#include <LigandDockProtocol.hh>

Inheritance diagram for protocols::ligand_docking::LigandDockProtocol:

Collaboration diagram for protocols::ligand_docking::LigandDockProtocol:

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)

virtual	~LigandDockProtocol ()

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

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

virtual std::string	get_name () const
	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=NULL) const
	Scores to be output that aren't normal scorefunction terms. More...

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

virtual	~LigandBaseProtocol ()

core::scoring::ScoreFunctionOP	get_scorefxn ()

core::scoring::ScoreFunctionCOP	get_scorefxn () const

core::Size	get_ligand_jump_id (core::pose::Pose const &pose) const

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

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

void	restrain_protein_Calphas (core::pose::Pose &pose, utility::vector1< bool > const &is_restrained, core::scoring::constraints::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	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

void	set_current_tag (std::string const &new_tag)

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

void	type (const std::string &type_in)

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

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

std::string	get_type () const

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

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

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

virtual bool	reinitialize_for_each_job () const
	this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	this function informs the job distributor (august 08 vintage) whether this object needs to be regenerated when the input pose is about to change (for example, if the mover has special code on the first apply() that is only valid for that one input pose). More...

virtual MoverOP	fresh_instance () const
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

Private Member Functions
	LigandDockProtocol (LigandDockProtocol const &that)

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)

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::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)

Protected Attributes inherited from protocols::ligand_docking::LigandBaseProtocol
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_

Detailed Description

Definition at line 51 of file LigandDockProtocol.hh.

Constructor & Destructor Documentation

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

Definition at line 96 of file LigandDockProtocol.cc.

References protocols::ligand_docking::LigandBaseProtocol::bb_interface_cutoff_, 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::sc_interface_padding_, start_from_pts_, and tether_ligand_.

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`
	)

Definition at line 140 of file LigandDockProtocol.cc.

References protocols::ligand_docking::LigandBaseProtocol::bb_interface_cutoff_, ligand_shear_moves_, and protocols::ligand_docking::LigandBaseProtocol::sc_interface_padding_.

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

virtual

Definition at line 194 of file LigandDockProtocol.cc.

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

private

Definition at line 185 of file LigandDockProtocol.cc.

Member Function Documentation

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

Definition at line 181 of file LigandDockProtocol.cc.

References start_from_pts_.

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 = `NULL`
	)		const

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

Definition at line 762 of file LigandDockProtocol.cc.

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(), 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(), start_from_pts_, protocols::rigid::RigidBodyTransMover::step_size(), core::pose::Pose::total_residue(), protocols::rigid::RigidBodyTransMover::trans_axis(), and core::conformation::Residue::xyz().

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

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

virtual

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.

Reimplemented in protocols::ligand_docking::LigandDockMain.

Definition at line 205 of file LigandDockProtocol.cc.

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

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

Definition at line 328 of file LigandDockProtocol.cc.

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_, protocols::moves::Mover::Mover(), repack_all_rsds_, rottrials_all_rsds_, protocols::ligand_docking::LigandBaseProtocol::sc_interface_padding_, and shear_min_protocol().

Referenced by apply().

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

virtual

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

Reimplemented from protocols::ligand_docking::LigandBaseProtocol.

Reimplemented in protocols::ligand_docking::LigandDockMain.

Definition at line 322 of file LigandDockProtocol.cc.

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.

Definition at line 694 of file LigandDockProtocol.cc.

References protocols::moves::no_stats.

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.

Definition at line 494 of file LigandDockProtocol.cc.

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::automorphic_rmsd(), core::pack::dunbrack::c, core::conformation::Residue::clone(), core::pose::Pose::conformation(), core::scoring::coordinate_constraint, 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::moves::Mover::name(), core::chemical::ResidueType::natoms(), core::conformation::Residue::nbr_atom_xyz(), core::chemical::ResidueType::nchi(), core::chemical::ResidueType::nheavyatoms(), core::conformation::Residue::nheavyatoms(), protocols::geometry::random_reorientation_matrix(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), RG(), core::scoring::rms, core::kinematics::Jump::rotation_by_matrix(), core::pose::Pose::set_jump(), core::pose::Pose::set_jump_now(), 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().

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

private

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

Definition at line 465 of file LigandDockProtocol.cc.

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

Referenced by apply().

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

private

Definition at line 878 of file LigandDockProtocol.cc.

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::total_residue().

Referenced by apply().

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

private

Definition at line 394 of file LigandDockProtocol.cc.

References protocols::ligand_docking::LigandBaseProtocol::get_ligand_id(), protocols::ligand_docking::LigandBaseProtocol::make_movemap(), minimize_all_rsds_, minimize_ligand_, minimize_water_, protocols::ligand_docking::my_RG(), core::pose::Pose::residue(), protocols::ligand_docking::LigandBaseProtocol::sc_interface_padding_, core::pose::Pose::set_chi(), and protocols::ligand_docking::TR().

Referenced by apply(), and classic_protocol().

Member Data Documentation

core::Real protocols::ligand_docking::LigandDockProtocol::ligand_chi_stddev_deg_

private

Definition at line 142 of file LigandDockProtocol.hh.

Referenced by LigandDockProtocol(), and restrain_ligand_chis().

bool protocols::ligand_docking::LigandDockProtocol::ligand_protonation_

private

Definition at line 141 of file LigandDockProtocol.hh.

Referenced by classic_protocol(), and LigandDockProtocol().

core::Size protocols::ligand_docking::LigandDockProtocol::ligand_shear_moves_

private

Definition at line 145 of file LigandDockProtocol.hh.

Referenced by classic_protocol(), and LigandDockProtocol().

core::Real protocols::ligand_docking::LigandDockProtocol::ligand_tether_stddev_Ang_

private

Definition at line 144 of file LigandDockProtocol.hh.

Referenced by apply(), and LigandDockProtocol().

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

private

Definition at line 151 of file LigandDockProtocol.hh.

Referenced by apply(), classic_protocol(), random_conformer(), and restrain_ligand_chis().

bool protocols::ligand_docking::LigandDockProtocol::minimize_all_rsds_

private

Definition at line 146 of file LigandDockProtocol.hh.

Referenced by apply(), classic_protocol(), LigandDockProtocol(), and shear_min_protocol().

bool protocols::ligand_docking::LigandDockProtocol::minimize_backbone_

private

Definition at line 139 of file LigandDockProtocol.hh.

Referenced by apply(), and LigandDockProtocol().

bool protocols::ligand_docking::LigandDockProtocol::minimize_ligand_

private

Definition at line 138 of file LigandDockProtocol.hh.

Referenced by apply(), classic_protocol(), LigandDockProtocol(), and shear_min_protocol().

bool protocols::ligand_docking::LigandDockProtocol::minimize_water_

private

Definition at line 149 of file LigandDockProtocol.hh.

Referenced by apply(), classic_protocol(), LigandDockProtocol(), and shear_min_protocol().

core::Real protocols::ligand_docking::LigandDockProtocol::protein_CA_stddev_Ang_

private

Definition at line 143 of file LigandDockProtocol.hh.

Referenced by apply(), and LigandDockProtocol().

std::string protocols::ligand_docking::LigandDockProtocol::protocol_

private

Definition at line 137 of file LigandDockProtocol.hh.

Referenced by apply(), and LigandDockProtocol().

bool protocols::ligand_docking::LigandDockProtocol::repack_all_rsds_

private

Definition at line 147 of file LigandDockProtocol.hh.

Referenced by classic_protocol(), and LigandDockProtocol().

bool protocols::ligand_docking::LigandDockProtocol::rottrials_all_rsds_

private

Definition at line 148 of file LigandDockProtocol.hh.

Referenced by classic_protocol(), and LigandDockProtocol().

utility::vector1< core::Vector > protocols::ligand_docking::LigandDockProtocol::start_from_pts_

private

Definition at line 150 of file LigandDockProtocol.hh.

Referenced by add_start_from(), append_ligand_docking_scores(), apply(), and LigandDockProtocol().

bool protocols::ligand_docking::LigandDockProtocol::tether_ligand_

private

Definition at line 140 of file LigandDockProtocol.hh.

Referenced by apply(), and LigandDockProtocol().

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

src/protocols/ligand_docking/LigandDockProtocol.hh
src/protocols/ligand_docking/LigandDockProtocol.cc

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_

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation