#include <FlexPepDockingProtocol.hh>

Inheritance diagram for protocols::flexpep_docking::FlexPepDockingProtocol:

[legend]

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

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

	~FlexPepDockingProtocol () override

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

void	view (bool view_in)
	setter More...

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

void	apply (core::pose::Pose &pose) override
	Main Method. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. 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 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

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 Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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...

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	place_peptide_on_binding_site (core::pose::Pose &pose)

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

void	SlideIntoContact (core::pose::Pose &pose, core::Vector translate_axis)

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	markInterfaceBySideChainContacts (ObjexxFCL::FArray1D_bool &native_interface_residues, core::Size distance) const

void	markNativeInterface (ObjexxFCL::FArray1D_bool &superpos_partner, ObjexxFCL::FArray1D_bool &native_interface_residues, bool mark_receptor_interface) 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...

core::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_
	flag for failures in class operation More...

FlexPepDockingFlags	flags_
	all flags loaded from cmd-line options More...

core::Size	nres_receptor_

core::Size	nres_peptide_

moves::MonteCarloOP	mc_

core::scoring::ScoreFunctionOP	scorefxn_

core::scoring::ScoreFunctionOP	scorefxn_lowres_
	for low-res optimization More...

FlexPepDockingPoseMetrics	fpdock_metrics_
	metrics calculator object More...

std::map< std::string, core::Real >	if_metrics_
	interface metrics More...

core::pack::task::TaskFactoryOP	allprotein_tf_
	taskfactory for all-protein repacking operations More...

core::pack::task::TaskFactoryOP	interface_tf_
	task factory that restricts packing to the interface More...

protocols::minimization_packing::PackRotamersMoverOP	interface_packer_
	for packing the docking interface More...

core::kinematics::MoveMapOP	movemap_
	the flexpepdock protocol movemap More...

core::kinematics::MoveMapOP	movemap_minimizer_
	movemap for the minimizer More...

protocols::relax::loop::LoopRelaxMoverOP	loop_relax_mover_
	loop mover for modeling loop closure More...

bool	fragment_files_need_load_ = false
	Do fragment files need to be loaded? More...

bool	is_trimmed_loops_

Additional Inherited Members
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

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...

Constructor & Destructor Documentation

◆ FlexPepDockingProtocol() [1/2]

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

constructor

References set_default().

◆ FlexPepDockingProtocol() [2/2]

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

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

◆ ~FlexPepDockingProtocol()

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

overridedefault

Member Function Documentation

◆ addLowResStatistics()

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

private

References protocols::jd2::add_string_real_pair_to_current_job(), protocols::simple_moves::SwitchResidueTypeSetMover::apply(), core::chemical::CENTROID, flags_, protocols::moves::Mover::get_native_pose(), core::pose::Pose::is_fullatom(), core::scoring::is_protein_backbone(), core::scoring::is_protein_CA(), markNativeInterface(), protocols::flexpep_docking::FlexPepDockingFlags::pep_fold_only, core::scoring::rmsd_no_super_subset(), core::scoring::rmsd_with_super(), scorefxn_lowres_, core::pose::Pose::size(), and protocols::TR().

Referenced by storeJobStatistics().

◆ apply()

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

◆ backrub_move()

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

private

References protocols::backrub::BackrubMover::add_mainchain_segments(), protocols::backrub::BackrubMover::apply(), protocols::backrub::BackrubMover::clear_segments(), flags_, core::pose::Pose::get_self_ptr(), protocols::flexpep_docking::FlexPepDockingFlags::peptide_first_res(), protocols::flexpep_docking::FlexPepDockingFlags::peptide_nres(), protocols::moves::Mover::set_input_pose(), and protocols::TR().

Referenced by apply().

◆ calcMetrics()

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

private

◆ check_filters()

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

private

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().

◆ clone()

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

overridevirtual

Return a clone of the Mover object.

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.

References flags_, fullatom_, rb_jump_, scorefxn_, and view_.

◆ extend_peptide()

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

private

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().

◆ flip_in_pcs()

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

private

References protocols::rigid::RigidBodyDeterministicSpinMover::apply(), flags_, protocols::flexpep_docking::FlexPepDockingFlags::peptide_first_res(), protocols::flexpep_docking::FlexPepDockingFlags::peptide_last_res(), rb_jump_, core::pose::Pose::residue(), protocols::flexpep_docking::FlexPepDockingFlags::sample_pc, protocols::TR(), and core::conformation::Residue::xyz().

Referenced by apply().

◆ get_name()

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ hires_fpdock_protocol()

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

private

Referenced by apply().

◆ markInterfaceBySideChainContacts()

void protocols::flexpep_docking::FlexPepDockingProtocol::markInterfaceBySideChainContacts	(	ObjexxFCL::FArray1D_bool &	native_interface_residues,
		core::Size	distance
	)		const

private

References core::kinematics::distance(), flags_, fpdock_metrics_, protocols::moves::Mover::get_native_pose(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::isInContact(), core::pose::Pose::pdb_info(), protocols::flexpep_docking::FlexPepDockingFlags::peptide_first_res(), protocols::flexpep_docking::FlexPepDockingFlags::peptide_last_res(), protocols::flexpep_docking::FlexPepDockingFlags::receptor_first_res(), protocols::flexpep_docking::FlexPepDockingFlags::receptor_last_res(), core::pose::Pose::residue(), and protocols::TR().

Referenced by storeJobStatistics().

◆ markNativeInterface()

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

private

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::flexpep_docking::FlexPepDockingFlags::receptor_first_res(), protocols::flexpep_docking::FlexPepDockingFlags::receptor_last_res(), protocols::TR(), and core::pose::Pose::update_residue_neighbors().

Referenced by addLowResStatistics(), and storeJobStatistics().

◆ minimize_only()

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

private

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

Referenced by apply().

◆ mover_name()

std::string protocols::flexpep_docking::FlexPepDockingProtocol::mover_name ( )

static

Referenced by get_name(), protocols::flexpep_docking::FlexPepDockingProtocolCreator::keyname(), provide_citation_info(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

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 force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

◆ peptide_random_loop_model()

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

private

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().

◆ place_peptide_on_binding_site()

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

private

References core::pose::Pose::conformation(), core::sequence::end, flags_, core::scoring::constraints::get_cst_file_option(), core::pose::Pose::jump(), protocols::flexpep_docking::FlexPepDockingFlags::peptide_first_res(), protocols::flexpep_docking::FlexPepDockingFlags::peptide_last_res(), rb_jump_, core::pose::Pose::residue(), core::kinematics::Jump::rotation_by_matrix(), core::pose::Pose::set_jump(), SlideIntoContact(), protocols::TR(), core::conformation::Conformation::upstream_jump_stub(), and core::conformation::Residue::xyz().

Referenced by apply().

◆ polyAla()

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

private

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

◆ prepack_only()

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

private

prepack protocol for flexpepdock

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::size(), and protocols::TR().

Referenced by apply().

◆ provide_citation_info()

void protocols::flexpep_docking::FlexPepDockingProtocol::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

References allprotein_tf_, flags_, interface_tf_, protocols::flexpep_docking::FlexPepDockingFlags::lowres_abinitio, mover_name(), scorefxn_, and scorefxn_lowres_.

◆ provide_xml_schema()

void protocols::flexpep_docking::FlexPepDockingProtocol::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::flexpep_docking::FlexPepDockingProtocolCreator::provide_xml_schema().

◆ random_peptide_phi_psi_perturbation()

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

private

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().

◆ random_rb_pert()

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

private

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

Referenced by apply().

◆ randomlySlidePeptideJump()

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

private

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(), protocols::TR(), and core::kinematics::FoldTree::upstream_jump_residue().

◆ rigidbody_monte_carlo_minimize()

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

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

Referenced by hires_fpdock_protocol().

◆ set_allowed_moves()

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

private

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().

◆ set_default()

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

◆ set_receptor_constraints()

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

private

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(), scorefxn_, and core::conformation::Conformation::xyz().

Referenced by apply().

◆ setup_foldtree()

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

private

setup the peptide docking fold tree

Referenced by apply().

◆ shear_moves()

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

private

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

Referenced by torsions_monte_carlo_minimize().

◆ SlideIntoContact()

void protocols::flexpep_docking::FlexPepDockingProtocol::SlideIntoContact	(	core::pose::Pose &	pose,
		core::Vector	translate_axis
	)

private

References core::scoring::ScoreFunctionFactory::create_score_function(), core::pose::Pose::energies(), core::scoring::interchain_vdw, rb_jump_, core::scoring::Energies::total_energies(), and protocols::TR().

Referenced by apply(), and place_peptide_on_binding_site().

◆ small_moves()

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

private

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

Referenced by torsions_monte_carlo_minimize().

◆ storeJobStatistics()

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

private

Referenced by apply().

◆ torsions_monte_carlo_minimize()

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
	)

private

References allprotein_tf_, protocols::minimization_packing::MinMover::apply(), protocols::minimization_packing::EnergyCutRotamerTrialsMover::apply(), interface_packer_, interface_tf_, movemap_minimizer_, scorefxn_, shear_moves(), small_moves(), and protocols::TR().

Referenced by hires_fpdock_protocol().

◆ view()

void protocols::flexpep_docking::FlexPepDockingProtocol::view ( bool view_in )

inline

setter

References view_.

Referenced by FlexPepDockingProtocol().

Member Data Documentation

◆ allprotein_tf_

core::pack::task::TaskFactoryOP protocols::flexpep_docking::FlexPepDockingProtocol::allprotein_tf_

private

taskfactory for all-protein repacking operations

Referenced by provide_citation_info(), rigidbody_monte_carlo_minimize(), set_default(), and torsions_monte_carlo_minimize().

◆ flags_

FlexPepDockingFlags protocols::flexpep_docking::FlexPepDockingProtocol::flags_

private

◆ fpdock_metrics_

FlexPepDockingPoseMetrics protocols::flexpep_docking::FlexPepDockingProtocol::fpdock_metrics_

private

metrics calculator object

Referenced by apply(), markInterfaceBySideChainContacts(), and storeJobStatistics().

◆ fragment_files_need_load_

bool protocols::flexpep_docking::FlexPepDockingProtocol::fragment_files_need_load_ = false

private

Do fragment files need to be loaded?

Done on first need (apply-time).

Referenced by apply(), and set_default().

◆ fullatom_

bool protocols::flexpep_docking::FlexPepDockingProtocol::fullatom_

private

information about the mode

Referenced by clone(), FlexPepDockingProtocol(), and set_default().

◆ if_metrics_

std::map< std::string, core::Real > protocols::flexpep_docking::FlexPepDockingProtocol::if_metrics_

private

interface metrics

Referenced by set_default(), and storeJobStatistics().

◆ interface_packer_

protocols::minimization_packing::PackRotamersMoverOP protocols::flexpep_docking::FlexPepDockingProtocol::interface_packer_

private

for packing the docking interface

Referenced by hires_fpdock_protocol(), rigidbody_monte_carlo_minimize(), set_default(), and torsions_monte_carlo_minimize().

◆ interface_tf_

core::pack::task::TaskFactoryOP protocols::flexpep_docking::FlexPepDockingProtocol::interface_tf_

private

task factory that restricts packing to the interface

Referenced by provide_citation_info(), rigidbody_monte_carlo_minimize(), set_default(), and torsions_monte_carlo_minimize().

◆ is_fail_

bool protocols::flexpep_docking::FlexPepDockingProtocol::is_fail_

private

flag for failures in class operation

◆ is_trimmed_loops_

bool protocols::flexpep_docking::FlexPepDockingProtocol::is_trimmed_loops_

private

◆ loop_relax_mover_

protocols::relax::loop::LoopRelaxMoverOP protocols::flexpep_docking::FlexPepDockingProtocol::loop_relax_mover_

private

loop mover for modeling loop closure

Referenced by apply(), peptide_random_loop_model(), and set_default().

◆ mc_

moves::MonteCarloOP protocols::flexpep_docking::FlexPepDockingProtocol::mc_

private

◆ movemap_

core::kinematics::MoveMapOP protocols::flexpep_docking::FlexPepDockingProtocol::movemap_

private

the flexpepdock protocol movemap

may change throughout the run

Referenced by apply(), peptide_random_loop_model(), set_allowed_moves(), set_default(), shear_moves(), and small_moves().

◆ movemap_minimizer_

core::kinematics::MoveMapOP protocols::flexpep_docking::FlexPepDockingProtocol::movemap_minimizer_

private

movemap for the minimizer

Referenced by hires_fpdock_protocol(), minimize_only(), rigidbody_monte_carlo_minimize(), set_allowed_moves(), set_default(), and torsions_monte_carlo_minimize().

◆ nres_peptide_

core::Size protocols::flexpep_docking::FlexPepDockingProtocol::nres_peptide_

private

◆ nres_receptor_

core::Size protocols::flexpep_docking::FlexPepDockingProtocol::nres_receptor_

private

◆ rb_jump_

core::Size protocols::flexpep_docking::FlexPepDockingProtocol::rb_jump_

private

the jump number across which to do rigid_body transformations

Referenced by apply(), clone(), flip_in_pcs(), markNativeInterface(), place_peptide_on_binding_site(), prepack_only(), random_rb_pert(), randomlySlidePeptideJump(), rigidbody_monte_carlo_minimize(), set_allowed_moves(), set_default(), SlideIntoContact(), and storeJobStatistics().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::flexpep_docking::FlexPepDockingProtocol::scorefxn_

private

Referenced by apply(), clone(), hires_fpdock_protocol(), minimize_only(), parse_my_tag(), prepack_only(), provide_citation_info(), rigidbody_monte_carlo_minimize(), set_default(), set_receptor_constraints(), storeJobStatistics(), and torsions_monte_carlo_minimize().

◆ scorefxn_lowres_

core::scoring::ScoreFunctionOP protocols::flexpep_docking::FlexPepDockingProtocol::scorefxn_lowres_

private

for low-res optimization

Referenced by addLowResStatistics(), apply(), parse_my_tag(), provide_citation_info(), and set_default().

◆ view_

bool protocols::flexpep_docking::FlexPepDockingProtocol::view_

private

whether or not to initialize the viewer (for opengl)

Referenced by apply(), clone(), FlexPepDockingProtocol(), set_default(), and view().

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

src/protocols/flexpep_docking/FlexPepDockingProtocol.hh
src/protocols/flexpep_docking/FlexPepDockingProtocol.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ FlexPepDockingProtocol() [1/2]

◆ FlexPepDockingProtocol() [2/2]

◆ ~FlexPepDockingProtocol()

Member Function Documentation

◆ addLowResStatistics()

◆ apply()

◆ backrub_move()

◆ calcMetrics()

◆ check_filters()

◆ clone()

◆ extend_peptide()

◆ flip_in_pcs()

◆ get_name()

◆ hires_fpdock_protocol()

◆ markInterfaceBySideChainContacts()

◆ markNativeInterface()

◆ minimize_only()

◆ mover_name()

◆ parse_my_tag()

◆ peptide_random_loop_model()

◆ place_peptide_on_binding_site()

◆ polyAla()

◆ prepack_only()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ random_peptide_phi_psi_perturbation()

◆ random_rb_pert()

◆ randomlySlidePeptideJump()

◆ rigidbody_monte_carlo_minimize()

◆ set_allowed_moves()

◆ set_default()

◆ set_receptor_constraints()

◆ setup_foldtree()

◆ shear_moves()

◆ SlideIntoContact()

◆ small_moves()

◆ storeJobStatistics()

◆ torsions_monte_carlo_minimize()

◆ view()

Member Data Documentation

◆ allprotein_tf_

◆ flags_

◆ fpdock_metrics_

◆ fragment_files_need_load_

◆ fullatom_

◆ if_metrics_

◆ interface_packer_

◆ interface_tf_

◆ is_fail_

◆ is_trimmed_loops_

◆ loop_relax_mover_

◆ mc_

◆ movemap_

◆ movemap_minimizer_

◆ nres_peptide_

◆ nres_receptor_

◆ rb_jump_

◆ scorefxn_

◆ scorefxn_lowres_

◆ view_