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Rosetta Protocols
2014.35
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Rosetta Protocols
2014.35
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#include <ZincHeterodimerMover.hh>
Public Member Functions | |
| ZincHeterodimerMover (utility::vector1< core::Size > const &metal_site, core::kinematics::Edge const &fixed_to_metal, core::kinematics::Edge const &metal_to_mobile) | |
| constructor More... | |
| virtual | ~ZincHeterodimerMover () |
| virtual void | apply (core::pose::Pose &pose) |
| 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 |
| void | set_type (std::string const &setting) |
| 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... | |
| 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... | |
| virtual MoverOP | fresh_instance () const |
| Generates a new Mover object freshly created with the default ctor. 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 Member Functions | |
| void | generate_scorefunctions () |
| constructor helper function - generates scorefunctions More... | |
| void | generate_factory () |
| constructor helper function - generates TaskFactory More... | |
| void | copy_to_centroid (core::pose::Pose const &pose, core::pose::Pose ¢roid, core::kinematics::FoldTree const ¢roid_tree, core::Size const metal_res) |
| apply helper function (ugly complex interface, I know) More... | |
Private Attributes | |
| core::scoring::ScoreFunctionOP | centroid_scorefunction_ |
| core::scoring::ScoreFunctionOP | fullatom_scorefunction_ |
| core::pack::task::TaskFactoryCOP | factory_ |
| core::kinematics::Edge const | fixed_to_metal_ |
| fixed_to_metal this is a core::kinematic::Edge which represents a bond from the metal center to a liganding residue on the "fixed" partner (the one without rigid-body freedom) More... | |
| core::kinematics::Edge const | metal_to_mobile_ |
| metal_to_mobile this is a core::kinematic::Edge which represents a bond from the metal center to a liganding residue on the mobile partner with rigid body freedom. The bond will be rotated by RotateJumpAxisMover More... | |
| utility::vector1< core::Size > const | metal_site_ |
| the residues involved in the metal site (generally 4 residues plus the metal for 5 total) 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 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. 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... | |
ZincHeterodimerMover is a mover for the ZincHeterodimerDesign protocol
| protocols::metal_interface::ZincHeterodimerMover::ZincHeterodimerMover | ( | utility::vector1< core::Size > const & | metal_site, |
| core::kinematics::Edge const & | fixed_to_metal, | ||
| core::kinematics::Edge const & | metal_to_mobile | ||
| ) |
constructor
| [in] | metal_site | this is the residues directly involved in metal binding (plus the metal itself) - these should not be repacked. |
| [in] | fixed_to_metal | this is a core::kinematic::Edge which represents a bond from the metal center to a liganding residue on the "fixed" partner (the one without rigid-body freedom) |
| [in] | metal_to_mobile | this is a core::kinematic::Edge which represents a bond from the metal center to a liganding residue on the mobile partner with rigid body freedom. The bond will be rotated by RotateJumpAxisMover |
constructor
References generate_factory(), and generate_scorefunctions().
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Implements protocols::moves::Mover.
References core::kinematics::FoldTree::add_edge(), protocols::moves::MoverContainer::add_mover(), protocols::moves::RandomMover::apply(), protocols::moves::DualMonteCarlo::boltzmann(), centroid, centroid_scorefunction_, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), copy_to_centroid(), core::pack::task::TaskFactory::create_packer_task(), protocols::metal_interface::dump_chis(), core::pack::task::EX_SIX_QUARTER_STEP_STDDEVS, factory_, fixed_res, fixed_to_metal_, core::pose::Pose::fold_tree(), fullatom_scorefunction_, protocols::stepwise::modeler::is_protein(), core::kinematics::Edge::label(), protocols::moves::DualMonteCarlo::MC(), protocols::moves::MonteCarlo::mc_accepted(), metal_to_mobile_, basic::options::OptionKeys::run::min_type, core::pack::task::PackerTask::nonconst_residue_task(), core::conformation::Conformation::num_chains(), basic::options::option, option, core::pack::task::ResidueLevelTask::or_ex1_sample_level(), core::pack::task::ResidueLevelTask::or_ex2_sample_level(), core::pack::task::ResidueLevelTask::or_ex3_sample_level(), core::pack::task::ResidueLevelTask::or_ex4_sample_level(), core::pack::task::ResidueLevelTask::or_fix_his_tautomer(), output_centroid, protocols::make_rot_lib::PEPTIDE, basic::options::OptionKeys::AnchoredDesign::perturb_cycles, perturb_cycles, perturb_show, basic::options::OptionKeys::AnchoredDesign::perturb_show, basic::options::OptionKeys::AnchoredDesign::perturb_temp, perturb_temp, protocols::moves::DualMonteCarlo::recover_low(), refine_cycles, basic::options::OptionKeys::AnchoredDesign::refine_cycles, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pack::task::PackerTask::restrict_to_repacking(), core::pack::task::PackerTask::restrict_to_residues(), core::kinematics::Edge::start(), core::kinematics::Edge::stop(), protocols::simple_moves::PackRotamersMover::task_factory(), core::pose::Pose::total_residue(), protocols::TR, and user.
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apply helper function (ugly complex interface, I know)
apply() needs to generate a centroid copy of the fullatom pose from time to time. Some of the things in the fullatom pose are not centroid safe (metal atom, possible hydrogen-lacking metal ligand residues) and must be removed before centroid-ization. This function takes care of that; unfortunately it needs a lot of help passed in.
References core::chemical::CENTROID, core::pose::Pose::fold_tree(), and core::util::switch_to_residue_type_set().
Referenced by apply().
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constructor helper function - generates TaskFactory
References end, factory_, metal_site_, option, protocols::TR, and user.
Referenced by ZincHeterodimerMover().
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constructor helper function - generates scorefunctions
References cbeta, cenpack, centroid_scorefunction_, env, fullatom_scorefunction_, core::scoring::get_score_function(), hbond_lr_bb, hbond_sr_bb, pair, protocols::TR, and vdw.
Referenced by ZincHeterodimerMover().
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Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
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Referenced by apply(), and generate_scorefunctions().
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Referenced by apply(), and generate_factory().
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fixed_to_metal this is a core::kinematic::Edge which represents a bond from the metal center to a liganding residue on the "fixed" partner (the one without rigid-body freedom)
Referenced by apply().
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Referenced by apply(), and generate_scorefunctions().
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the residues involved in the metal site (generally 4 residues plus the metal for 5 total)
Referenced by generate_factory().
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metal_to_mobile this is a core::kinematic::Edge which represents a bond from the metal center to a liganding residue on the mobile partner with rigid body freedom. The bond will be rotated by RotateJumpAxisMover
Referenced by apply().
1.8.7