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Rosetta 3.5
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Rosetta 3.5
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#include <MultiThreadingMover.hh>
Public Types | |
| typedef core::sequence::SequenceAlignment | Alignment |
| typedef utility::vector1 < Alignment > | Alignments |
| typedef utility::vector1 < core::pose::Pose > | Poses |
 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 |
Public Member Functions | |
| MultiThreadingMover (Alignments const &aligns, Poses const &template_poses) | |
| align describes the association between the query and template sequences, template_pose is the conformation from which to build a threading model. More... | |
| virtual | ~MultiThreadingMover () |
| void | build_loops (bool setting) |
| Returns the SequenceAlignments used in threading. More... | |
| void | randomize_loop_coords (bool setting) |
| void | repack_query (bool setting) |
| bool | build_loops () const |
| bool | repack_query () const |
| bool | randomize_loop_coords () |
| void | min_loop_size (core::Size const new_size) |
| Size | min_loop_size () const |
| utility::vector1 < core::fragment::FragSetOP > | frag_libs () const |
| void | frag_libs (utility::vector1< core::fragment::FragSetOP > new_libs) |
| virtual void | apply (core::pose::Pose &query_pose) |
| Threads the given Pose onto the template_pose with the SequenceAlignment provided. More... | |
| virtual std::string | get_name () const |
| Each derived class must specify its name. The class name. More... | |
| 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 |
Private Member Functions | |
| void | check_internals () const |
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. 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 35 of file MultiThreadingMover.hh.
| typedef core::sequence::SequenceAlignment protocols::comparative_modeling::MultiThreadingMover::Alignment |
Definition at line 38 of file MultiThreadingMover.hh.
| typedef utility::vector1< Alignment > protocols::comparative_modeling::MultiThreadingMover::Alignments |
Definition at line 39 of file MultiThreadingMover.hh.
| typedef utility::vector1< core::pose::Pose > protocols::comparative_modeling::MultiThreadingMover::Poses |
Definition at line 40 of file MultiThreadingMover.hh.
| protocols::comparative_modeling::MultiThreadingMover::MultiThreadingMover | ( | Alignments const & | aligns, |
| Poses const & | template_poses | ||
| ) |
align describes the association between the query and template sequences, template_pose is the conformation from which to build a threading model.
Definition at line 73 of file MultiThreadingMover.cc.
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inlinevirtual |
Definition at line 52 of file MultiThreadingMover.hh.
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virtual |
Threads the given Pose onto the template_pose with the SequenceAlignment provided.
Implements protocols::moves::Mover.
Definition at line 130 of file MultiThreadingMover.cc.
References alignments_, protocols::comparative_modeling::ThreadingMover::apply(), protocols::comparative_modeling::ThreadingMover::build_loops(), check_internals(), core::pose::initialize_atomid_map(), core::conformation::Residue::natoms(), protocols::comparative_modeling::ThreadingMover::randomize_loop_coords(), protocols::comparative_modeling::randomize_selected_atoms(), protocols::comparative_modeling::ThreadingMover::repack_query(), core::pose::Pose::residue(), core::sequence::SequenceAlignment::sequence_mapping(), template_poses_, core::pose::Pose::total_residue(), and protocols::comparative_modeling::tr().
| void protocols::comparative_modeling::MultiThreadingMover::build_loops | ( | bool | setting) |
Returns the SequenceAlignments used in threading.
Manipulate the SequenceAlignments associated with this object.
Definition at line 87 of file MultiThreadingMover.cc.
References build_query_loops_.
| bool protocols::comparative_modeling::MultiThreadingMover::build_loops | ( | ) | const |
Definition at line 100 of file MultiThreadingMover.cc.
References build_query_loops_.
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private |
Definition at line 178 of file MultiThreadingMover.cc.
References alignments_, and template_poses_.
Referenced by apply().
| utility::vector1< core::fragment::FragSetOP > protocols::comparative_modeling::MultiThreadingMover::frag_libs | ( | ) | const |
Definition at line 120 of file MultiThreadingMover.cc.
References frag_libs_.
| void protocols::comparative_modeling::MultiThreadingMover::frag_libs | ( | utility::vector1< core::fragment::FragSetOP > | new_libs) |
Definition at line 124 of file MultiThreadingMover.cc.
References frag_libs_.
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virtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
Definition at line 174 of file MultiThreadingMover.cc.
| void protocols::comparative_modeling::MultiThreadingMover::min_loop_size | ( | core::Size const | new_size) |
Definition at line 112 of file MultiThreadingMover.cc.
References min_loop_size_.
| core::Size protocols::comparative_modeling::MultiThreadingMover::min_loop_size | ( | ) | const |
Definition at line 116 of file MultiThreadingMover.cc.
References min_loop_size_.
| void protocols::comparative_modeling::MultiThreadingMover::randomize_loop_coords | ( | bool | setting) |
Definition at line 91 of file MultiThreadingMover.cc.
References randomize_loop_coords_.
| bool protocols::comparative_modeling::MultiThreadingMover::randomize_loop_coords | ( | ) |
Definition at line 108 of file MultiThreadingMover.cc.
References randomize_loop_coords_.
| void protocols::comparative_modeling::MultiThreadingMover::repack_query | ( | bool | setting) |
Definition at line 95 of file MultiThreadingMover.cc.
References repack_query_.
| bool protocols::comparative_modeling::MultiThreadingMover::repack_query | ( | ) | const |
Definition at line 104 of file MultiThreadingMover.cc.
References repack_query_.
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private |
Definition at line 99 of file MultiThreadingMover.hh.
Referenced by apply(), and check_internals().
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private |
Definition at line 100 of file MultiThreadingMover.hh.
Referenced by build_loops().
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private |
Definition at line 105 of file MultiThreadingMover.hh.
Referenced by frag_libs().
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private |
Definition at line 103 of file MultiThreadingMover.hh.
Referenced by min_loop_size().
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private |
Definition at line 102 of file MultiThreadingMover.hh.
Referenced by randomize_loop_coords().
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private |
Definition at line 101 of file MultiThreadingMover.hh.
Referenced by repack_query().
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private |
Definition at line 98 of file MultiThreadingMover.hh.
Referenced by apply(), and check_internals().
1.8.4