Rosetta
2016.11
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#include <ParsedProtocol.hh>
Classes | |
class | MoverFilterPair |
Public Types | |
typedef core::Real | Real |
typedef core::pose::Pose | Pose |
typedef utility::vector1 < MoverFilterPair > | MoverFilterVector |
typedef MoverFilterVector::iterator | iterator |
typedef MoverFilterVector::const_iterator | const_iterator |
Public Types inherited from protocols::moves::Mover | |
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 | |
ParsedProtocol () | |
virtual | ~ParsedProtocol () |
virtual void | apply (Pose &pose) |
virtual core::pose::PoseOP | get_additional_output () |
virtual std::string | get_name () const |
Each derived class must specify its name. The class name. More... | |
void | final_scorefxn (core::scoring::ScoreFunctionCOP scorefxn) |
core::scoring::ScoreFunctionCOP | final_scorefxn () const |
void | final_score (core::pose::Pose &pose) const |
void | report_all (Pose const &pose) const |
void | report_filters_to_pose (Pose &pose) |
void | report_filters_to_job (Pose const &pose) const |
virtual void | add_values_to_job (Pose const &pose, protocols::jd2::Job &) const |
protocols::moves::MoverCOP | get_mover (core::Size const mover_number) const |
MoverFilterPair | get_mover_filter_pair (core::Size const mover_number) const |
void | add_mover_filter_pair (protocols::moves::MoverOP mover, std::string const &mover_name, protocols::filters::FilterOP filter, bool const report_filter_at_end=false) |
Add a mover-filter pair. More... | |
void | set_resid (core::Size const resid) |
protocols::moves::MoverOP | clone () const |
Return a clone of the Mover object. More... | |
protocols::moves::MoverOP | fresh_instance () const |
Generates a new Mover object freshly created with the default ctor. More... | |
virtual void | parse_my_tag (utility::tag::TagCOP, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &) |
Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
void | clear () |
std::string | mode () const |
iterator | begin () |
const_iterator | begin () const |
iterator | end () |
const_iterator | end () const |
void | apply_probability (utility::vector1< core::Real > const a) |
utility::vector1< core::Real > | apply_probability () |
core::Size | size () |
core::Size | last_attempted_mover_idx () |
void | last_attempted_mover_idx (core::Size const s) |
bool | report_call_order () const |
void | report_call_order (bool const c) |
std::string | call_order () const |
Public Member Functions inherited from protocols::moves::Mover | |
Mover () | |
virtual | ~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... | |
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 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 |
virtual void | show (std::ostream &output=std::cout) const |
Outputs details about the Mover, including current settings. More... | |
Public Member Functions inherited from protocols::moves::ResId | |
ResId () | |
ResId (core::Size const r) | |
virtual core::Size | get_resid () const |
virtual core::Size & | get_resid () |
virtual bool | modifiable () const |
should another method be able to modify resid_. This is used by modify_ResId_based_object as a test More... | |
virtual void | modifiable (bool const u) |
virtual | ~ResId () |
Private Member Functions | |
void | finish_protocol (Pose &pose) |
void | apply_mover (Pose &pose, MoverFilterPair const &mover_pair) |
apply the mover of the pair More... | |
bool | apply_filter (Pose &pose, MoverFilterPair const &mover_pair) |
apply the filter of the pair More... | |
void | sequence_protocol (Pose &pose, MoverFilterVector::const_iterator mover_it_in) |
void | random_order_protocol (Pose &pose) |
void | random_single_protocol (Pose &pose) |
Private Attributes | |
MoverFilterVector | movers_ |
core::scoring::ScoreFunctionCOP | final_scorefxn_ |
std::string | mode_ |
utility::vector1< core::Real > | apply_probability_ |
core::Size | last_attempted_mover_idx_ |
bool | report_call_order_ |
std::string | call_order_ |
protocols::moves::MoverOP | last_mover_ |
bool | resume_support_ |
Additional Inherited Members | |
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... | |
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... | |
typedef MoverFilterVector::const_iterator protocols::rosetta_scripts::ParsedProtocol::const_iterator |
typedef MoverFilterVector::iterator protocols::rosetta_scripts::ParsedProtocol::iterator |
typedef utility::vector1< MoverFilterPair > protocols::rosetta_scripts::ParsedProtocol::MoverFilterVector |
protocols::rosetta_scripts::ParsedProtocol::ParsedProtocol | ( | ) |
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void protocols::rosetta_scripts::ParsedProtocol::add_mover_filter_pair | ( | protocols::moves::MoverOP | mover, |
std::string const & | mover_name, | ||
protocols::filters::FilterOP | filter, | ||
bool const | report_filter_at_end = false |
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Implements protocols::jd2::JobOutputterObserver.
References protocols::jd2::Job::add_string_real_pair(), and movers_.
Referenced by report_filters_to_job().
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Takes care of the docking, design and filtering moves. pre_cycle and pose_cycle can be setup in derived classes to setup variables before and after these cycles.
Implements protocols::moves::Mover.
References apply_filter(), protocols::jd2::JobDistributor::current_job(), protocols::moves::FAIL_RETRY, final_score(), protocols::jd2::JobDistributor::get_instance(), protocols::moves::Mover::get_last_move_status(), protocols::moves::Mover::get_self_ptr(), protocols::jd2::jd2_used(), last_mover_, mode_, movers_, protocols::moves::MS_SUCCESS, random_order_protocol(), random_single_protocol(), resume_support_, sequence_protocol(), and protocols::moves::Mover::set_last_move_status().
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apply the filter of the pair
References protocols::filters::Filter::apply(), protocols::nonlocal::current_job(), end(), protocols::moves::FAIL_RETRY, protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair::filter(), protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair::first, protocols::jd2::JobDistributor::get_instance(), protocols::filters::Filter::get_user_defined_name(), protocols::moves::Mover::info(), protocols::moves::MS_SUCCESS, protocols::filters::Filter::report(), protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair::report_filter_at_end_, protocols::filters::Filter::report_sm(), protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair::second, protocols::moves::Mover::set_last_move_status(), and core::pose::Pose::update_residue_neighbors().
Referenced by apply(), get_additional_output(), random_order_protocol(), random_single_protocol(), and sequence_protocol().
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apply the mover of the pair
References protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair::first, protocols::moves::Mover::get_native_pose(), and last_mover_.
Referenced by get_additional_output(), random_order_protocol(), random_single_protocol(), and sequence_protocol().
void protocols::rosetta_scripts::ParsedProtocol::apply_probability | ( | utility::vector1< core::Real > const | a | ) |
References core::pose::motif::a(), apply_probability_, and movers_.
utility::vector1< core::Real > protocols::rosetta_scripts::ParsedProtocol::apply_probability | ( | ) |
References apply_probability_.
Referenced by parse_my_tag(), and random_single_protocol().
ParsedProtocol::iterator protocols::rosetta_scripts::ParsedProtocol::begin | ( | ) |
References movers_.
ParsedProtocol::const_iterator protocols::rosetta_scripts::ParsedProtocol::begin | ( | ) | const |
References movers_.
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References call_order_.
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References movers_.
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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.
ParsedProtocol::iterator protocols::rosetta_scripts::ParsedProtocol::end | ( | ) |
References movers_.
Referenced by apply_filter().
ParsedProtocol::const_iterator protocols::rosetta_scripts::ParsedProtocol::end | ( | ) | const |
References movers_.
void protocols::rosetta_scripts::ParsedProtocol::final_score | ( | core::pose::Pose & | pose | ) | const |
References final_scorefxn(), core::pose::symmetry::is_symmetric(), and core::scoring::symmetry::symmetrize_scorefunction().
Referenced by apply().
void protocols::rosetta_scripts::ParsedProtocol::final_scorefxn | ( | core::scoring::ScoreFunctionCOP | scorefxn | ) |
References final_scorefxn_.
core::scoring::ScoreFunctionCOP protocols::rosetta_scripts::ParsedProtocol::final_scorefxn | ( | ) | const |
References final_scorefxn_.
Referenced by final_score().
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References protocols::nonlocal::current_job(), protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair::first, protocols::jd2::JobDistributor::get_instance(), movers_, protocols::moves::MS_SUCCESS, report_all(), report_call_order(), report_filters_to_pose(), and protocols::moves::Mover::set_last_move_status().
Referenced by random_order_protocol(), random_single_protocol(), and sequence_protocol().
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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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Looks for any submovers that have additional output poses to process. If any are found, run remainder of parsed protocol.
Reimplemented from protocols::moves::Mover.
References apply_filter(), apply_mover(), mode_, movers_, protocols::moves::MS_SUCCESS, report_all(), report_filters_to_pose(), resume_support_, and protocols::moves::Mover::set_last_move_status().
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References movers_.
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References movers_.
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Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References protocols::rosetta_scripts::ParsedProtocolCreator::mover_name().
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References last_attempted_mover_idx_.
Referenced by random_single_protocol().
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References last_attempted_mover_idx_.
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References mode_.
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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 stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.
Reimplemented from protocols::moves::Mover.
References apply_probability(), mode_, movers_, protocols::rosetta_scripts::parse_mover_subtag(), report_call_order(), and resume_support_.
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References apply_filter(), apply_mover(), finish_protocol(), movers_, and core::scoring::rg.
Referenced by apply().
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References apply_filter(), apply_mover(), apply_probability(), finish_protocol(), last_attempted_mover_idx(), movers_, protocols::simple_moves::bb_sampler::probability, and core::scoring::rg.
Referenced by apply().
void protocols::rosetta_scripts::ParsedProtocol::report_all | ( | Pose const & | pose | ) | const |
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References report_call_order_.
Referenced by finish_protocol(), and parse_my_tag().
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References core::pack::dunbrack::c, and report_call_order_.
void protocols::rosetta_scripts::ParsedProtocol::report_filters_to_job | ( | Pose const & | pose | ) | const |
void protocols::rosetta_scripts::ParsedProtocol::report_filters_to_pose | ( | Pose & | pose | ) |
References movers_, and core::pose::setPoseExtraScore().
Referenced by finish_protocol(), and get_additional_output().
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References apply_filter(), apply_mover(), finish_protocol(), and movers_.
Referenced by apply().
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sets resid for the constituent filters and movers
Reimplemented from protocols::moves::ResId.
References protocols::moves::modify_ResId_based_object(), and movers_.
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References movers_.
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Referenced by apply_probability().
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Referenced by call_order().
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Referenced by final_scorefxn().
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Referenced by last_attempted_mover_idx().
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Referenced by apply(), and apply_mover().
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Referenced by apply(), get_additional_output(), mode(), and parse_my_tag().
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Referenced by add_mover_filter_pair(), add_values_to_job(), apply(), apply_probability(), begin(), clear(), end(), finish_protocol(), get_additional_output(), get_mover(), get_mover_filter_pair(), parse_my_tag(), random_order_protocol(), random_single_protocol(), report_all(), report_filters_to_pose(), sequence_protocol(), set_resid(), and size().
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Referenced by report_call_order().
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Referenced by apply(), get_additional_output(), and parse_my_tag().