wraps protein-interface specific considerations around the general multistate design / genetic algorithm framework More...
#include <ProteinInterfaceMultiStateDesignMover.hh>
Public Types | |
| typedef multistate_design::PosType | PosType |
| typedef core::pack::task::PackerTaskCOP | PackerTaskCOP |
| typedef utility::pointer::shared_ptr< genetic_algorithm::GeneticAlgorithm > | GeneticAlgorithmOP |
 Public Types inherited from protocols::minimization_packing::PackRotamersMover | |
| typedef core::pack::interaction_graph::AnnealableGraphBaseOP | AnnealableGraphBaseOP |
| typedef core::pack::interaction_graph::AnnealableGraphBaseCOP | AnnealableGraphBaseCOP |
| typedef core::pack::rotamer_set::RotamerSetsOP | RotamerSetsOP |
| typedef core::pack::rotamer_set::RotamerSetsCOP | RotamerSetsCOP |
| typedef core::pack::task::PackerTaskCOP | PackerTaskCOP |
| typedef core::pack::task::TaskFactoryCOP | TaskFactoryCOP |
| typedef core::scoring::ScoreFunctionCOP | ScoreFunctionCOP |
| 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 |
Public Member Functions | |
| ProteinInterfaceMultiStateDesignMover () | |
| ~ProteinInterfaceMultiStateDesignMover () override | |
| void | apply (Pose &) override |
| Performs side-chain packing based on the input PackerTask using the input ScoreFunction. More... | |
| void | output_results (Pose &) |
| void | parse_my_tag (TagCOP, basic::datacache::DataMap &) override |
| parse XML (specifically in the context of the parser/scripting scheme) More... | |
| moves::MoverOP | fresh_instance () const override |
| required in the context of the parser/scripting scheme More... | |
| moves::MoverOP | clone () const override |
| required in the context of the parser/scripting scheme More... | |
| void | restrict_sequence_profile (core::pose::Pose const &pose, core::pack::task::PackerTaskOP const ptask) const |
| unsigned long | sequence_space (core::pack::task::PackerTaskCOP ptask) const |
| void | output_alternative_states (core::pose::Pose const &output_pose) const |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
| Public Member Functions inherited from protocols::minimization_packing::PackRotamersMover | |
| PackRotamersMover () | |
| default constructor; reads the nloop_ value from the global options system. More... | |
| PackRotamersMover (utility::options::OptionCollection const &options) | |
| constructor that reads from the (possibly local) options collection object More... | |
| PackRotamersMover (std::string const &) | |
| constructor with typename; reads the nloop_ value from the global options system. More... | |
| PackRotamersMover (ScoreFunctionCOP scorefxn, PackerTaskCOP task=nullptr, core::Size nloop=1) | |
| Constructs a PackRotamersMover with PackerTask <task> evaluated using <scorefxn> More... | |
| ~PackRotamersMover () override | |
| PackRotamersMover (PackRotamersMover const &other) | |
| void | show (std::ostream &output=std::cout) const override |
| Outputs details about the Mover, including current settings. More... | |
| bool | task_is_valid (Pose const &pose) const |
| when the PackerTask was not generated locally, verify compatibility with pose More... | |
| virtual void | parse_score_function (TagCOP, basic::datacache::DataMap const &) |
| parse "scorefxn" XML option (can be employed virtually by derived Packing movers) More... | |
| virtual void | parse_task_operations (TagCOP, basic::datacache::DataMap const &) |
| parse "task_operations" XML option (can be employed virtually by derived Packing movers) More... | |
| void | initialize_task_factory_with_operations (std::list< core::pack::task::operation::TaskOperationCOP > const &) |
| void | score_function (ScoreFunctionCOP sf) |
| Sets the ScoreFunction to <sf> More... | |
| virtual void | task_factory (TaskFactoryCOP tf) |
| Sets the TaskFactory to <tf> More... | |
| void | task (PackerTaskCOP t) |
| Sets the PackerTask to <t> More... | |
| void | nloop (core::Size nloop_in) |
| ScoreFunctionCOP | score_function () const |
| Returns the ScoreFunction. More... | |
| PackerTaskCOP | task () const |
| Returns the PackerTask. More... | |
| core::Size | nloop () const |
| TaskFactoryCOP | task_factory () const |
| Returns the TaskFactory. More... | |
| RotamerSetsCOP | rotamer_sets () const |
| Returns the RotamerSets object being used for packing. More... | |
| void | set_annealer_observer (core::pack::annealer::AnnealerObserverOP observer) |
| 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... | |
| 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 std::string | mover_name () |
| static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
| Static Public Member Functions inherited from protocols::minimization_packing::PackRotamersMover | |
| static std::string | mover_name () |
| static utility::tag::XMLSchemaComplexTypeGeneratorOP | complex_type_generator_for_pack_rotamers_mover (utility::tag::XMLSchemaDefinition &xsd) |
| static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
| static void | list_options_read (utility::options::OptionKeyList &opts) |
| 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... | |
Private Member Functions | |
| void | initialize (Pose &) |
| void | run () |
| void | add_states (Pose const &) |
| add target and competitor states More... | |
Additional Inherited Members | |
| Protected Member Functions inherited from protocols::minimization_packing::PackRotamersMover | |
| virtual void | setup (Pose &pose) |
| get rotamers, energies. Also performs lazy initialization of ScoreFunction, PackerTask. More... | |
| virtual core::PackerEnergy | run (Pose &pose, utility::vector0< int > rot_to_pack=utility::vector0< int >()) const |
| virtual void | cleanup (core::pose::Pose &pose) |
| Clean up cached pose and mover data after the fact. More... | |
| virtual void | note_packertask_settings (Pose const &) |
| note PackerTask's packable and designable residues as string info 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... | |
Detailed Description
wraps protein-interface specific considerations around the general multistate design / genetic algorithm framework
Member Typedef Documentation
◆ GeneticAlgorithmOP
| typedef utility::pointer::shared_ptr< genetic_algorithm::GeneticAlgorithm > protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::GeneticAlgorithmOP |
◆ PackerTaskCOP
| typedef core::pack::task::PackerTaskCOP protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::PackerTaskCOP |
◆ PosType
| typedef multistate_design::PosType protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::PosType |
Constructor & Destructor Documentation
◆ ProteinInterfaceMultiStateDesignMover()
| protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::ProteinInterfaceMultiStateDesignMover | ( | ) |
References saved_state_poses_, state_poses_, state_positive_, state_unbound_, and state_unfolded_.
◆ ~ProteinInterfaceMultiStateDesignMover()
|
overridedefault |
Member Function Documentation
◆ add_states()
|
private |
add target and competitor states
we build one target (bound) and two competitor (unbound and unfolded) states.
References input_is_positive_, multistate_packer_, protocols::protein_interface_design::movers::part_complex(), rb_jump_, saved_state_poses_, scorefxn_, state_poses_, state_positive_, state_task_factory_, state_unbound_, state_unfolded_, protocols::minimization_packing::PackRotamersMover::task_factory(), unbound_, protocols::protein_interface_design::movers::unfold_complex(), core::scoring::unfolded, and unfolded_.
Referenced by initialize().
◆ apply()
|
overridevirtual |
Performs side-chain packing based on the input PackerTask using the input ScoreFunction.
example(s): packmover.apply(pose) See Also: PackerTask ScoreFunction
Reimplemented from protocols::minimization_packing::PackRotamersMover.
References initialize(), output_alternative_states(), output_results(), and run().
◆ clone()
|
overridevirtual |
required in the context of the parser/scripting scheme
Reimplemented from protocols::minimization_packing::PackRotamersMover.
◆ fresh_instance()
|
overridevirtual |
required in the context of the parser/scripting scheme
Reimplemented from protocols::minimization_packing::PackRotamersMover.
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Reimplemented from protocols::minimization_packing::PackRotamersMover.
References mover_name().
◆ initialize()
|
private |
References protocols::cluster::calibur::aa, add_states(), core::pack::task::ResidueLevelTask::allowed_residue_types(), anchor_offset_, core::pack::task::ResidueLevelTask::being_designed(), boltz_temp_, checkpoint_gz_, checkpoint_interval_, checkpoint_prefix_, checkpoint_rename_, compare_energy_to_ground_state_, core::sequence::end, fraction_by_recombination_, gen_alg_, generations_, protocols::moves::Mover::info(), core::chemical::ResidueTypeBase::is_protein(), multistate_packer_, mutate_rate_, num_packs_, pop_from_ss_, pop_size_, core::pose::Pose::residue_type(), restrict_sequence_profile(), scorefxn_, protocols::hybridization::t, protocols::minimization_packing::PackRotamersMover::task(), protocols::minimization_packing::PackRotamersMover::task_factory(), protocols::multistate_design::PosType::to_string(), and protocols::protein_interface_design::movers::TR().
Referenced by apply().
◆ mover_name()
|
static |
◆ output_alternative_states()
| void protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::output_alternative_states | ( | core::pose::Pose const & | output_pose | ) | const |
References core::pose::Pose::dump_scored_pdb(), fname_prefix_, core::pack::pack_rotamers(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), saved_state_poses_, scorefxn_, core::pose::Pose::size(), state_positive_, protocols::minimization_packing::PackRotamersMover::task_factory(), protocols::protein_interface_design::movers::TR(), and core::pose::Pose::update_residue_neighbors().
Referenced by apply().
◆ output_results()
| void protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::output_results | ( | Pose & | pose | ) |
References core::sequence::end, core::chemical::element::F, protocols::genetic_algorithm::Entity::fitness(), gen_alg_, protocols::moves::Mover::info(), multistate_packer_, numresults_, scorefxn_, protocols::protein_interface_design::movers::TR(), and protocols::genetic_algorithm::Entity::traits().
Referenced by apply().
◆ parse_my_tag()
|
overridevirtual |
parse XML (specifically in the context of the parser/scripting scheme)
Reimplemented from protocols::minimization_packing::PackRotamersMover.
References anchor_offset_, boltz_temp_, bump_threshold_, checkpoint_gz_, checkpoint_interval_, checkpoint_prefix_, checkpoint_rename_, compare_energy_to_ground_state_, fname_prefix_, fraction_by_recombination_, generations_, input_is_positive_, mutate_rate_, num_packs_, numresults_, core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), core::import_pose::PDB_file, pop_from_ss_, pop_size_, core::import_pose::pose_from_file(), rb_jump_, saved_state_poses_, scorefxn_, state_poses_, state_positive_, state_task_factory_, state_unbound_, state_unfolded_, protocols::minimization_packing::PackRotamersMover::task_factory(), protocols::protein_interface_design::movers::TR(), unbound_, core::scoring::unfolded, unfolded_, and use_unbound_for_sequence_profile_.
◆ provide_xml_schema()
|
static |
References core::scoring::attributes_for_parse_score_function(), core::pack::task::attributes_for_parse_task_operations(), mover_name(), protocols::protein_interface_design::movers::subtag_for_msd(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().
Referenced by protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMoverCreator::provide_xml_schema().
◆ restrict_sequence_profile()
| void protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::restrict_sequence_profile | ( | core::pose::Pose const & | pose, |
| core::pack::task::PackerTaskOP const | ptask | ||
| ) | const |
References core::conformation::Residue::aa(), protocols::cluster::calibur::aa, core::chemical::aa_ala, core::pack::task::ResidueLevelTask::allowed_residue_types(), core::pack::task::ResidueLevelTask::being_designed(), bump_threshold_, core::sequence::end, core::scoring::fa_rep, core::chemical::ResidueTypeBase::is_protein(), core::conformation::Residue::name3(), core::chemical::num_canonical_aas, core::pack::pack_rotamers(), protocols::protein_interface_design::movers::part_complex(), core::pack::task::ResidueLevelTask::prevent_repacking(), rb_jump_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pack::task::ResidueLevelTask::restrict_absent_canonical_aas(), core::pack::rotamer_trials(), scorefxn_, sequence_space(), core::pose::Pose::size(), protocols::hybridization::t, protocols::protein_interface_design::movers::TR(), and use_unbound_for_sequence_profile_.
Referenced by initialize().
◆ run()
|
private |
References gen_alg_, and protocols::protein_interface_design::movers::TR().
Referenced by apply().
◆ sequence_space()
| unsigned long protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::sequence_space | ( | core::pack::task::PackerTaskCOP | ptask | ) | const |
Member Data Documentation
◆ anchor_offset_
|
private |
Referenced by initialize(), and parse_my_tag().
◆ boltz_temp_
|
private |
Referenced by initialize(), and parse_my_tag().
◆ bump_threshold_
|
private |
Referenced by parse_my_tag(), and restrict_sequence_profile().
◆ checkpoint_gz_
|
private |
Referenced by initialize(), and parse_my_tag().
◆ checkpoint_interval_
|
private |
Referenced by initialize(), and parse_my_tag().
◆ checkpoint_prefix_
|
private |
Referenced by initialize(), and parse_my_tag().
◆ checkpoint_rename_
|
private |
Referenced by initialize(), and parse_my_tag().
◆ compare_energy_to_ground_state_
|
private |
Referenced by initialize(), and parse_my_tag().
◆ fname_prefix_
|
private |
Referenced by output_alternative_states(), and parse_my_tag().
◆ fraction_by_recombination_
|
private |
Referenced by initialize(), and parse_my_tag().
◆ gen_alg_
|
private |
Referenced by initialize(), output_results(), and run().
◆ generations_
|
private |
Referenced by initialize(), and parse_my_tag().
◆ input_is_positive_
|
private |
Referenced by add_states(), and parse_my_tag().
◆ multistate_packer_
|
private |
Referenced by add_states(), initialize(), and output_results().
◆ mutate_rate_
|
private |
Referenced by initialize(), and parse_my_tag().
◆ num_packs_
|
private |
Referenced by initialize(), and parse_my_tag().
◆ numresults_
|
private |
Referenced by output_results(), and parse_my_tag().
◆ pop_from_ss_
|
private |
Referenced by initialize(), and parse_my_tag().
◆ pop_size_
|
private |
Referenced by initialize(), and parse_my_tag().
◆ rb_jump_
|
private |
Referenced by add_states(), parse_my_tag(), and restrict_sequence_profile().
◆ saved_state_poses_
|
private |
Referenced by add_states(), output_alternative_states(), parse_my_tag(), and ProteinInterfaceMultiStateDesignMover().
◆ scorefxn_
|
private |
Referenced by add_states(), initialize(), output_alternative_states(), output_results(), parse_my_tag(), and restrict_sequence_profile().
◆ state_poses_
|
private |
states
Referenced by add_states(), parse_my_tag(), and ProteinInterfaceMultiStateDesignMover().
◆ state_positive_
|
private |
for dumping out pdbs of negative states at the end
Referenced by add_states(), output_alternative_states(), parse_my_tag(), and ProteinInterfaceMultiStateDesignMover().
◆ state_task_factory_
|
private |
Referenced by add_states(), and parse_my_tag().
◆ state_unbound_
|
private |
Referenced by add_states(), parse_my_tag(), and ProteinInterfaceMultiStateDesignMover().
◆ state_unfolded_
|
private |
Referenced by add_states(), parse_my_tag(), and ProteinInterfaceMultiStateDesignMover().
◆ unbound_
|
private |
Referenced by add_states(), and parse_my_tag().
◆ unfolded_
|
private |
Referenced by add_states(), and parse_my_tag().
◆ use_unbound_for_sequence_profile_
|
private |
Referenced by parse_my_tag(), and restrict_sequence_profile().
The documentation for this class was generated from the following files:
- src/protocols/protein_interface_design/movers/ProteinInterfaceMultiStateDesignMover.hh
- src/protocols/protein_interface_design/movers/ProteinInterfaceMultiStateDesignMover.cc
