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Rosetta
2021.16
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Rosetta
2021.16
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The full trRosetta structure prediction protocol from Yang et al, converted to C++ and implemented as a mover. More...
#include <trRosettaProtocolMover.hh>
Public Member Functions | |
| trRosettaProtocolMover () | |
| Constructors ///. More... | |
| trRosettaProtocolMover (basic::options::OptionCollection const &options) | |
| Options constructor. More... | |
| ~trRosettaProtocolMover () override | |
| Destructor (important for properly forward-declaring smart-pointer members) More... | |
| void | apply (core::pose::Pose &pose) override |
| Mover Methods ///. More... | |
| void | show (std::ostream &output=std::cout) const override |
| Show the contents of the Mover. More... | |
| void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override |
| Rosetta Scripts Support ///. More... | |
| protocols::moves::MoverOP | fresh_instance () const override |
| required in the context of the parser/scripting scheme More... | |
| protocols::moves::MoverOP | clone () const override |
| required in the context of the parser/scripting scheme More... | |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
| void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const override |
| This mover is unpublished. It returns Vikram K. Mulligan as its author. It also adds Yang et al. (2020) as a citiation for trRosetta itself. 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 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... | |
Static Public Member Functions | |
| static void | register_options (bool const only_constraint_generator_options=false) |
| Indicate commandline flags that are relevant to this mover. More... | |
| static std::string | get_randomization_mode_string_from_enum (trRosettaProtocolBackboneRandomizationMode const mode_enum) |
| Given a backbone randomization mode enum, get a string corresponding to the enum. More... | |
| static trRosettaProtocolBackboneRandomizationMode | get_randomization_mode_enum_from_string (std::string const &mode_name) |
| Given a backbone randomization mode name, get the enum corresponding to the name. More... | |
| static std::string | get_minimization_mode_string_from_enum (trRosettaProtocolBackboneMinimizationMode const mode_enum) |
| Given a backbone minimization mode enum, get a string corresponding to the enum. More... | |
| static trRosettaProtocolBackboneMinimizationMode | get_minimization_mode_enum_from_string (std::string const &mode_name) |
| Given a backbone minimization mode name, get the enum corresponding to the name. More... | |
| 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... | |
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... | |
The full trRosetta structure prediction protocol from Yang et al, converted to C++ and implemented as a mover.
| protocols::trRosetta_protocols::movers::trRosettaProtocolMover::trRosettaProtocolMover | ( | ) |
Constructors ///.
Default constructor.
Initializes from the global options system.
Default constructor
Initializes from the global options system.
| protocols::trRosetta_protocols::movers::trRosettaProtocolMover::trRosettaProtocolMover | ( | basic::options::OptionCollection const & | options | ) |
Options constructor.
Initializes from a local options collection.
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overridedefault |
Destructor (important for properly forward-declaring smart-pointer members)
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overridevirtual |
Mover Methods ///.
Apply the mover
Implements protocols::moves::Mover.
References core::simple_metrics::RealMetric::apply(), protocols::trRosetta_protocols::movers::classic0, protocols::trRosetta_protocols::movers::classic1, protocols::trRosetta_protocols::movers::classic2, protocols::moves::Mover::get_native_pose(), core::sequence::read_fasta_file(), core::id::to_string(), and protocols::TR().
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overridevirtual |
required in the context of the parser/scripting scheme
Reimplemented from protocols::moves::Mover.
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overridevirtual |
required in the context of the parser/scripting scheme
Reimplemented from protocols::moves::Mover.
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static |
Given a backbone minimization mode name, get the enum corresponding to the name.
Throws if an invalid name is provided.
References protocols::trRosetta_protocols::movers::classic2, get_minimization_mode_string_from_enum(), and protocols::trRosetta_protocols::movers::NUM_ENTRIES.
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static |
Given a backbone minimization mode enum, get a string corresponding to the enum.
This function must be updated if entries are added to the trRosettaProtocolBackboneMinimizationMode enum class!
References protocols::trRosetta_protocols::movers::classic0, protocols::trRosetta_protocols::movers::classic1, protocols::trRosetta_protocols::movers::classic2, and core::id::to_string().
Referenced by get_minimization_mode_enum_from_string().
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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 |
Given a backbone randomization mode name, get the enum corresponding to the name.
Throws if an invalid name is provided.
References protocols::trRosetta_protocols::movers::classic, get_randomization_mode_string_from_enum(), and protocols::trRosetta_protocols::movers::NUM_ENTRIES.
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static |
Given a backbone randomization mode enum, get a string corresponding to the enum.
This function must be updated if entries are added to the trRosettaProtocolBackboneRandomizationMode enum class!
References protocols::trRosetta_protocols::movers::bins, protocols::trRosetta_protocols::movers::classic, protocols::trRosetta_protocols::movers::ramachandran, and core::id::to_string().
Referenced by get_randomization_mode_enum_from_string().
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overridevirtual |
Rosetta Scripts Support ///.
RosettaScripts Support ///.
parse XML tag (to use this Mover in Rosetta Scripts)
Reimplemented from protocols::moves::Mover.
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overridevirtual |
This mover is unpublished. It returns Vikram K. Mulligan as its author. It also adds Yang et al. (2020) as a citiation for trRosetta itself.
Reimplemented from protocols::moves::Mover.
References protocols::trRosetta::trRosettaProtocol_v1::get_trRosetta_neural_net_citation(), core::simple_metrics::metrics::RMSDMetric::provide_citation_info(), core::simple_metrics::metrics::TimingProfileMetric::provide_citation_info(), core::simple_metrics::metrics::TotalEnergyMetric::provide_citation_info(), and protocols::relax::FastRelax::provide_citation_info().
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static |
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static |
Indicate commandline flags that are relevant to this mover.
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overridevirtual |
Show the contents of the Mover.
Reimplemented from protocols::moves::Mover.
References protocols::moves::Mover::show().
Referenced by protocols::trRosetta_protocols::movers::operator<<().
1.8.7