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Rosetta 3.5
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Rosetta 3.5
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#include <cluster.hh>
Public Member Functions | |
| ClusterBase () | |
| virtual std::string | get_name () const |
| Each derived class must specify its name. The class name. More... | |
| void | set_cluster_radius (core::Real cluster_radius) |
| void | set_population_weight (core::Real population_weight) |
| core::Real | get_cluster_radius () |
| core::Real | get_median_rms () |
| void | calculate_distance_matrix () |
| void | add_structure (core::pose::Pose &pose) |
| void | remove_highest_energy_member_of_each_group () |
| void | sort_each_group_by_energy () |
| void | sort_groups_by_energy () |
| void | remove_singletons () |
| void | export_only_low (bool value=false) |
| void | limit_groupsize (int limit=-1) |
| void | limit_groupsize (core::Real percent_limit) |
| void | random_limit_groupsize (core::Real percent_limit) |
| void | limit_groups (int limit=-1) |
| void | limit_total_structures (int limit=-1) |
| void | clean_pose_store () |
| void | print_summary () |
| void | print_raw_numbers () |
| void | print_cluster_assignment () |
| void | print_cluster_PDBs (std::string prefix) |
| void | print_clusters_silentfile (std::string prefix) |
| std::vector< core::pose::PoseOP > | return_lowest_poses_in_clusters () |
| std::vector< core::pose::PoseOP > | return_top_poses_in_clusters (core::Size count) |
| void | create_constraints (std::string prefix, EnsembleConstraints &constraint_maker) |
| std::vector< Cluster > const & | get_cluster_list () const |
 Public Member Functions inherited from protocols::cluster::GatherPosesMover | |
| GatherPosesMover () | |
| void | set_score_function (core::scoring::ScoreFunctionOP sfxn) |
| void | set_filter (core::Real filter) |
| virtual void | apply (core::pose::Pose &pose) |
| bool | check_tag (const std::string &query_tag) |
| void | push_back (const core::pose::Pose &pose) |
| void | clear () |
| void | set_cluster_by_protein_backbone (bool const &setting) |
| void | set_cluster_by_all_atom (bool const &setting) |
| int | processed () const |
| std::vector< core::pose::Pose > & | get_pose_list () |
| std::vector< std::string > const & | get_tag_list () const |
| virtual core::Real | get_distance_measure (const core::pose::Pose &pose1, const core::pose::Pose &pose2) const |
| Public Member Functions inherited from protocols::moves::Mover | |
| Mover () | |
| virtual | ~Mover () |
| virtual MoverSP | create () |
| virtual void | apply (core::io::serialization::PipeMap &pmap) |
| virtual void | parse_state (SerializableState const &state) |
| virtual void | parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache) |
| virtual void | save_state (SerializableState &state) |
| 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 |
| 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... | |
| 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) |
| virtual MoverOP | clone () const |
| clone has to be overridden only if clone invocation is expected. More... | |
| virtual void | parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose) |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| 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 |
| this function informs 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 |
| this function informs 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... | |
| virtual MoverOP | fresh_instance () const |
| this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More... | |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
Protected Attributes | |
| ObjexxFCL::FArray2D< core::Real > | distance_matrix |
| std::vector< Cluster > | clusterlist |
| bool | export_only_low_ |
| core::Real | median_rms_ |
| core::Real | population_weight_ |
| core::Real | cluster_radius_ |
| Protected Attributes inherited from protocols::cluster::GatherPosesMover | |
| std::vector< core::pose::Pose > | poselist |
Additional Inherited Members | |
| Public Types inherited from protocols::moves::Mover | |
| typedef utility::tag::TagPtr | TagPtr |
| typedef core::pose::Pose | Pose |
| typedef core::pose::PoseCOP | PoseCOP |
| typedef protocols::filters::Filters_map | Filters_map |
| typedef std::list< std::string > | Strings |
| 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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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... | |
Definition at line 196 of file cluster.hh.
| protocols::cluster::ClusterBase::ClusterBase | ( | ) |
Definition at line 277 of file cluster.cc.
| void protocols::cluster::ClusterBase::add_structure | ( | core::pose::Pose & | pose) |
Definition at line 356 of file cluster.cc.
References clusterlist, get_cluster_radius(), protocols::cluster::GatherPosesMover::get_distance_measure(), protocols::cluster::GatherPosesMover::poselist, core::scoring::rms, and protocols::cluster::tr().
| void protocols::cluster::ClusterBase::calculate_distance_matrix | ( | ) |
Definition at line 302 of file cluster.cc.
References distance_matrix, protocols::cluster::GatherPosesMover::get_distance_measure(), get_median_rms(), median_rms_, protocols::cluster::GatherPosesMover::poselist, and protocols::cluster::tr().
Referenced by protocols::cluster::ClusterPhilStyle::do_clustering().
| void protocols::cluster::ClusterBase::clean_pose_store | ( | ) |
Definition at line 586 of file cluster.cc.
References clusterlist, protocols::cluster::GatherPosesMover::poselist, and protocols::cluster::tr().
| void protocols::cluster::ClusterBase::create_constraints | ( | std::string | prefix, |
| EnsembleConstraints & | constraint_maker | ||
| ) |
Definition at line 793 of file cluster.cc.
References protocols::cluster::GatherPosesMover::clear(), clusterlist, protocols::cluster::EnsembleConstraints::createConstraints(), protocols::cluster::GatherPosesMover::poselist, protocols::cluster::GatherPosesMover::push_back(), core::io::serialization::size(), and protocols::cluster::tr().
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Definition at line 217 of file cluster.hh.
References export_only_low_.
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Definition at line 236 of file cluster.hh.
References clusterlist.
| Real protocols::cluster::ClusterBase::get_cluster_radius | ( | ) |
Definition at line 298 of file cluster.cc.
References cluster_radius_.
Referenced by add_structure(), and protocols::cluster::ClusterPhilStyle::do_clustering().
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Definition at line 204 of file cluster.hh.
References median_rms_.
Referenced by calculate_distance_matrix(), and protocols::cluster::ClusterPhilStyle::do_clustering().
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Each derived class must specify its name. The class name.
Reimplemented from protocols::cluster::GatherPosesMover.
Reimplemented in protocols::cluster::ClusterPhilStyle_Loop, and protocols::cluster::ClusterPhilStyle.
Definition at line 286 of file cluster.cc.
| void protocols::cluster::ClusterBase::limit_groups | ( | int | limit = -1) |
Definition at line 543 of file cluster.cc.
References clusterlist, protocols::cluster::GatherPosesMover::poselist, core::io::serialization::size(), and protocols::cluster::tr().
| void protocols::cluster::ClusterBase::limit_groupsize | ( | int | limit = -1) |
Definition at line 498 of file cluster.cc.
References clusterlist, protocols::cluster::Cluster::size(), and protocols::cluster::tr().
| void protocols::cluster::ClusterBase::limit_groupsize | ( | core::Real | percent_limit) |
Definition at line 512 of file cluster.cc.
References clusterlist, protocols::cluster::Cluster::size(), and protocols::cluster::tr().
| void protocols::cluster::ClusterBase::limit_total_structures | ( | int | limit = -1) |
Definition at line 563 of file cluster.cc.
References protocols::cluster::Cluster::clear(), clusterlist, protocols::cluster::Cluster::push_back(), core::io::serialization::size(), protocols::cluster::Cluster::size(), and protocols::cluster::tr().
| void protocols::cluster::ClusterBase::print_cluster_assignment | ( | ) |
Definition at line 651 of file cluster.cc.
References clusterlist, core::pose::extract_tag_from_pose(), protocols::cluster::GatherPosesMover::poselist, core::io::serialization::size(), and protocols::cluster::tr().
| void protocols::cluster::ClusterBase::print_cluster_PDBs | ( | std::string | prefix) |
Definition at line 662 of file cluster.cc.
References core::pose::add_comment(), protocols::idealize::IdealizeMover::apply(), clusterlist, core::pose::Pose::dump_pdb(), core::sequence::end, export_only_low_, protocols::idealize::IdealizeMover::fast(), core::pose::get_all_comments(), core::pose::get_all_score_line_strings(), protocols::cluster::GatherPosesMover::poselist, and core::io::serialization::size().
| void protocols::cluster::ClusterBase::print_clusters_silentfile | ( | std::string | prefix) |
Definition at line 750 of file cluster.cc.
References protocols::idealize::IdealizeMover::apply(), clusterlist, export_only_low_, protocols::idealize::IdealizeMover::fast(), protocols::cluster::GatherPosesMover::poselist, and core::io::serialization::size().
| void protocols::cluster::ClusterBase::print_raw_numbers | ( | ) |
Definition at line 640 of file cluster.cc.
References clusterlist, core::io::serialization::size(), and protocols::cluster::tr().
| void protocols::cluster::ClusterBase::print_summary | ( | ) |
Definition at line 611 of file cluster.cc.
References clusterlist, core::pose::extract_tag_from_pose(), core::pose::getPoseExtraScores(), protocols::cluster::GatherPosesMover::poselist, core::io::serialization::size(), and protocols::cluster::tr().
| void protocols::cluster::ClusterBase::random_limit_groupsize | ( | core::Real | percent_limit) |
Definition at line 527 of file cluster.cc.
References clusterlist, protocols::cluster::Cluster::shuffle(), protocols::cluster::Cluster::size(), and protocols::cluster::tr().
| void protocols::cluster::ClusterBase::remove_highest_energy_member_of_each_group | ( | ) |
Definition at line 425 of file cluster.cc.
References clusterlist, protocols::cluster::compareIndexEnergyPair(), core::pose::getPoseExtraScores(), protocols::cluster::GatherPosesMover::poselist, protocols::cluster::GatherPosesMover::push_back(), core::io::serialization::size(), and protocols::cluster::tr().
| void protocols::cluster::ClusterBase::remove_singletons | ( | ) |
Definition at line 477 of file cluster.cc.
References clusterlist.
| std::vector< PoseOP > protocols::cluster::ClusterBase::return_lowest_poses_in_clusters | ( | ) |
Definition at line 714 of file cluster.cc.
References clusterlist, protocols::cluster::GatherPosesMover::poselist, and core::io::serialization::size().
| std::vector< core::pose::PoseOP > protocols::cluster::ClusterBase::return_top_poses_in_clusters | ( | core::Size | count) |
Definition at line 724 of file cluster.cc.
References clusterlist, protocols::cluster::GatherPosesMover::poselist, and core::io::serialization::size().
| void protocols::cluster::ClusterBase::set_cluster_radius | ( | core::Real | cluster_radius) |
Definition at line 290 of file cluster.cc.
References cluster_radius_.
| void protocols::cluster::ClusterBase::set_population_weight | ( | core::Real | population_weight) |
Definition at line 294 of file cluster.cc.
References population_weight_.
| void protocols::cluster::ClusterBase::sort_each_group_by_energy | ( | ) |
Definition at line 401 of file cluster.cc.
References clusterlist, protocols::cluster::compareIndexEnergyPair(), core::pose::getPoseExtraScores(), protocols::cluster::GatherPosesMover::poselist, protocols::cluster::GatherPosesMover::push_back(), core::io::serialization::size(), and protocols::cluster::tr().
| void protocols::cluster::ClusterBase::sort_groups_by_energy | ( | ) |
Definition at line 447 of file cluster.cc.
References clusterlist, protocols::cluster::compareIndexEnergyPair(), core::pose::getPoseExtraScores(), population_weight_, protocols::cluster::GatherPosesMover::poselist, and protocols::cluster::tr().
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Definition at line 245 of file cluster.hh.
Referenced by protocols::cluster::ClusterPhilStyle::do_clustering(), get_cluster_radius(), and set_cluster_radius().
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Definition at line 240 of file cluster.hh.
Referenced by add_structure(), clean_pose_store(), create_constraints(), protocols::cluster::ClusterPhilStyle::do_clustering(), protocols::cluster::ClusterPhilStyle::do_redistribution(), get_cluster_list(), limit_groups(), limit_groupsize(), limit_total_structures(), print_cluster_assignment(), print_cluster_PDBs(), print_clusters_silentfile(), print_raw_numbers(), print_summary(), random_limit_groupsize(), remove_highest_energy_member_of_each_group(), remove_singletons(), return_lowest_poses_in_clusters(), return_top_poses_in_clusters(), sort_each_group_by_energy(), and sort_groups_by_energy().
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Definition at line 239 of file cluster.hh.
Referenced by calculate_distance_matrix(), protocols::cluster::ClusterPhilStyle::do_clustering(), and protocols::cluster::ClusterPhilStyle::do_redistribution().
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Definition at line 242 of file cluster.hh.
Referenced by export_only_low(), print_cluster_PDBs(), and print_clusters_silentfile().
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Definition at line 243 of file cluster.hh.
Referenced by calculate_distance_matrix(), and get_median_rms().
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Definition at line 244 of file cluster.hh.
Referenced by set_population_weight(), and sort_groups_by_energy().
1.8.4