class that will identify the region around the ligand, remove it, and then do a repack. It can also calculate the following parameters: E diff after the repack, (in essence a crude delta G calc) rmsd of the repacked site after the repack and rmsd of catalytic residues More...

#include <EnzdesMovers.hh>

Inheritance diagram for protocols::enzdes::RepackLigandSiteWithoutLigandMover:

[legend]

Collaboration diagram for protocols::enzdes::RepackLigandSiteWithoutLigandMover:

[legend]

Public Member Functions
	RepackLigandSiteWithoutLigandMover ()

	RepackLigandSiteWithoutLigandMover (core::scoring::ScoreFunctionCOP sfxn, bool calculate_silent_Es)

	~RepackLigandSiteWithoutLigandMover ()

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

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

void	set_cstio (toolbox::match_enzdes_util::EnzConstraintIOCOP enzcst_io)

void	set_sfxn (core::scoring::ScoreFunctionCOP sfxn)

void	set_calculate_silent_Es (bool calculate)

utility::vector1 < core::io::silent::SilentEnergy > const &	silent_Es ()

core::pack::task::PackerTaskCOP	get_ptask () const

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 Member Functions
void	separate_protein_and_ligand (core::pose::Pose &pose) const

Private Attributes
core::scoring::ScoreFunctionCOP	sfxn_

core::Size	lig_seqpos_

toolbox::match_enzdes_util::EnzConstraintIOCOP	enzcst_io_

bool	calculate_silent_Es_

core::pack::task::PackerTaskOP	ptask_

utility::vector1 < core::io::silent::SilentEnergy >	silent_Es_

Additional Inherited Members
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

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

class that will identify the region around the ligand, remove it, and then do a repack. It can also calculate the following parameters: E diff after the repack, (in essence a crude delta G calc) rmsd of the repacked site after the repack and rmsd of catalytic residues

Definition at line 205 of file EnzdesMovers.hh.

Constructor & Destructor Documentation

protocols::enzdes::RepackLigandSiteWithoutLigandMover::RepackLigandSiteWithoutLigandMover ( )

Definition at line 383 of file EnzdesMovers.cc.

References silent_Es_.

protocols::enzdes::RepackLigandSiteWithoutLigandMover::RepackLigandSiteWithoutLigandMover	(	core::scoring::ScoreFunctionCOP	sfxn,
		bool	calculate_silent_Es
	)

Definition at line 389 of file EnzdesMovers.cc.

References silent_Es_.

protocols::enzdes::RepackLigandSiteWithoutLigandMover::~RepackLigandSiteWithoutLigandMover ( )

Definition at line 397 of file EnzdesMovers.cc.

Member Function Documentation

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

virtual

Implements protocols::moves::Mover.

Definition at line 421 of file EnzdesMovers.cc.

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, calculate_silent_Es_, core::pose::Pose::conformation(), core::scoring::coordinate_constraint, core::pack::task::TaskFactory::create_task_and_apply_taskoperations(), core::conformation::Conformation::delete_residue_slow(), core::scoring::dihedral_constraint, enzcst_io_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), protocols::ligand_docking::get_ligand_seqpos(), core::chemical::ResidueType::is_ligand(), core::conformation::Residue::is_protein(), core::scoring::is_protein_sidechain_heavyatom(), lig_seqpos_, ptask_, core::pack::task::TaskFactory::push_back(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::scoring::rmsd_no_super_subset(), separate_protein_and_ligand(), sfxn_, and silent_Es_.

Referenced by protocols::enzdes::RepackWithoutLigandFilter::compute(), and protocols::enzdes::EnzdesScorefileFilter::examine_pose().

std::string protocols::enzdes::RepackLigandSiteWithoutLigandMover::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 513 of file EnzdesMovers.cc.

core::pack::task::PackerTaskCOP protocols::enzdes::RepackLigandSiteWithoutLigandMover::get_ptask ( ) const

Definition at line 528 of file EnzdesMovers.cc.

References ptask_.

Referenced by protocols::enzdes::RepackWithoutLigandFilter::compute().

void protocols::enzdes::RepackLigandSiteWithoutLigandMover::separate_protein_and_ligand ( core::pose::Pose & pose) const

private

Definition at line 519 of file EnzdesMovers.cc.

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_jump_that_builds_residue(), lig_seqpos_, and protocols::rigid::RigidBodyTransMover::step_size().

Referenced by apply().

void protocols::enzdes::RepackLigandSiteWithoutLigandMover::set_calculate_silent_Es ( bool calculate)

Definition at line 414 of file EnzdesMovers.cc.

References calculate_silent_Es_.

void protocols::enzdes::RepackLigandSiteWithoutLigandMover::set_cstio ( toolbox::match_enzdes_util::EnzConstraintIOCOP enzcst_io)

Definition at line 407 of file EnzdesMovers.cc.

References enzcst_io_.

Referenced by protocols::enzdes::EnzdesScorefileFilter::examine_pose().

void protocols::enzdes::RepackLigandSiteWithoutLigandMover::set_sfxn ( core::scoring::ScoreFunctionCOP sfxn)

Definition at line 400 of file EnzdesMovers.cc.

References sfxn_.

utility::vector1< core::io::silent::SilentEnergy > const& protocols::enzdes::RepackLigandSiteWithoutLigandMover::silent_Es ( )

inline

Definition at line 236 of file EnzdesMovers.hh.

References silent_Es_.

Referenced by protocols::enzdes::EnzdesScorefileFilter::examine_pose().

Member Data Documentation

bool protocols::enzdes::RepackLigandSiteWithoutLigandMover::calculate_silent_Es_

private

Definition at line 249 of file EnzdesMovers.hh.

Referenced by apply(), and set_calculate_silent_Es().

toolbox::match_enzdes_util::EnzConstraintIOCOP protocols::enzdes::RepackLigandSiteWithoutLigandMover::enzcst_io_

private

Definition at line 248 of file EnzdesMovers.hh.

Referenced by apply(), and set_cstio().

core::Size protocols::enzdes::RepackLigandSiteWithoutLigandMover::lig_seqpos_

private

Definition at line 247 of file EnzdesMovers.hh.

Referenced by apply(), and separate_protein_and_ligand().

core::pack::task::PackerTaskOP protocols::enzdes::RepackLigandSiteWithoutLigandMover::ptask_

private

Definition at line 250 of file EnzdesMovers.hh.

Referenced by apply(), and get_ptask().

core::scoring::ScoreFunctionCOP protocols::enzdes::RepackLigandSiteWithoutLigandMover::sfxn_

private

Definition at line 246 of file EnzdesMovers.hh.

Referenced by apply(), and set_sfxn().

utility::vector1< core::io::silent::SilentEnergy > protocols::enzdes::RepackLigandSiteWithoutLigandMover::silent_Es_

private

Definition at line 251 of file EnzdesMovers.hh.

Referenced by apply(), RepackLigandSiteWithoutLigandMover(), and silent_Es().

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

src/protocols/enzdes/EnzdesMovers.hh
src/protocols/enzdes/EnzdesMovers.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation