generates random rbconfs until a total of num_total_rbconfs_ are present in the cacheable observer. The diversifier is used to ensure that all newly generated confs are different. note: no scorefunction used More...

#include <ModifyStoredLigandRBConfsMovers.hh>

Inheritance diagram for protocols::enzdes::GenerateStoredRBConfs:

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Collaboration diagram for protocols::enzdes::GenerateStoredRBConfs:

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Public Types
typedef ModifyStoredRBConfs	parent

Public Types inherited from protocols::enzdes::ModifyStoredRBConfs
typedef core::Size	Size

typedef core::Real	Real

typedef protocols::moves::Mover	parent

typedef utility::vector1 < utility::vector1 < core::conformation::ResidueCOP > >	RBConfLists

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
	GenerateStoredRBConfs (Size num_total_rbconfs, bool include_metals)

	~GenerateStoredRBConfs ()

void	apply (core::pose::Pose &pose)
	two things happen: More...

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

Public Member Functions inherited from protocols::enzdes::ModifyStoredRBConfs
	ModifyStoredRBConfs (std::string const name)

	~ModifyStoredRBConfs ()

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

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
Size	num_total_rbconfs_

bool	include_metals_

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::enzdes::ModifyStoredRBConfs
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...

Detailed Description

generates random rbconfs until a total of num_total_rbconfs_ are present in the cacheable observer. The diversifier is used to ensure that all newly generated confs are different. note: no scorefunction used

Definition at line 106 of file ModifyStoredLigandRBConfsMovers.hh.

Member Typedef Documentation

typedef ModifyStoredRBConfs protocols::enzdes::GenerateStoredRBConfs::parent

Definition at line 109 of file ModifyStoredLigandRBConfsMovers.hh.

Constructor & Destructor Documentation

protocols::enzdes::GenerateStoredRBConfs::GenerateStoredRBConfs	(	Size	num_total_rbconfs,
		bool	include_metals
	)

Definition at line 149 of file ModifyStoredLigandRBConfsMovers.cc.

protocols::enzdes::GenerateStoredRBConfs::~GenerateStoredRBConfs ( )

Definition at line 155 of file ModifyStoredLigandRBConfsMovers.cc.

Member Function Documentation

void protocols::enzdes::GenerateStoredRBConfs::apply ( core::pose::Pose & pose)

virtual

two things happen:

for ligands which already have multiple conformations stored, their number will be increased to num_total_rbconfs_ in case there are already more rb_confs than num_total_rb_confs_, nothing happens
for ligands that don't have multiple conformations stored, num_total_rbconfs_ will be generated

Implements protocols::enzdes::ModifyStoredRBConfs.

Definition at line 169 of file ModifyStoredLigandRBConfsMovers.cc.

References core::conformation::Residue::clone(), protocols::moves::Mover::clone(), protocols::enzdes::DiversifyStoredRBConfs::diversify_all_confs(), protocols::enzdes::ModifyStoredRBConfs::get_rigid_body_confs(), include_metals_, core::chemical::ResidueType::is_ligand(), core::conformation::Residue::name(), core::chemical::ResidueType::natoms(), num_total_rbconfs_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::enzdes::ModifyStoredRBConfs::set_rigid_body_confs_for_seqpos(), core::io::serialization::size(), core::pose::Pose::total_residue(), and protocols::enzdes::tr().