function, rather, it shares one with other classes – CAUTION: the score function is externally modifiable, but this is probably the way users expect this to behave when they use this mover).
Referenced by apply(), score_function(), and scorefxn().
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private |
use a PackerTask ONLY for fixed-sequence work. WARNING TO ANY DESIGNER WHO PASSES IN A TASK: YOUR DESIGN STEPS WILL BE UNDONE AS THIS TASK CONCEIVES OF THE INPUT SEQUENCE THAT CORRESPONDS TO THE ORIGINAL SEQUENCE If a factory is present it overwrites this task with each call to apply()
Referenced by RotamerTrialsMinMover(), and task().