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Rosetta Protocols
2014.35
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Rosetta Protocols
2014.35
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#include <ConstrainToIdealMover.hh>
Public Member Functions | |
| ConstrainToIdealMover () | |
| parse XML (specifically in the context of the parser/scripting scheme) More... | |
| ConstrainToIdealMover (ConstrainToIdealMover const &rhs) | |
| ConstrainToIdealMover & | operator= (ConstrainToIdealMover const &rhs) |
| virtual | ~ConstrainToIdealMover () |
| virtual void | apply (core::pose::Pose &pose) |
| virtual std::string | get_name () const |
| Each derived class must specify its name. The class name. More... | |
| virtual moves::MoverOP | fresh_instance () const |
| Generates a new Mover object freshly created with the default ctor. More... | |
| virtual moves::MoverOP | clone () const |
| Return a clone of the Mover object. More... | |
| void | set_movemap (core::kinematics::MoveMapOP movemap) |
| supply a MoveMap to be further modified by this mover; otherwise it will modify a blank one More... | |
| core::kinematics::MoveMapOP | get_movemap () const |
| get the MoveMap last created during apply() More... | |
| void | set_AllowInsert (protocols::toolbox::AllowInsertOP allow_insert) |
| setter for AllowInsert; makes a shallow copy More... | |
| protocols::toolbox::AllowInsertOP | get_AllowInsert () const |
| getter for AllowInsert 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 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... | |
| 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 | vary_bond_geometry (core::pose::Pose &pose, core::pose::Pose const &pose_reference) |
| parse XML (specifically in the context of the parser/scripting scheme) More... | |
| virtual void | create_pose_reference (core::pose::Pose const &pose, core::pose::Pose &pose_reference) |
| this function generates a "reference pose" for the input pose that has the same chemistry (as best as possible), but has ideal angles and bond lengths. These are then used to generate the constraints later. Virtual in case you want to make the reference in a different fashion. More... | |
| virtual bool | i_want_this_atom_to_move (core::pose::Pose const &pose, core::id::AtomID const &atom_id) |
| maps to other version of function; should this type of atom be moved during idealization? More... | |
| virtual bool | i_want_this_atom_to_move (core::conformation::Residue const &residue2, core::Size const &k) |
| returns whether or not this atom should move during idealiation categorically; mostly boils down to "don't move the sidechains". Virtual in case you want to deny using a different metric. More... | |
| bool | check_if_really_connected (core::pose::Pose const &pose, core::id::AtomID const &atom_id1, core::id::AtomID const &atom_id2) |
| bool | check_in_bonded_list (core::id::AtomID const &atom_id1, core::id::AtomID const &atom_id2, utility::vector1< std::pair< core::id::AtomID, core::id::AtomID > > &bonded_atom_list) |
| bool | check_in_bond_angle_list (core::id::AtomID const &atom_id1, core::id::AtomID const &atom_id2, core::id::AtomID const &atom_id3, utility::vector1< std::pair< core::id::AtomID, std::pair< core::id::AtomID, core::id::AtomID > > > &bond_angle_list) |
| void | add_bond_angle_constraint (core::id::AtomID const &atom_id1, core::id::AtomID const &atom_id2, core::id::AtomID const &atom_id3, utility::vector1< std::pair< core::id::AtomID, std::pair< core::id::AtomID, core::id::AtomID > > > &bond_angle_list, core::pose::Pose const &pose, core::pose::Pose const &pose_reference, core::scoring::constraints::ConstraintSetOP &cst_set) |
| void | add_bond_constraint (core::id::AtomID const &atom_id1, core::id::AtomID const &atom_id2, utility::vector1< std::pair< core::id::AtomID, core::id::AtomID > > &bonded_atom_list, core::pose::Pose const &pose, core::pose::Pose const &pose_reference, core::scoring::constraints::ConstraintSetOP &cst_set) |
Private Attributes | |
| protocols::toolbox::AllowInsertOP | allow_insert_ |
| sort of like a MoveMap? Allowed to maintain use w/Rhiju's RNA code. More... | |
| core::kinematics::MoveMapOP | mm_ |
| MoveMap used to allow bond and angle torsions. More... | |
| bool | supplied_movemap_ |
| does the mm_ variable contain a movemap filled by apply(), or a movemap supplied to be modified? Necessary to know if a self-generated movemap needs to be tossed out at the beginning of apply() 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... | |
Idealization is generally performed by adding constraints to the Pose that keep bond lengths and angles within the appropriate ranges; then freeing those DOFs and performing minimization or sampling. This protocols::moves::Mover creates bond and angle constraints compatible with idealization; it does not modify the input Pose other than by adding constraints. If your pose is already ideal, this is likely to unidealize it. Also, it will add a LOT of degrees of freedom to your minimization, which may lead to significant slowdowns!
| protocols::simple_moves::ConstrainToIdealMover::ConstrainToIdealMover | ( | ) |
parse XML (specifically in the context of the parser/scripting scheme)
Referenced by clone(), and fresh_instance().
| protocols::simple_moves::ConstrainToIdealMover::ConstrainToIdealMover | ( | ConstrainToIdealMover const & | rhs | ) |
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References core::scoring::constraints::ConstraintSet::add_constraint(), angle_radians(), core::id::AtomID::atomno(), check_in_bond_angle_list(), degrees(), has, radians(), core::pose::Pose::residue(), rna_bond_geometry, core::id::AtomID::rsd(), protocols::simple_moves::TR, and protocols::kinmatch::xyz().
Referenced by vary_bond_geometry().
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References core::scoring::constraints::ConstraintSet::add_constraint(), core::id::AtomID::atomno(), check_in_bonded_list(), has, length, core::pose::Pose::residue(), rna_bond_geometry, core::id::AtomID::rsd(), protocols::simple_moves::TR, and protocols::kinmatch::xyz().
Referenced by vary_bond_geometry().
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This code will modify your input pose by adding constraints which will trend bond lengths and angles towards ideal. If you input a movemap via set_movemap, that movemap will be modified to free the same set of bond lengths and angles (needs some testing) and will be available from get_movemap.
Implements protocols::moves::Mover.
References allow_insert_, create_pose_reference(), mm_, supplied_movemap_, and vary_bond_geometry().
Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::apply(), and protocols::farna::RNA_Minimizer::setup_movemap().
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References core::kinematics::AtomTree::atom(), core::pose::Pose::atom_tree(), and core::id::AtomID::rsd().
Referenced by vary_bond_geometry().
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Referenced by add_bond_angle_constraint().
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Referenced by add_bond_constraint().
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Return a clone of the Mover object.
clone is meant to return an OP'ed deep copy of this object. 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.
Reimplemented from protocols::moves::Mover.
References ConstrainToIdealMover().
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privatevirtual |
this function generates a "reference pose" for the input pose that has the same chemistry (as best as possible), but has ideal angles and bond lengths. These are then used to generate the constraints later. Virtual in case you want to make the reference in a different fashion.
References protocols::simple_moves::apply_ideal_coordinates_for_alternative_pucker(), core::chemical::ChemicalManager::get_instance(), make_pose_from_sequence(), core::chemical::ChemicalManager::residue_type_set(), and core::pose::Pose::sequence().
Referenced by apply().
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virtual |
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 ConstrainToIdealMover().
| protocols::toolbox::AllowInsertOP protocols::simple_moves::ConstrainToIdealMover::get_AllowInsert | ( | ) | const |
| core::kinematics::MoveMapOP protocols::simple_moves::ConstrainToIdealMover::get_movemap | ( | ) | const |
get the MoveMap last created during apply()
get the MoveMap last created during apply(); it has the bond and angles free for minimization
References mm_.
Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::apply(), operator=(), and protocols::farna::RNA_Minimizer::setup_movemap().
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Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
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privatevirtual |
maps to other version of function; should this type of atom be moved during idealization?
References core::id::AtomID::atomno(), core::pose::Pose::residue(), residue, and core::id::AtomID::rsd().
Referenced by vary_bond_geometry().
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privatevirtual |
returns whether or not this atom should move during idealiation categorically; mostly boils down to "don't move the sidechains". Virtual in case you want to deny using a different metric.
References allow_insert_, core::chemical::rna::first_base_atom_index(), core::conformation::Residue::first_sidechain_atom(), utility::pointer::owning_ptr< T >::get(), core::conformation::Residue::is_virtual(), and core::conformation::Residue::seqpos().
| ConstrainToIdealMover & protocols::simple_moves::ConstrainToIdealMover::operator= | ( | ConstrainToIdealMover const & | rhs | ) |
References allow_insert_, core::kinematics::MoveMap::clone(), get_AllowInsert(), get_movemap(), mm_, and supplied_movemap_.
| void protocols::simple_moves::ConstrainToIdealMover::set_AllowInsert | ( | protocols::toolbox::AllowInsertOP | allow_insert | ) |
setter for AllowInsert; makes a shallow copy
setter for AllowInsert; shallow copy
References allow_insert_.
Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::apply(), and protocols::farna::RNA_Minimizer::setup_movemap().
| void protocols::simple_moves::ConstrainToIdealMover::set_movemap | ( | core::kinematics::MoveMapOP | movemap | ) |
supply a MoveMap to be further modified by this mover; otherwise it will modify a blank one
supply a MoveMap to be further modified by this mover; otherwise it will modify a blank one; notice it sets a boolean flag to mark the source of the movemap
References mm_, and supplied_movemap_.
Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::apply(), and protocols::farna::RNA_Minimizer::setup_movemap().
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parse XML (specifically in the context of the parser/scripting scheme)
of the work happens here. This modifies the movemap (member variable) and adds constraints to the Pose that will gently idealize angles and bond lengths
References add_bond_angle_constraint(), add_bond_constraint(), allow_insert_, core::kinematics::AtomTree::atom(), core::pose::Pose::atom_tree(), core::id::AtomID::atomno(), core::conformation::Conformation::bonded_neighbor_all_res(), check_if_really_connected(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), D, utility::pointer::owning_ptr< T >::get(), i_want_this_atom_to_move(), mm_, nres, PHI, q, core::pose::Pose::residue(), residue, core::id::AtomID::rsd(), core::kinematics::MoveMap::set(), THETA, and core::pose::Pose::total_residue().
Referenced by apply().
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sort of like a MoveMap? Allowed to maintain use w/Rhiju's RNA code.
Referenced by apply(), get_AllowInsert(), i_want_this_atom_to_move(), operator=(), set_AllowInsert(), and vary_bond_geometry().
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MoveMap used to allow bond and angle torsions.
Referenced by apply(), get_movemap(), operator=(), set_movemap(), and vary_bond_geometry().
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does the mm_ variable contain a movemap filled by apply(), or a movemap supplied to be modified? Necessary to know if a self-generated movemap needs to be tossed out at the beginning of apply()
Referenced by apply(), operator=(), and set_movemap().
1.8.7