Shared functionality for protocols that dock ligands. More...

#include <LigandBaseProtocol.hh>

Inheritance diagram for protocols::ligand_docking::LigandBaseProtocol:

Public Member Functions
	LigandBaseProtocol ()

	~LigandBaseProtocol () override

LigandBaseProtocolOP	shared_from_this ()

core::scoring::ScoreFunctionOP	get_scorefxn ()

core::scoring::ScoreFunctionCOP	get_scorefxn () const

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

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

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

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...

Static Public Member Functions
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
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)

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...

Protected Attributes
bool	use_soft_rep_

core::scoring::ScoreFunctionOP	scorefxn_

core::scoring::ScoreFunctionOP	hard_scorefxn_

core::scoring::ScoreFunctionOP	soft_scorefxn_

core::Real	sc_interface_padding_

core::Real	bb_interface_cutoff_

core::pack::rotamer_set::UnboundRotamersOperationOP	unboundrot_

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

Detailed Description

Shared functionality for protocols that dock ligands.

Includes score function setup, interface definitions, and ligand flexibility.

Constructor & Destructor Documentation

protocols::ligand_docking::LigandBaseProtocol::LigandBaseProtocol ( )

References core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::get_score_function(), hard_scorefxn_, make_tweaked_scorefxn(), scorefxn_, soft_scorefxn_, protocols::ligand_docking::TR(), unboundrot_, and use_soft_rep_.

protocols::ligand_docking::LigandBaseProtocol::~LigandBaseProtocol ( )

overridedefault

Member Function Documentation

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

Reimplemented in protocols::ligand_docking::LigandDockProtocol.

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

protected

References protocols::geometry::centroids_by_jump(), and core::scoring::rg.

Referenced by move_ligand_to_desired_centroid().

void protocols::ligand_docking::LigandBaseProtocol::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

protected

Find residues that would most benefit docking by backbone movement. Based on absolute distance to CA/CB – being near the end of a long sc is no reason its backbone should move. This is a new invention; not taken from Rosetta++.

References core::pose::Pose::fold_tree(), core::conformation::Residue::has(), core::conformation::Residue::is_lower_terminus(), core::chemical::ResidueTypeBase::is_polymer(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_upper_terminus(), protocols::mean_field::max(), protocols::mean_field::min(), core::conformation::Residue::nheavyatoms(), core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), protocols::ligand_docking::TR(), and core::conformation::Residue::xyz().

Referenced by make_movemap(), and setup_bbmin_foldtree().

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

protected

References core::pose::Pose::fold_tree(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_radius(), core::conformation::Residue::nheavyatoms(), core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::ligand_docking::TR(), and core::conformation::Residue::xyz().

Referenced by make_movemap(), and make_packer_task().

core::Size protocols::ligand_docking::LigandBaseProtocol::get_ligand_id ( core::pose::Pose const & pose )

static

Return the residue sequence number for our ligand.

Only works with single residue ligands, really. Reconsider this in the future.

References get_ligand_jump_id().

Referenced by protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::enzdes::EnzdesFixBBProtocol::apply(), protocols::ligand_docking::LigandDockProtocol::apply(), protocols::enzdes::LigBurialFilter::compute(), protocols::enzdes::LigInterfaceEnergyFilter::compute(), protocols::enzdes::EnzScoreFilter::compute(), protocols::enzdes::DiffAtomSasaFilter::compute(), protocols::enzdes::EnzdesBaseProtocol::create_enzdes_movemap(), reorder_foldtree_around_mobile_regions(), setup_bbmin_foldtree(), protocols::enzdes::EnzdesBaseProtocol::setup_bbmin_ft_and_csts(), and protocols::ligand_docking::LigandDockProtocol::shear_min_protocol().

core::Size protocols::ligand_docking::LigandBaseProtocol::get_ligand_id	(	core::pose::Pose const &	pose,
		core::Size	jump_id
	)

static

Return the residue sequence number for our ligand.

Only works with single residue ligands, really. Reconsider this in the future.

References core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::conformation::Residue::is_polymer(), core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::residue(), and core::pose::Pose::size().

core::Size protocols::ligand_docking::LigandBaseProtocol::get_ligand_jump_id ( core::pose::Pose const & pose )

static

References core::pose::Pose::num_jump().

Referenced by protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::ligand_docking::LigandDockProtocol::apply(), and get_ligand_id().

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

overridevirtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::ligand_docking::LigandDockProtocol.

void protocols::ligand_docking::LigandBaseProtocol::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

References core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::pose::Pose::residue(), core::pose::Pose::residue_type_ptr(), and core::pose::Pose::size().

Referenced by protocols::enzdes::EnzdesBaseProtocol::exchange_ligands_in_pose(), and protocols::enzdes::EnzdesBaseProtocol::generate_explicit_ligand_rotamer_poses().

core::scoring::ScoreFunctionOP protocols::ligand_docking::LigandBaseProtocol::get_scorefxn ( )

References scorefxn_.

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

core::scoring::ScoreFunctionCOP protocols::ligand_docking::LigandBaseProtocol::get_scorefxn ( ) const

References scorefxn_.

core::kinematics::MoveMapOP protocols::ligand_docking::LigandBaseProtocol::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

protected

References bb_interface_cutoff_, find_interface_backbone(), find_interface_rsds(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_residue_edge(), core::conformation::Residue::has_property(), core::kinematics::Edge::is_jump(), core::conformation::Residue::is_polymer(), core::kinematics::Edge::label(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and protocols::ligand_docking::TR().

Referenced by protocols::ligand_docking::LigandDockProtocol::apply(), protocols::ligand_docking::LigandDockProtocol::classic_protocol(), and protocols::ligand_docking::LigandDockProtocol::shear_min_protocol().

core::pack::task::PackerTaskOP protocols::ligand_docking::LigandBaseProtocol::make_packer_task	(	core::pose::Pose const &	pose,
		ObjexxFCL::FArray1D_bool const &	allow_repack,
		bool	ligand_protonation
	)		const

protected

Shared machinery for the next two.

Referenced by protocols::ligand_docking::LigandDockProtocol::classic_protocol(), make_packer_task(), and make_packer_task_ligand_only().

core::pack::task::PackerTaskOP protocols::ligand_docking::LigandBaseProtocol::make_packer_task	(	core::pose::Pose const &	pose,
		int	jump_id,
		core::Real	sc_padding,
		bool	include_all_rsds,
		bool	ligand_protonation
	)		const

protected

Receptor (interface?) plus ligand.

References find_interface_rsds(), make_packer_task(), and core::pose::Pose::size().

core::pack::task::PackerTaskOP protocols::ligand_docking::LigandBaseProtocol::make_packer_task_ligand_only	(	core::pose::Pose const &	pose,
		int	jump_id,
		bool	ligand_protonation
	)		const

protected

Just ligand, not the receptor.

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

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

protected

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::chainbreak, core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, core::scoring::methods::EnergyMethodOptions::exclude_protein_protein_fa_elec(), core::scoring::fa_elec, core::scoring::fa_intra_rep, core::scoring::hbond_bb_sc, core::scoring::hbond_sc, core::scoring::omega, and core::scoring::rama.

Referenced by LigandBaseProtocol().

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

protected

References choose_desired_centroid().

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

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

protected

References protocols::rigid::RigidBodyTransMover::apply(), protocols::geometry::downstream_centroid_by_jump(), protocols::rigid::RigidBodyTransMover::step_size(), and protocols::rigid::RigidBodyTransMover::trans_axis().

void protocols::ligand_docking::LigandBaseProtocol::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

have zero effect on the non-mobile regions. for every contiguous string of mobile regions, the downstream non-mobile stretch will be connected to the upstream non-mobile stretch through a jump. further, a cutpoint will be introduced into every mobile stretch. the ligand will be connected to the nearest non-mobile residue. Note: every contiguous stretch in the mobile regions must be at least 4 residues long

References core::kinematics::FoldTree::add_edge(), core::pose::add_variant_type_to_pose_residue(), protocols::loops::Loop::cut(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::kinematics::FoldTree::delete_extra_vertices(), core::pose::Pose::fold_tree(), get_ligand_id(), core::conformation::Residue::has(), core::conformation::Residue::is_polymer(), core::conformation::Residue::is_terminus(), protocols::mean_field::max(), protocols::mean_field::min(), core::conformation::Residue::nbr_atom_xyz(), core::kinematics::FoldTree::num_jump(), protocols::make_rot_lib::PEPTIDE, core::pose::Pose::residue(), core::scoring::rg, core::pose::Pose::size(), protocols::loops::Loop::start(), protocols::loops::start, protocols::loops::Loop::stop(), protocols::loops::stop, protocols::ligand_docking::TR(), and core::conformation::Residue::xyz().

Referenced by setup_bbmin_foldtree(), and protocols::enzdes::EnzdesBaseProtocol::setup_bbmin_ft_and_csts().

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

protected

Depends on atomtree topology; atomtree setup should be finished before calling this. Returns the newly created Constraint for future reference, but also adds it to the Pose.

References core::pose::Pose::add_constraint(), core::pose::Pose::atom_tree(), core::scoring::coordinate_constraint, core::pose::Pose::residue(), core::kinematics::AtomTree::root(), scorefxn_, and protocols::ligand_docking::TR().

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

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

Depends on atomtree topology; atomtree setup should be finished before calling this.

References core::pose::Pose::add_constraint(), core::chemical::ResidueType::atom_index(), core::pose::Pose::atom_tree(), core::scoring::coordinate_constraint, core::conformation::Residue::is_protein(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::kinematics::AtomTree::root(), scorefxn_, core::pose::Pose::size(), protocols::ligand_docking::TR(), and core::conformation::Residue::xyz().

Referenced by setup_bbmin_foldtree(), and protocols::enzdes::EnzdesBaseProtocol::setup_bbmin_ft_and_csts().

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

protected

This function actually alters both the pose, and the jump_id to be docked. The pose will have chainbreak variant types and distance constraints added.

References find_interface_backbone(), get_ligand_id(), reorder_foldtree_around_mobile_regions(), restrain_protein_Calphas(), and core::pose::Pose::size().

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

LigandBaseProtocolOP protocols::ligand_docking::LigandBaseProtocol::shared_from_this ( )

inline