#include <FlexPepDockingProtocol.hh>

Inheritance diagram for protocols::flexpep_docking::FlexPepDockingProtocol:

Collaboration diagram for protocols::flexpep_docking::FlexPepDockingProtocol:

Public Member Functions
	FlexPepDockingProtocol (Size const rb_jump_in=1)
	constructor More...

	FlexPepDockingProtocol (Size const rb_jump_in, bool const fullatom, bool const view=false)

	~FlexPepDockingProtocol ()

void	set_default ()
	setup that is called from constructor More...

void	view (bool view_in)
	setter More...

virtual protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

virtual void	apply (core::pose::Pose &pose)
	main flexible peptide docking protocol More...

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

virtual void	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &data, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. 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)

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	setup_foldtree (core::pose::Pose &pose)
	setup the peptide docking fold tree More...

void	minimize_only (core::pose::Pose &pose, const std::string &min_type, const float min_func_tol)

void	prepack_only (core::pose::Pose &pose, bool ppk_receptor, bool ppk_peptide)
	prepack protocol for flexpepdock More...

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

void	set_allowed_moves ()

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

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

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

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

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

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

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

bool	check_filters (core::pose::Pose &pose)

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

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

void	torsions_monte_carlo_minimize (core::pose::Pose &pose, const int cycles, const std::string &min_type, const float minimization_threshold, const float min_func_tol)

void	rigidbody_monte_carlo_minimize (core::pose::Pose &pose, const int cycles, const std::string &min_type, const float trans_magnitude, const float rot_magnitude, const float minimization_threshold, const float func_tol)

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

void	markNativeInterface (ObjexxFCL::FArray1D_bool &superpos_partner, ObjexxFCL::FArray1D_bool &native_interface_residues) const

void	addLowResStatistics (core::pose::Pose const &start_pose, core::pose::Pose &pose_after_lowres) const

void	storeJobStatistics (core::pose::Pose const &start_pose, core::pose::Pose &pose_after_lowres, core::pose::Pose &final_pose)

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

Private Attributes
bool	fullatom_
	information about the mode More...

Size	rb_jump_
	the jump number across which to do rigid_body transformations More...

bool	view_
	whether or not to initialize the viewer (for opengl) More...

bool	is_fail_

FlexPepDockingFlags	flags_

core::Size	nres_receptor_

core::Size	nres_peptide_

moves::MonteCarloOP	mc_

core::scoring::ScoreFunctionOP	scorefxn_

core::scoring::ScoreFunctionOP	scorefxn_lowres_

FlexPepDockingPoseMetrics	fpdock_metrics_

std::map< std::string, core::Real >	if_metrics_

core::pack::task::TaskFactoryOP	allprotein_tf_

core::pack::task::TaskFactoryOP	interface_tf_

protocols::simple_moves::PackRotamersMoverOP	interface_packer_

core::pack::task::operation::RestrictResidueToRepackingOP	receptor_protector_oper_

core::pack::task::PackerTaskOP	design_task_

protocols::simple_moves::PackRotamersMoverOP	design_mover_

core::kinematics::MoveMapOP	movemap_

core::kinematics::MoveMapOP	movemap_minimizer_

protocols::comparative_modeling::LoopRelaxMoverOP	loop_relax_mover_

bool	is_trimmed_loops_

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

Definition at line 52 of file FlexPepDockingProtocol.hh.

Constructor & Destructor Documentation

protocols::flexpep_docking::FlexPepDockingProtocol::FlexPepDockingProtocol ( Size const rb_jump_in = 1)

constructor

Definition at line 113 of file FlexPepDockingProtocol.cc.

References set_default().

Referenced by clone(), and protocols::flexpep_docking::FlexPepDockingProtocolCreator::create_mover().

protocols::flexpep_docking::FlexPepDockingProtocol::FlexPepDockingProtocol	(	Size const	rb_jump_in,
		bool const	fullatom,
		bool const	view = `false`
	)

Definition at line 125 of file FlexPepDockingProtocol.cc.

References fullatom_, set_default(), view(), and view_.

protocols::flexpep_docking::FlexPepDockingProtocol::~FlexPepDockingProtocol ( )

Definition at line 142 of file FlexPepDockingProtocol.cc.

Member Function Documentation

void protocols::flexpep_docking::FlexPepDockingProtocol::addLowResStatistics	(	core::pose::Pose const &	start_pose,
		core::pose::Pose &	pose_after_lowres
	)		const

private

Definition at line 1136 of file FlexPepDockingProtocol.cc.

References protocols::simple_moves::SwitchResidueTypeSetMover::apply(), core::chemical::CENTROID, protocols::nonlocal::current_job(), protocols::moves::Mover::get_native_pose(), core::scoring::is_protein_backbone(), core::scoring::is_protein_CA(), markNativeInterface(), core::scoring::rmsd_no_super_subset(), scorefxn_lowres_, and protocols::TR().

Referenced by storeJobStatistics().

void protocols::flexpep_docking::FlexPepDockingProtocol::apply ( core::pose::Pose & pose)

virtual

main flexible peptide docking protocol

FlexPepDocking apply

Detailed:: Main function for peptide docking. Includes the following steps: 1) Optional centroid mode docking, with alternating MCM cycles of rigid-body movement and peptide torsion relaxation 2) High-resolution peptide docking, with alternating MCM cycles of rigid-body movement and peptide torsion relaxation with side-chain repacking on-the-fly Prepack mode: prepare a starting structure for later runs OR: Score only mode Minimize only mode

IMPORTANT NOTE: Apply should not change the internal state of this object in a way that will affect the behaviour of subsequent apply() invocations (because, e.g., the job distributor may invoke apply() for multiple decoys, using the same mover object)

Implements protocols::moves::Mover.

Definition at line 978 of file FlexPepDockingProtocol.cc.

void protocols::flexpep_docking::FlexPepDockingProtocol::backrub_move ( core::pose::Pose & pose)

private

Definition at line 598 of file FlexPepDockingProtocol.cc.

References protocols::backrub::BackrubMover::clear_segments(), flags_, protocols::flexpep_docking::FlexPepDockingFlags::peptide_first_res(), protocols::flexpep_docking::FlexPepDockingFlags::peptide_nres(), and protocols::TR().

Referenced by apply().

void protocols::flexpep_docking::FlexPepDockingProtocol::calcMetrics ( core::pose::Pose & pose)

private

bool protocols::flexpep_docking::FlexPepDockingProtocol::check_filters ( core::pose::Pose & pose)

private

Definition at line 660 of file FlexPepDockingProtocol.cc.

References flags_, protocols::flexpep_docking::FlexPepDockingFlags::hb_filter, protocols::flexpep_docking::FlexPepDockingFlags::hotspot_filter, protocols::flexpep_docking::FlexPepDockingFlags::score_filter, and protocols::TR().

Referenced by apply().

protocols::moves::MoverOP protocols::flexpep_docking::FlexPepDockingProtocol::clone ( ) const

virtual

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

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

Definition at line 147 of file FlexPepDockingProtocol.cc.

References flags_, FlexPepDockingProtocol(), fullatom_, rb_jump_, scorefxn_, and view_.

void protocols::flexpep_docking::FlexPepDockingProtocol::extend_peptide ( core::pose::Pose & pose)

private

Definition at line 515 of file FlexPepDockingProtocol.cc.

References flags_, protocols::flexpep_docking::FlexPepDockingFlags::peptide_first_res(), protocols::flexpep_docking::FlexPepDockingFlags::peptide_nres(), core::pose::Pose::set_phi(), and core::pose::Pose::set_psi().

Referenced by apply().

std::string protocols::flexpep_docking::FlexPepDockingProtocol::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 1087 of file FlexPepDockingProtocol.cc.

void protocols::flexpep_docking::FlexPepDockingProtocol::hires_fpdock_protocol ( core::pose::Pose & pose)

private

Definition at line 860 of file FlexPepDockingProtocol.cc.

Referenced by apply().

void protocols::flexpep_docking::FlexPepDockingProtocol::markNativeInterface	(	ObjexxFCL::FArray1D_bool &	superpos_partner,
		ObjexxFCL::FArray1D_bool &	native_interface_residues
	)		const

private

Definition at line 1102 of file FlexPepDockingProtocol.cc.

References flags_, protocols::moves::Mover::get_native_pose(), protocols::flexpep_docking::FlexPepDockingFlags::pep_fold_only, protocols::flexpep_docking::FlexPepDockingFlags::peptide_first_res(), protocols::flexpep_docking::FlexPepDockingFlags::peptide_last_res(), rb_jump_, protocols::TR(), and core::pose::Pose::update_residue_neighbors().

Referenced by addLowResStatistics(), and storeJobStatistics().

void protocols::flexpep_docking::FlexPepDockingProtocol::minimize_only	(	core::pose::Pose &	pose,
		const std::string &	min_type,
		const float	min_func_tol
	)

private

Definition at line 391 of file FlexPepDockingProtocol.cc.

References protocols::simple_moves::MinMover::apply(), movemap_minimizer_, and scorefxn_.

Referenced by apply().

void protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag	(	utility::tag::TagPtr const	tag,
		protocols::moves::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)

virtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

Definition at line 1344 of file FlexPepDockingProtocol.cc.

void protocols::flexpep_docking::FlexPepDockingProtocol::peptide_random_loop_model ( core::pose::Pose & pose)

private

Definition at line 834 of file FlexPepDockingProtocol.cc.

References flags_, loop_relax_mover_, movemap_, protocols::flexpep_docking::FlexPepDockingFlags::peptide_first_res(), protocols::flexpep_docking::FlexPepDockingFlags::peptide_last_res(), and protocols::flexpep_docking::FlexPepDockingFlags::peptide_nres().

Referenced by hires_fpdock_protocol().

void protocols::flexpep_docking::FlexPepDockingProtocol::polyAla ( core::pose::Pose & pose)

private

Definition at line 633 of file FlexPepDockingProtocol.cc.

References core::conformation::ResidueFactory::create_residue(), flags_, core::chemical::ChemicalManager::get_instance(), protocols::flexpep_docking::FlexPepDockingFlags::peptide_first_res(), protocols::flexpep_docking::FlexPepDockingFlags::peptide_nres(), and core::pose::Pose::replace_residue().

void protocols::flexpep_docking::FlexPepDockingProtocol::prepack_only	(	core::pose::Pose &	pose,
		bool	ppk_receptor,
		bool	ppk_peptide
	)

private

prepack protocol for flexpepdock

create and apply prepack mover

Definition at line 419 of file FlexPepDockingProtocol.cc.

References core::pack::task::operation::NoRepackDisulfides::apply(), flags_, protocols::flexpep_docking::FlexPepDockingFlags::pep_fold_only, rb_jump_, protocols::flexpep_docking::FlexPepDockingFlags::receptor_nres(), scorefxn_, core::pose::Pose::total_residue(), and protocols::TR().

Referenced by apply().

void protocols::flexpep_docking::FlexPepDockingProtocol::random_peptide_phi_psi_perturbation ( core::pose::Pose & pose)

private

Definition at line 489 of file FlexPepDockingProtocol.cc.

References flags_, protocols::flexpep_docking::FlexPepDockingFlags::peptide_first_res(), protocols::flexpep_docking::FlexPepDockingFlags::peptide_nres(), core::pose::Pose::phi(), core::pose::Pose::psi(), protocols::flexpep_docking::FlexPepDockingFlags::random_phi_psi_pert_size, core::pose::Pose::set_phi(), and core::pose::Pose::set_psi().

Referenced by apply().

void protocols::flexpep_docking::FlexPepDockingProtocol::random_rb_pert ( core::pose::Pose & pose)

private

Definition at line 532 of file FlexPepDockingProtocol.cc.

References flags_, rb_jump_, protocols::flexpep_docking::FlexPepDockingFlags::rb_rot_size, and protocols::flexpep_docking::FlexPepDockingFlags::rb_trans_size.

Referenced by apply().

void protocols::flexpep_docking::FlexPepDockingProtocol::randomlySlidePeptideJump ( core::pose::Pose & pose)

private

Definition at line 684 of file FlexPepDockingProtocol.cc.

References flags_, core::pose::Pose::fold_tree(), protocols::flexpep_docking::FlexPepDockingFlags::peptide_first_res(), protocols::flexpep_docking::FlexPepDockingFlags::peptide_nres(), rb_jump_, core::kinematics::FoldTree::slide_jump(), and protocols::TR().

void protocols::flexpep_docking::FlexPepDockingProtocol::rigidbody_monte_carlo_minimize	(	core::pose::Pose &	pose,
		const int	cycles,
		const std::string &	min_type,
		const float	trans_magnitude,
		const float	rot_magnitude,
		const float	minimization_threshold,
		const float	func_tol
	)

private

Definition at line 770 of file FlexPepDockingProtocol.cc.

References allprotein_tf_, protocols::simple_moves::EnergyCutRotamerTrialsMover::apply(), protocols::rigid::RigidBodyPerturbMover::apply(), protocols::simple_moves::MinMover::apply(), interface_packer_, interface_tf_, movemap_minimizer_, rb_jump_, scorefxn_, and protocols::TR().

Referenced by hires_fpdock_protocol().

void protocols::flexpep_docking::FlexPepDockingProtocol::set_allowed_moves ( )

private

Definition at line 353 of file FlexPepDockingProtocol.cc.

References flags_, protocols::flexpep_docking::FlexPepDockingFlags::min_receptor_bb, movemap_, movemap_minimizer_, protocols::flexpep_docking::FlexPepDockingFlags::pep_fold_only, protocols::flexpep_docking::FlexPepDockingFlags::peptide_first_res(), protocols::flexpep_docking::FlexPepDockingFlags::peptide_last_res(), rb_jump_, protocols::flexpep_docking::FlexPepDockingFlags::receptor_first_res(), and protocols::flexpep_docking::FlexPepDockingFlags::receptor_last_res().

Referenced by apply().

void protocols::flexpep_docking::FlexPepDockingProtocol::set_default ( )

setup that is called from constructor

Definition at line 160 of file FlexPepDockingProtocol.cc.

References allprotein_tf_, core::scoring::CENTROID_WTS, core::scoring::ScoreFunctionFactory::create_score_function(), flags_, fullatom_, core::scoring::getScoreFunction(), if_metrics_, interface_packer_, interface_tf_, loop_relax_mover_, movemap_, movemap_minimizer_, protocols::flexpep_docking::FlexPepDockingFlags::pep_fold_only, rb_jump_, protocols::loops::read_loop_fragments(), scorefxn_, scorefxn_lowres_, and view_.

Referenced by FlexPepDockingProtocol().

void protocols::flexpep_docking::FlexPepDockingProtocol::set_receptor_constraints ( core::pose::Pose & pose)

private

Definition at line 317 of file FlexPepDockingProtocol.cc.

References core::conformation::Residue::atom_index(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, flags_, protocols::flexpep_docking::FlexPepDockingFlags::receptor_first_res(), protocols::flexpep_docking::FlexPepDockingFlags::receptor_last_res(), core::pose::Pose::residue(), and scorefxn_.

Referenced by apply().

void protocols::flexpep_docking::FlexPepDockingProtocol::setup_foldtree ( core::pose::Pose & pose)

private

setup the peptide docking fold tree

Definition at line 235 of file FlexPepDockingProtocol.cc.

Referenced by apply().

void protocols::flexpep_docking::FlexPepDockingProtocol::shear_moves ( core::pose::Pose & pose)

private

Definition at line 579 of file FlexPepDockingProtocol.cc.

References flags_, movemap_, and protocols::flexpep_docking::FlexPepDockingFlags::smove_angle_range.

Referenced by torsions_monte_carlo_minimize().

void protocols::flexpep_docking::FlexPepDockingProtocol::small_moves ( core::pose::Pose & pose)

private

Definition at line 560 of file FlexPepDockingProtocol.cc.

References flags_, movemap_, and protocols::flexpep_docking::FlexPepDockingFlags::smove_angle_range.

Referenced by torsions_monte_carlo_minimize().

void protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics	(	core::pose::Pose const &	start_pose,
		core::pose::Pose &	pose_after_lowres,
		core::pose::Pose &	final_pose
	)

private

Definition at line 1200 of file FlexPepDockingProtocol.cc.

Referenced by apply().

void protocols::flexpep_docking::FlexPepDockingProtocol::torsions_monte_carlo_minimize	(	core::pose::Pose &	pose,
		const int	cycles,
		const std::string &	min_type,
		const float	minimization_threshold,
		const float	min_func_tol
	)