small mover that takes an invrot tree More...
#include <AlignPoseToInvrotTreeMover.hh>
Inheritance diagram for protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover:
Public Types | |
| typedef core::Size | Size |
 Public Types inherited from protocols::moves::Mover | |
| typedef utility::tag::TagCOP | TagCOP |
| typedef core::pose::Pose | Pose |
| typedef core::pose::PoseCOP | PoseCOP |
| typedef std::list< std::string > | Strings |
Public Member Functions | |
| AlignPoseToInvrotTreeMover (InvrotTreeCOP invrot_tree, AllowedSeqposForGeomCstCOP seqpos) | |
| the invrot tree and the seqpos object that are being passed in need to be initialized More... | |
| ~AlignPoseToInvrotTreeMover () override | |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
| void | apply (core::pose::Pose &pose) override |
| void | set_add_target_to_pose (bool const setting) |
| void | set_geomcst_for_superposition_from_enz_io (EnzConstraintIOCOP enzcst_io) |
| void | setup_foldtree_around_anchor_invrot (core::pose::Pose &pose, core::Size const anchor_seqpos, core::Size const first_target_seqpos) const |
| sets up a foldtree such that the anchor residue doesn't move, i.e. a backward edge from anchor to 1 and a forward edge from anchor to seqpos also need to setup the jumps at anchor res More... | |
| core::conformation::ResidueCOP | switch_residue_type_set (core::conformation::ResidueCOP residue, core::chemical::TypeSetMode desired_restype_set) const |
| silly helper function to get the equivalent of a certain residue in a new residue type set note if the passed in residue is already of the required residue type set, nothing changes, just passes back input pointer More... | |
| Public Member Functions inherited from protocols::moves::Mover | |
| Mover () | |
| virtual MoverOP | create () |
| MoverCOP | get_self_ptr () const |
| MoverOP | get_self_ptr () |
| MoverCAP | get_self_weak_ptr () const |
| MoverAP | get_self_weak_ptr () |
| Mover (std::string const &type_name) | |
| sets the type for a mover; name_ has been removed (2010/05/14) More... | |
| 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... | |
| virtual MoverOP | clone () const |
| Return a clone of the Mover object. 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... | |
| 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... | |
| void | set_type (std::string const &setting) |
| Set the 'type' string. More... | |
| std::string | get_type () const |
| void | type (const std::string &type_in) |
| Set the 'type' string. More... | |
| std::string const & | type () const |
| Get the set 'type' string. More... | |
| 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 | parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
| virtual void | set_current_tag (std::string const &new_tag) |
| 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... | |
| virtual void | show (std::ostream &output=std::cout) const |
| Outputs details about the Mover, including current settings. More... | |
| virtual core::Real | last_proposal_density_ratio () |
| 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 void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
| Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More... | |
Private Attributes | |
| bool | add_target_to_pose_ |
| InvrotTreeCOP | invrot_tree_ |
| AllowedSeqposForGeomCstCOP | seqpos_ |
| utility::vector1< InvrotCollectorCOP > | all_invrots_ |
| utility::vector1< core::Size > | geomcsts_for_superposition_ |
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... | |
| 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... | |
Detailed Description
small mover that takes an invrot tree
Member Typedef Documentation
◆ Size
Constructor & Destructor Documentation
◆ AlignPoseToInvrotTreeMover()
| protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::AlignPoseToInvrotTreeMover | ( | InvrotTreeCOP | invrot_tree, |
| AllowedSeqposForGeomCstCOP | seqpos | ||
| ) |
the invrot tree and the seqpos object that are being passed in need to be initialized
References all_invrots_, and geomcsts_for_superposition_.
◆ ~AlignPoseToInvrotTreeMover()
|
overridedefault |
Member Function Documentation
◆ apply()
|
overridevirtual |
this function does two things
- align one of the seqpos in the pose onto one of the invrots in the tree
- grab the InvrotTarget residues and add them to the pose this entails setting up the foldtree such that the target residues are upstream of the rest of the pose WARNING: right now this absolutely only works for InvrotTrees where the target is one ligand
Implements protocols::moves::Mover.
References add_target_to_pose_, all_invrots_, core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::atom_index(), core::id::AtomID::BOGUS_ATOM_ID(), core::pose::Pose::conformation(), geomcsts_for_superposition_, core::pose::initialize_atomid_map(), invrot_tree_, core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::conformation::Conformation::residue_typeset_mode(), seqpos_, core::id::AtomID_Map< T >::set(), setup_foldtree_around_anchor_invrot(), core::pose::Pose::size(), core::scoring::superimpose_pose(), and switch_residue_type_set().
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
◆ set_add_target_to_pose()
| void protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::set_add_target_to_pose | ( | bool const | setting | ) |
References add_target_to_pose_.
◆ set_geomcst_for_superposition_from_enz_io()
| void protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::set_geomcst_for_superposition_from_enz_io | ( | EnzConstraintIOCOP | enzcst_io | ) |
◆ setup_foldtree_around_anchor_invrot()
| void protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::setup_foldtree_around_anchor_invrot | ( | core::pose::Pose & | pose, |
| core::Size const | anchor_seqpos, | ||
| core::Size const | first_target_seqpos | ||
| ) | const |
sets up a foldtree such that the anchor residue doesn't move, i.e. a backward edge from anchor to 1 and a forward edge from anchor to seqpos also need to setup the jumps at anchor res
the simplest possible implementation for now assumes the pose only has one chain
References core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::check_fold_tree(), core::pose::Pose::fold_tree(), core::kinematics::Edge::PEPTIDE, and core::pose::Pose::size().
Referenced by apply().
◆ switch_residue_type_set()
| core::conformation::ResidueCOP protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::switch_residue_type_set | ( | core::conformation::ResidueCOP | residue, |
| core::chemical::TypeSetMode | desired_restype_set | ||
| ) | const |
silly helper function to get the equivalent of a certain residue in a new residue type set note if the passed in residue is already of the required residue type set, nothing changes, just passes back input pointer
References core::util::switch_to_residue_type_set().
Referenced by apply().
Member Data Documentation
◆ add_target_to_pose_
|
private |
Referenced by apply(), and set_add_target_to_pose().
◆ all_invrots_
|
private |
Referenced by AlignPoseToInvrotTreeMover(), and apply().
◆ geomcsts_for_superposition_
|
private |
Referenced by AlignPoseToInvrotTreeMover(), apply(), and set_geomcst_for_superposition_from_enz_io().
◆ invrot_tree_
|
private |
Referenced by apply().
◆ seqpos_
|
private |
Referenced by apply().
The documentation for this class was generated from the following files:
- src/protocols/toolbox/match_enzdes_util/AlignPoseToInvrotTreeMover.hh
- src/protocols/toolbox/match_enzdes_util/AlignPoseToInvrotTreeMover.cc
