small mover that takes an invrot tree More...

#include <AlignPoseToInvrotTreeMover.hh>

Inheritance diagram for protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover:

Collaboration diagram for protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover:

Public Types
typedef core::Size	Size

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr	TagPtr

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

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 ()

virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...

virtual void	apply (core::pose::Pose &pose)

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, Size const anchor_seqpos, 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, std::string const desired_restype_set_name) 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	~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

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
	clone has to be overridden only if clone invocation is expected. More...

virtual void	parse_my_tag (TagPtr const tag, 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
	this function informs 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
	this function informs 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
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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

Definition at line 48 of file AlignPoseToInvrotTreeMover.hh.

Member Typedef Documentation

typedef core::Size protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::Size

Definition at line 51 of file AlignPoseToInvrotTreeMover.hh.

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

Definition at line 59 of file AlignPoseToInvrotTreeMover.cc.

References all_invrots_, and geomcsts_for_superposition_.

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

Definition at line 72 of file AlignPoseToInvrotTreeMover.cc.

Member Function Documentation

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

virtual

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.

Definition at line 89 of file AlignPoseToInvrotTreeMover.cc.

References add_target_to_pose_, all_invrots_, core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::atom_index(), core::id::BOGUS_ATOM_ID, geomcsts_for_superposition_, core::pose::initialize_atomid_map(), invrot_tree_, core::chemical::ResidueTypeSet::name(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), seqpos_, core::id::AtomID_Map< T >::set(), setup_foldtree_around_anchor_invrot(), core::io::serialization::size(), core::scoring::superimpose_pose(), switch_residue_type_set(), and core::pose::Pose::total_residue().

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

virtual

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

Implements protocols::moves::Mover.

Definition at line 75 of file AlignPoseToInvrotTreeMover.cc.

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

Definition at line 175 of file AlignPoseToInvrotTreeMover.cc.

References add_target_to_pose_.

void protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::set_geomcst_for_superposition_from_enz_io ( EnzConstraintIOCOP enzcst_io)

Definition at line 183 of file AlignPoseToInvrotTreeMover.cc.

References geomcsts_for_superposition_, and protocols::moves::Mover::info().

void protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::setup_foldtree_around_anchor_invrot	(	core::pose::Pose &	pose,
		Size const	anchor_seqpos,
		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

Definition at line 217 of file AlignPoseToInvrotTreeMover.cc.

References core::kinematics::FoldTree::add_edge(), core::pose::Pose::fold_tree(), and core::pose::Pose::total_residue().

Referenced by apply().

core::conformation::ResidueCOP protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::switch_residue_type_set	(	core::conformation::ResidueCOP	residue,
		std::string const	desired_restype_set_name
	)		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

Definition at line 239 of file AlignPoseToInvrotTreeMover.cc.

References core::util::switch_to_residue_type_set().

Referenced by apply().