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Rosetta Protocols
2014.16.56682
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Rosetta Protocols
2014.16.56682
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Public Member Functions | |
| LigandDockMain () | |
| virtual | ~LigandDockMain () |
| virtual void | apply (core::pose::Pose &pose) |
| Creates a new hierarchy of Movers for each Pose passed in. More... | |
| virtual std::string | get_name () const |
| Each derived class must specify its name. The class name. More... | |
| virtual protocols::moves::MoverOP | fresh_instance () const |
| Generates a new Mover object freshly created with the default ctor. 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... | |
 Public Member Functions inherited from protocols::ligand_docking::LigandDockProtocol | |
| LigandDockProtocol () | |
| LigandDockProtocol (std::string const protocol, bool const minimize_ligand, bool const minimize_backbone, bool const tether_ligand, bool const mutate_same_name3, core::Real const ligand_chi_stddev_deg, core::Real const protein_CA_stddev_Ang, core::Real const ligand_tether_stddev_Ang_=-1, core::Size const ligand_shear_moves=0) | |
| virtual | ~LigandDockProtocol () |
| void | add_start_from (core::Real x, core::Real y, core::Real z) |
| void | append_ligand_docking_scores (core::pose::Pose const &before, core::pose::Pose const &after, core::scoring::ScoreFunctionCOP scorefxn, std::map< std::string, core::Real > &scores, protocols::toolbox::match_enzdes_util::EnzConstraintIOCOP constraint_io=NULL) const |
| Scores to be output that aren't normal scorefunction terms. More... | |
| Public Member Functions inherited from protocols::ligand_docking::LigandBaseProtocol | |
| LigandBaseProtocol () | |
| virtual | ~LigandBaseProtocol () |
| core::scoring::ScoreFunctionOP | get_scorefxn () |
| core::scoring::ScoreFunctionCOP | get_scorefxn () const |
| core::Size | get_ligand_jump_id (core::pose::Pose const &pose) const |
| core::Size | get_ligand_id (core::pose::Pose const &pose) const |
| Return the residue sequence number for our ligand. More... | |
| core::Size | get_ligand_id (core::pose::Pose const &pose, core::Size jump_id) const |
| Return the residue sequence number for our ligand. More... | |
| void | restrain_protein_Calphas (core::pose::Pose &pose, utility::vector1< bool > const &is_restrained, core::scoring::func::FuncOP restr_func) const |
| void | reorder_foldtree_around_mobile_regions (core::pose::Pose &pose, core::Size const &jump_id, utility::vector1< bool > const &mobile_bb, core::Size const &lig_id) const |
| reorders a fold tree such that movement in the mobile regions will More... | |
| void | get_non_bb_clashing_rotamers (core::pose::Pose const &pose, core::Size seqpos, core::scoring::ScoreFunctionCOP scofx, utility::vector1< core::conformation::ResidueCOP > &accepted_rotamers) 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 |
| Return a clone of the Mover object. More... | |
| virtual void | parse_my_tag (TagCOP tag, basic::datacache::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... | |
| 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... | |
Private Attributes | |
| core::pose::PoseOP | native_ |
| protocols::toolbox::match_enzdes_util::EnzConstraintIOOP | constraints_ |
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inline |
References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, constraints_, core::scoring::coordinate_constraint, basic::options::OptionKeys::enzdes::cstfile, core::scoring::dihedral_constraint, core::chemical::FA_STANDARD, core::chemical::ChemicalManager::get_instance(), protocols::ligand_docking::LigandBaseProtocol::get_scorefxn(), protocols::moves::Mover::name(), basic::options::OptionKeys::in::file::native, native_, basic::options::option, core::import_pose::pose_from_pdb(), basic::options::OptionKeys::run::preserve_header, core::chemical::ChemicalManager::residue_type_set(), and user.
Referenced by fresh_instance().
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inlinevirtual |
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inlinevirtual |
Creates a new hierarchy of Movers for each Pose passed in.
Some Movers (e.g. repack) require knowledge of the Pose to create, and are only valid for that Pose and other conformations of it (i.e. poses with the same number of residues, jumps, etc). In general, we expect each Pose coming in here to be from a different PDB file. The cost of creating these objects anew should be minimal compared to the processing work they do.
Reimplemented from protocols::ligand_docking::LigandDockProtocol.
References protocols::jd2::Job::add_string_real_pair(), protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::ligand_docking::LigandDockProtocol::apply(), constraints_, protocols::nonlocal::current_job(), end, protocols::jd2::JobDistributor::get_instance(), protocols::ligand_docking::LigandBaseProtocol::get_scorefxn(), core::import_pose::atom_tree_diffs::map_of_weighted_scores(), and native_.
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inlinevirtual |
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.
References LigandDockMain().
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inlinevirtual |
Each derived class must specify its name. The class name.
Reimplemented from protocols::ligand_docking::LigandDockProtocol.
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inlinevirtual |
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use.
Movers default to not regenerating
Reimplemented from protocols::moves::Mover.
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inlinevirtual |
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).
Movers default to not regenerating
Reimplemented from protocols::moves::Mover.
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private |
Referenced by apply(), and LigandDockMain().
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private |
Referenced by apply(), and LigandDockMain().
1.8.7