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protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover Class Reference

small mover that takes an invrot tree More...

#include <AlignPoseToInvrotTreeMover.hh>

Inheritance diagram for protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover:
Inheritance graph
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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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Private Attributes

bool add_target_to_pose_
 
InvrotTreeCOP invrot_tree_
 
AllowedSeqposForGeomCstCOP seqpos_
 
utility::vector1
< InvrotCollectorCOP
all_invrots_
 
utility::vector1< core::Sizegeomcsts_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

Constructor & Destructor Documentation

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_.

protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::~AlignPoseToInvrotTreeMover ( )
overridedefault

Member Function Documentation

void protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::apply ( core::pose::Pose pose)
overridevirtual

this function does two things

  1. align one of the seqpos in the pose onto one of the invrots in the tree
  2. 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().

std::string protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::get_name ( ) const
overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

void protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::set_add_target_to_pose ( bool const  setting)

References add_target_to_pose_.

void protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::set_geomcst_for_superposition_from_enz_io ( EnzConstraintIOCOP  enzcst_io)
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::pose::Pose::fold_tree(), protocols::make_rot_lib::PEPTIDE, and core::pose::Pose::size().

Referenced by apply().

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

bool protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::add_target_to_pose_
private

Referenced by apply(), and set_add_target_to_pose().

utility::vector1< InvrotCollectorCOP > protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::all_invrots_
private
utility::vector1< core::Size > protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::geomcsts_for_superposition_
private
InvrotTreeCOP protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::invrot_tree_
private

Referenced by apply().

AllowedSeqposForGeomCstCOP protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::seqpos_
private

Referenced by apply().


The documentation for this class was generated from the following files: