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Rosetta Protocols
2014.35
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Rosetta Protocols
2014.35
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virtual base class that has some common functionality More...
#include <ModifyStoredLigandRBConfsMovers.hh>
Public Member Functions | |
| ModifyStoredRBConfs (std::string const name) | |
| ~ModifyStoredRBConfs () | |
| virtual void | apply (core::pose::Pose &pose)=0 |
| virtual std::string | get_name () const |
| Each derived class must specify its name. The class name. More... | |
| void | swap_coordinates_in_pose (core::pose::Pose &pose, core::conformation::Residue &rescoords) const |
| helper function to exchange coordinates in a pose this function doesn't actually exchange the residues, but sets all the coords of pose.residue( rescoords.seqpos() ) to what is in rescoords and vice versa More... | |
| utility::vector1< Real > | closest_orient_atoms_msd (core::pose::Pose const &pose, utility::vector1< core::conformation::ResidueCOP > const &confs) const |
| calculates the closest orient atom (i.e. atoms used in rotamer placement msd between every conf and the confs coming before it in the pose or in the vector 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... | |
Protected Member Functions | |
| RBConfLists | get_rigid_body_confs (core::pose::Pose const &pose) const |
| this function is the function that all derived classes should call to get access to pose stored additional rb confs. right now it only returns the confs in the proper format, but in the future some logic might be added as to for which seqpos to return the stored confs More... | |
| void | set_rigid_body_confs (RBConfLists rbs, core::pose::Pose &pose) const |
| same as for above function. all derived classes should use this function to communicate new/changed rigid body confs back to the pose/enzdes cacheable observer More... | |
| void | set_rigid_body_confs_for_seqpos (core::Size seqpos, utility::vector1< core::conformation::ResidueCOP > &confs, core::pose::Pose &pose) const |
| see comments for set_rigid_body_confs 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... | |
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. More... | |
virtual base class that has some common functionality
| typedef utility::vector1< utility::vector1< core::conformation::ResidueCOP > > protocols::enzdes::ModifyStoredRBConfs::RBConfLists |
| protocols::enzdes::ModifyStoredRBConfs::ModifyStoredRBConfs | ( | std::string const | name | ) |
| protocols::enzdes::ModifyStoredRBConfs::~ModifyStoredRBConfs | ( | ) |
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pure virtual |
| utility::vector1< ModifyStoredRBConfs::Real > protocols::enzdes::ModifyStoredRBConfs::closest_orient_atoms_msd | ( | core::pose::Pose const & | pose, |
| utility::vector1< core::conformation::ResidueCOP > const & | confs | ||
| ) | const |
calculates the closest orient atom (i.e. atoms used in rotamer placement msd between every conf and the confs coming before it in the pose or in the vector
References core::conformation::Residue::atom_name(), center, numeric::xyzVector< class >::distance_squared(), distance_squared(), core::conformation::Residue::name3(), protocols::sic_dock::scores::nbr1, protocols::sic_dock::scores::nbr2, core::pose::Pose::residue(), runtime_assert, core::conformation::Residue::xyz(), and protocols::kinmatch::xyz().
Referenced by protocols::enzdes::DiversifyStoredRBConfs::diversify_all_confs().
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virtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
Reimplemented in protocols::enzdes::DiversifyStoredRBConfs, protocols::enzdes::MinimizeStoredRBConfs, protocols::enzdes::ApplyRandomStoredRBConf, and protocols::enzdes::GenerateStoredRBConfs.
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protected |
this function is the function that all derived classes should call to get access to pose stored additional rb confs. right now it only returns the confs in the proper format, but in the future some logic might be added as to for which seqpos to return the stored confs
References protocols::toolbox::match_enzdes_util::get_enzdes_observer(), core::chemical::ResidueType::is_ligand(), core::pose::Pose::residue(), and core::conformation::Residue::type().
Referenced by protocols::enzdes::GenerateStoredRBConfs::apply(), protocols::enzdes::ApplyRandomStoredRBConf::apply(), protocols::enzdes::MinimizeStoredRBConfs::apply(), and protocols::enzdes::DiversifyStoredRBConfs::apply().
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protected |
same as for above function. all derived classes should use this function to communicate new/changed rigid body confs back to the pose/enzdes cacheable observer
References set_rigid_body_confs_for_seqpos(), and size().
Referenced by protocols::enzdes::ApplyRandomStoredRBConf::apply().
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protected |
see comments for set_rigid_body_confs
References protocols::toolbox::match_enzdes_util::get_enzdes_observer().
Referenced by protocols::enzdes::GenerateStoredRBConfs::apply(), protocols::enzdes::MinimizeStoredRBConfs::apply(), protocols::enzdes::DiversifyStoredRBConfs::apply(), and set_rigid_body_confs().
| void protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose | ( | core::pose::Pose & | pose, |
| core::conformation::Residue & | rescoords | ||
| ) | const |
helper function to exchange coordinates in a pose this function doesn't actually exchange the residues, but sets all the coords of pose.residue( rescoords.seqpos() ) to what is in rescoords and vice versa
References core::conformation::Residue::atom_index(), core::conformation::Residue::atom_name(), core::chemical::ResidueType::name3(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), runtime_assert, core::conformation::Residue::seqpos(), core::pose::Pose::set_xyz(), core::conformation::Residue::set_xyz(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().
Referenced by protocols::enzdes::ApplyRandomStoredRBConf::apply(), protocols::enzdes::DiversifyStoredRBConfs::diversify_all_confs(), and protocols::enzdes::MinimizeStoredRBConfs::rb_minimize_all_confs().
1.8.7