#include <LigandDockProtocol.hh>

Inheritance diagram for protocols::ligand_docking::LigandDockProtocol:

[legend]

Public Member Functions
	LigandDockProtocol ()

	LigandDockProtocol (std::string const &protocol, bool const minimize_ligand, bool const minimize_backbone, bool const tether_ligand, bool const mutate_same_name3, core::Real const ligand_chi_stddev_deg, core::Real const protein_CA_stddev_Ang, core::Real const ligand_tether_stddev_Ang_=-1, core::Size const ligand_shear_moves=0)

	~LigandDockProtocol () override

LigandDockProtocolOP	shared_from_this ()

void	add_start_from (core::Real x, core::Real y, core::Real z)

void	apply (core::pose::Pose &pose) override
	Creates a new hierarchy of Movers for each Pose passed in. More...

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

void	append_ligand_docking_scores (core::pose::Pose const &before, core::pose::Pose const &after, core::scoring::ScoreFunctionCOP scorefxn, std::map< std::string, core::Real > &scores, protocols::toolbox::match_enzdes_util::EnzConstraintIOCOP constraint_io=nullptr) const
	Scores to be output that aren't normal scorefunction terms. More...

Public Member Functions inherited from protocols::ligand_docking::LigandBaseProtocol
	LigandBaseProtocol ()

	~LigandBaseProtocol () override

LigandBaseProtocolOP	shared_from_this ()

core::scoring::ScoreFunctionOP	get_scorefxn ()

core::scoring::ScoreFunctionCOP	get_scorefxn () const

void	restrain_protein_Calphas (core::pose::Pose &pose, utility::vector1< bool > const &is_restrained, core::scoring::func::FuncOP restr_func)

void	reorder_foldtree_around_mobile_regions (core::pose::Pose &pose, core::Size const &jump_id, utility::vector1< bool > const &mobile_bb, core::Size const &lig_id) const
	reorders a fold tree such that movement in the mobile regions will More...

void	get_non_bb_clashing_rotamers (core::pose::Pose const &pose, core::Size seqpos, core::scoring::ScoreFunctionCOP scofx, utility::vector1< core::conformation::ResidueCOP > &accepted_rotamers) const

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 MoverOP	clone () const
	Return a clone of the Mover object. 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

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

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...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Member Functions
	LigandDockProtocol (LigandDockProtocol const &)=delete

void	classic_protocol (core::pose::Pose &pose, int jump_id, core::scoring::ScoreFunctionOP scorefxn, protocols::moves::MonteCarloOP monteCarlo, core::Size num_cycles, core::Size repack_every_Nth) const

void	shear_min_protocol (core::pose::Pose &pose, int jump_id, core::scoring::ScoreFunctionOP scorefxn, protocols::moves::MonteCarloOP monteCarlo, core::Size num_cycles) const

void	optimize_orientation3 (core::pose::Pose &pose, int jump_id, core::Size lig_id)
	Repeatedly randomize ligand orientation in a given location to find where some ligand rotamer has minimal clashes with the backbone. More...

void	random_conformer (core::pose::Pose &pose) const
	Replace current ligand(s) with conformers picked randomly from the library. More...

protocols::moves::MoverOP	make_dockmcm_mover (core::pose::Pose const &pose, int jump_id, protocols::moves::MoverOP repack_mover, protocols::moves::MoverOP rigbod_mover, core::kinematics::MoveMapOP movemap, core::scoring::ScoreFunctionOP scorefxn, protocols::moves::MonteCarloOP monteCarlo) const
	Build Mover for Monte Carlo Minimization protocol. More...

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

Private Attributes
std::string	protocol_

bool	minimize_ligand_

bool	minimize_backbone_

bool	tether_ligand_

bool	ligand_protonation_

core::Real	ligand_chi_stddev_deg_

core::Real	protein_CA_stddev_Ang_

core::Real	ligand_tether_stddev_Ang_

core::Size	ligand_shear_moves_

bool	minimize_all_rsds_

bool	repack_all_rsds_

bool	rottrials_all_rsds_

bool	minimize_water_

utility::vector1< core::Vector >	start_from_pts_

utility::vector1< protocols::ligand_docking::ResidueTorsionRestraintsOP >	ligand_torsion_restraints_

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

Static Public Member Functions inherited from protocols::ligand_docking::LigandBaseProtocol
static core::Size	get_ligand_jump_id (core::pose::Pose const &pose)

static core::Size	get_ligand_id (core::pose::Pose const &pose)
	Return the residue sequence number for our ligand. More...

static core::Size	get_ligand_id (core::pose::Pose const &pose, core::Size jump_id)
	Return the residue sequence number for our ligand. More...

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...

Protected Member Functions inherited from protocols::ligand_docking::LigandBaseProtocol
core::scoring::ScoreFunctionOP	make_tweaked_scorefxn (std::string const &weights_tag, bool estat_exclude_protein, bool estat_upweight, bool hbonds_downweight)

core::Vector	choose_desired_centroid (core::pose::Pose const &pose, core::Size jump_id, utility::vector1< core::Vector >)

void	move_ligand_to_desired_centroid (core::pose::Pose &pose, core::Size jump_id, utility::vector1< core::Vector > start_from_pts)

void	move_ligand_to_desired_centroid (core::pose::Pose &pose, core::Size jump_id, core::Vector desired_centroid)

core::kinematics::MoveMapOP	make_movemap (core::pose::Pose const &pose, core::Size jump_id, core::Real sc_padding, bool include_all_rsds, bool include_backbone, bool include_ligands, bool include_water) const

core::pack::task::PackerTaskOP	make_packer_task (core::pose::Pose const &pose, ObjexxFCL::FArray1D_bool const &allow_repack, bool ligand_protonation) const
	Shared machinery for the next two. More...

core::pack::task::PackerTaskOP	make_packer_task (core::pose::Pose const &pose, int jump_id, core::Real sc_padding, bool include_all_rsds, bool ligand_protonation) const
	Receptor (interface?) plus ligand. More...

core::pack::task::PackerTaskOP	make_packer_task_ligand_only (core::pose::Pose const &pose, int jump_id, bool ligand_protonation) const
	Just ligand, not the receptor. More...

void	find_interface_rsds (core::pose::Pose const &pose, int jump_id, core::Real padding, ObjexxFCL::FArray1D_bool &is_interface) const

void	find_interface_backbone (core::pose::Pose const &pose, int jump_id, core::Real cutoff_dist, utility::vector1< bool > &is_interface, utility::vector1< bool > &is_around_interface) const

core::scoring::constraints::ConstraintOP	restrain_ligand_nbr_atom (core::pose::Pose &pose, core::Size lig_id, core::Real stddev_Angstroms) const

void	setup_bbmin_foldtree (core::pose::Pose &pose, core::Size const &jump_id, core::Real cutoff_dist, core::Real stddev_Angstroms)

core::pack::rotamer_set::UnboundRotamersOperationOP	unboundrot ()
	Nonconst access to the unboundrot_ object. More...

core::scoring::ScoreFunctionOP	scorefxn ()
	Access the scorefunction. More...

void	set_scorefxn (core::scoring::ScoreFunctionCOP const &sfxn_in)
	Set the scorefunction (cloning the input). More...

core::scoring::ScoreFunctionOP	hard_scorefxn ()
	Access the hard scorefunction. More...

core::scoring::ScoreFunctionOP	soft_scorefxn ()
	Access the soft scorefunction. More...

core::Real	sc_interface_padding () const
	Access the sc_interface_padding. More...

core::Real	bb_interface_cutoff () const
	Access the bb_interface_cutoff. More...

void	set_sc_interface_padding (core::Real const setting)
	Set the sc_interface_padding. More...

void	set_bb_interface_cutoff (core::Real const setting)
	Set the bb_interface_cutoff. More...

bool	use_soft_rep () const
	Are we using soft repulsion? 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...

Constructor & Destructor Documentation

◆ LigandDockProtocol() [1/3]

protocols::ligand_docking::LigandDockProtocol::LigandDockProtocol ( )

References ligand_chi_stddev_deg_, ligand_protonation_, ligand_shear_moves_, ligand_tether_stddev_Ang_, minimize_all_rsds_, minimize_backbone_, minimize_ligand_, minimize_water_, protein_CA_stddev_Ang_, protocol_, repack_all_rsds_, rottrials_all_rsds_, protocols::ligand_docking::LigandBaseProtocol::set_bb_interface_cutoff(), protocols::ligand_docking::LigandBaseProtocol::set_sc_interface_padding(), start_from_pts_, and tether_ligand_.

◆ LigandDockProtocol() [2/3]

protocols::ligand_docking::LigandDockProtocol::LigandDockProtocol	(	std::string const &	protocol,
		bool const	minimize_ligand,
		bool const	minimize_backbone,
		bool const	tether_ligand,
		bool const	mutate_same_name3,
		core::Real const	ligand_chi_stddev_deg,
		core::Real const	protein_CA_stddev_Ang,
		core::Real const	ligand_tether_stddev_Ang_ = `-1`,
		core::Size const	ligand_shear_moves = `0`
	)

References ligand_shear_moves_, protocols::ligand_docking::LigandBaseProtocol::set_bb_interface_cutoff(), and protocols::ligand_docking::LigandBaseProtocol::set_sc_interface_padding().

◆ ~LigandDockProtocol()

protocols::ligand_docking::LigandDockProtocol::~LigandDockProtocol ( )

overridedefault

◆ LigandDockProtocol() [3/3]

protocols::ligand_docking::LigandDockProtocol::LigandDockProtocol ( LigandDockProtocol const & )

privatedelete

Member Function Documentation

◆ add_start_from()

void protocols::ligand_docking::LigandDockProtocol::add_start_from	(	core::Real	x,
		core::Real	y,
		core::Real	z
	)

References start_from_pts_.

◆ append_ligand_docking_scores()

void protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores	(	core::pose::Pose const &	before,
		core::pose::Pose const &	after,
		core::scoring::ScoreFunctionCOP	scorefxn,
		std::map< std::string, core::Real > &	scores,
		protocols::toolbox::match_enzdes_util::EnzConstraintIOCOP	constraint_io = `nullptr`
	)		const

Scores to be output that aren't normal scorefunction terms.

References protocols::rigid::RigidBodyTransMover::apply(), core::scoring::automorphic_rmsd(), core::scoring::calc_total_sasa(), protocols::geometry::centroids_by_jump(), protocols::ligand_docking::count_buried_unsat_Hbonds(), core::scoring::fa_rep, core::pose::Pose::fold_tree(), protocols::ligand_docking::frac_atoms_within(), protocols::ligand_docking::LigandBaseProtocol::get_ligand_id(), protocols::ligand_docking::LigandBaseProtocol::get_ligand_jump_id(), core::conformation::Residue::is_polymer(), protocols::mean_field::min(), core::scoring::n_score_types, core::scoring::name_from_score_type(), core::conformation::Residue::nchi(), core::conformation::Residue::nheavyatoms(), core::kinematics::FoldTree::partition_by_jump(), protocols::ligand_docking::print_buried_unsat_Hbonds(), core::pose::Pose::residue(), protocols::ligand_docking::LigandBaseProtocol::scorefxn(), core::pose::Pose::size(), start_from_pts_, protocols::rigid::RigidBodyTransMover::step_size(), protocols::rigid::RigidBodyTransMover::trans_axis(), and core::conformation::Residue::xyz().

Referenced by protocols::ligand_docking::LigandDockMain::apply().

◆ apply()

void protocols::ligand_docking::LigandDockProtocol::apply ( core::pose::Pose & pose )

overridevirtual

Creates a new hierarchy of Movers for each Pose passed in.

Some Movers (e.g. repack) require knowledge of the Pose to create, and are only valid for that Pose and other conformations of it (i.e. poses with the same number of residues, jumps, etc). In general, we expect each Pose coming in here to be from a different PDB file. The cost of creating these objects anew should be minimal compared to the processing work they do.

Reimplemented from protocols::ligand_docking::LigandBaseProtocol.

Referenced by protocols::ligand_docking::LigandDockMain::apply().

◆ classic_protocol()

void protocols::ligand_docking::LigandDockProtocol::classic_protocol	(	core::pose::Pose &	pose,
		int	jump_id,
		core::scoring::ScoreFunctionOP	scorefxn,
		protocols::moves::MonteCarloOP	monteCarlo,
		core::Size	num_cycles,
		core::Size	repack_every_Nth
	)		const

private

References ligand_protonation_, ligand_shear_moves_, ligand_torsion_restraints_, protocols::ligand_docking::LigandBaseProtocol::make_movemap(), protocols::ligand_docking::LigandBaseProtocol::make_packer_task(), minimize_all_rsds_, minimize_ligand_, minimize_water_, repack_all_rsds_, rottrials_all_rsds_, protocols::ligand_docking::LigandBaseProtocol::sc_interface_padding(), protocols::ligand_docking::LigandBaseProtocol::scorefxn(), and shear_min_protocol().

Referenced by apply().

◆ get_name()

std::string protocols::ligand_docking::LigandDockProtocol::get_name ( ) const

overridevirtual

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

Reimplemented from protocols::ligand_docking::LigandBaseProtocol.

◆ make_dockmcm_mover()

protocols::moves::MoverOP protocols::ligand_docking::LigandDockProtocol::make_dockmcm_mover	(	core::pose::Pose const &	pose,
		int	jump_id,
		protocols::moves::MoverOP	repack_mover,
		protocols::moves::MoverOP	rigbod_mover,
		core::kinematics::MoveMapOP	movemap,
		core::scoring::ScoreFunctionOP	scorefxn,
		protocols::moves::MonteCarloOP	monteCarlo
	)		const

private

Build Mover for Monte Carlo Minimization protocol.

References protocols::moves::no_stats, and protocols::ligand_docking::LigandBaseProtocol::scorefxn().

◆ optimize_orientation3()

void protocols::ligand_docking::LigandDockProtocol::optimize_orientation3	(	core::pose::Pose &	pose,
		int	jump_id,
		core::Size	lig_id
	)

private

Repeatedly randomize ligand orientation in a given location to find where some ligand rotamer has minimal clashes with the backbone.

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::automorphic_rmsd(), core::conformation::Residue::clone(), core::pose::Pose::conformation(), core::scoring::coordinate_constraint, core::pack::task::TaskFactory::create_packer_task(), core::scoring::dihedral_constraint, core::conformation::Conformation::downstream_jump_stub(), protocols::ligand_docking::grid_rotamer_trials_atr_rep(), protocols::ligand_docking::grid_score_atr_rep(), core::pose::Pose::jump(), protocols::ligand_docking::make_atr_rep_grid(), protocols::mean_field::max(), protocols::moves::Mover::name(), core::chemical::ResidueType::natoms(), core::conformation::Residue::nbr_atom_xyz(), core::chemical::ResidueType::nchi(), core::conformation::Residue::nheavyatoms(), core::chemical::ResidueType::nheavyatoms(), protocols::geometry::random_reorientation_matrix(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::scoring::rg, core::scoring::rms, core::kinematics::Jump::rotation_by_matrix(), core::pose::Pose::set_jump(), core::kinematics::Jump::set_rb_center(), core::scoring::ScoreFunction::set_weight(), core::pose::Pose::set_xyz(), protocols::ligand_docking::TR(), core::conformation::Conformation::upstream_jump_stub(), and protocols::kinmatch::xyz().

Referenced by apply().

◆ random_conformer()

void protocols::ligand_docking::LigandDockProtocol::random_conformer ( core::pose::Pose & pose ) const

private

Replace current ligand(s) with conformers picked randomly from the library.

References core::conformation::Residue::is_polymer(), ligand_torsion_restraints_, core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by apply().

◆ restrain_ligand_chis()

void protocols::ligand_docking::LigandDockProtocol::restrain_ligand_chis ( core::pose::Pose & pose )

private

References protocols::ligand_docking::constrain_ligand_torsions(), core::conformation::Residue::is_polymer(), ligand_chi_stddev_deg_, ligand_torsion_restraints_, core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by apply().

◆ shared_from_this()

LigandDockProtocolOP protocols::ligand_docking::LigandDockProtocol::shared_from_this ( )

inline

◆ shear_min_protocol()

void protocols::ligand_docking::LigandDockProtocol::shear_min_protocol	(	core::pose::Pose &	pose,
		int	jump_id,
		core::scoring::ScoreFunctionOP	scorefxn,
		protocols::moves::MonteCarloOP	monteCarlo,
		core::Size	num_cycles
	)		const