Ligand Docking protocol using Genetic Algorithm. More...

#include <GALigandDock.hh>

Inheritance diagram for protocols::ligand_docking::ga_ligand_dock::GALigandDock:

Public Member Functions
	GALigandDock ()

void	apply (Pose &pose) override
	main apply of GA ligand docking More...

core::pose::PoseOP	get_additional_output () override

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

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

void	setup_params_for_runmode (std::string runmode)
	parse options based on umbrella runmode option 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...

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...

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...

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...

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 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
core::pose::Pose	run_docking (LigandConformer const &gene_initial, GridScorerOP gridscore, LigandAligner &aligner, OutputStructureStore &outputs)
	main function running on single ligand type More...

utility::vector1< core::Size >	get_movable_scs (core::pose::Pose const &pose, GridScorerCOP gridscore, utility::vector1< core::Size > const &lig_resnos) const

void	idealize_and_repack_pose (core::pose::Pose &pose, utility::vector1< core::Size > const &movable_scs, utility::vector1< core::Size > const &lig_resnos) const

LigandAligner	setup_ligand_aligner (core::pose::Pose const &pose, utility::vector1< core::Size > const &lig_resnos, utility::vector1< core::Size > movable_scs_in_ref) const
	generate object containing binding-motif search results More...

LigandConformers	generate_perturbed_structures (LigandConformer const &gene_initial, GridScorerOP gridscorer, core::Size npool, LigandAligner aligner) const
	generate an initial set of perturbed structures More...

core::pose::PoseOP	make_starting_pose_for_virtual_screening (core::pose::Pose const &pose_apo, core::Size const &lig_resno, std::string const ligand_name) const
	replace ligand to a new ideal res named by ligand_name More...

void	load_initial_pool (LigandConformer const &gene_initial, LigandConformers &genes_sel) const
	load the initial pool More...

void	load_reference_pool (LigandConformer const &gene_initial, utility::vector1< ConstraintInfo > &ref_ligs) const

GAOptimizerOP	get_optimizer (LigandConformer const &gene_initial, GridScorerOP gridscorer) const
	create and initialize the grid optimizer More...

core::Real	calculate_free_receptor_score (core::pose::Pose pose, utility::vector1< core::Size > const &lig_resnos, utility::vector1< core::Size > const &moving_scs, bool simple=true) const

core::Real	calculate_free_ligand_score (core::pose::Pose pose, utility::vector1< core::Size > const &lig_resnos) const

void	apply_coord_cst_to_sctip (core::pose::PoseOP pose, utility::vector1< core::Size > const &moving_scs) const

void	premin_ligand (core::pose::Pose &pose, utility::vector1< core::Size > const &lig_resnos) const
	pre cart-min ligand before docking More...

void	final_exact_cartmin (core::Size nneigh, LigandConformer &gene, core::pose::Pose &pose)
	final optimization cycle More...

void	final_exact_scmin (LigandConformer const &gene, core::pose::Pose &pose)
	alternate final optimization cycle More...

void	final_cartligmin (LigandConformer const &gene, core::pose::Pose &pose)
	alternate final optimization cycle More...

void	final_solvate (LigandConformer &gene, core::pose::Pose &pose)
	solvate pose before final relax More...

Private Attributes
core::scoring::ScoreFunctionOP	scfxn_

core::scoring::ScoreFunctionOP	scfxn_relax_

std::string	runmode_

core::pose::PoseOP	pose_native_

core::Real	grid_

core::Real	padding_

core::Real	hashsize_

core::Size	subhash_

bool	exact_

bool	debug_

core::Real	fa_rep_grid_

core::Real	grid_bound_penalty_

std::string	ligid_

std::string	sidechains_

core::select::residue_selector::ResidueSelectorCOP	frozen_residues_

core::Real	sc_edge_buffer_

bool	move_water_

bool	use_pharmacophore_

core::Real	max_rot_cumulative_prob_

core::Real	rot_energy_cutoff_

core::Real	random_oversample_

core::Real	reference_oversample_

core::Real	reference_frac_

bool	reference_frac_auto_

std::string	initial_pool_

std::string	reference_pool_

bool	premin_ligand_

bool	sample_ring_conformers_

core::Real	torsion_sampler_percentage_

TorsionSampler	torsion_sampler_

std::string	final_exact_minimize_

bool	cartmin_lig_

bool	min_neighbor_

bool	final_solvate_

bool	redefine_flexscs_at_relax_

std::string	fast_relax_script_file_

std::vector< std::string >	fast_relax_lines_

core::Real	favor_native_

bool	optimize_input_H_

bool	full_repack_before_finalmin_

core::Size	nrelax_

core::Size	nreport_

bool	estimate_dG_

bool	use_mean_maxRad_

core::Real	stdev_multiplier_

core::Real	multi_ligands_maxRad_

core::Size	ngen_

core::Size	npool_

core::Real	rmsdthreshold_

core::Real	pmut_

core::Real	maxiter_

core::Real	packer_cycles_

core::Real	smoothing_

utility::vector1< core::Real >	ramp_schedule_

utility::vector1 < GADockStageParams >	protocol_

utility::vector1< std::string >	multiple_ligands_

OutputStructureStore	remaining_outputs_

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...

Detailed Description

Ligand Docking protocol using Genetic Algorithm.

Runs ligand docking using pre-computed full-atom grid score, binding-motif search, and genetic algorithm search on Ligand & flexible sidechains at receptor conformations. This docking method supports full on-the-fly search of ligand conformation hence ligand "conformer" generation is not required.

Constructor & Destructor Documentation

protocols::ligand_docking::ga_ligand_dock::GALigandDock::GALigandDock ( )

References core::scoring::get_score_function().

Member Function Documentation

void protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply ( pose::Pose & pose )

overridevirtual

main apply of GA ligand docking

Implements protocols::moves::Mover.

References protocols::membrane::com(), core::conformation::Residue::connected_residue_at_resconn(), core::sequence::end, core::conformation::get_residue_from_name(), core::pose::get_resnum_list_ordered(), core::pose::getPoseExtraScore(), core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), core::conformation::Residue::is_polymer(), core::conformation::Residue::is_virtual_residue(), protocols::sewing::data_storage::ligand, core::scoring::lk_ball, core::scoring::lk_ball_wtd, core::chemical::ResidueType::lower_connect_id(), protocols::mean_field::max(), core::pose::Pose::residue(), core::scoring::rms, protocols::hybridization::score, protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_sample_ring_conformers(), protocols::loops::start, core::pose::Pose::total_residue(), protocols::ligand_docking::ga_ligand_dock::TR(), core::conformation::Residue::type(), and core::chemical::ResidueType::upper_connect_id().

void protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply_coord_cst_to_sctip	(	core::pose::PoseOP	pose,
		utility::vector1< core::Size > const &	moving_scs
	)		const

private

Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::calculate_free_ligand_score	(	core::pose::Pose	pose,
		utility::vector1< core::Size > const &	lig_resnos
	)		const

private

References core::pose::addVirtualResAsRoot(), core::scoring::coordinate_constraint, core::pose::initialize_disulfide_bonds(), core::pose::Pose::residue(), and protocols::kinmatch::xyz().

Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::calculate_free_receptor_score	(	core::pose::Pose	pose,
		utility::vector1< core::Size > const &	lig_resnos,
		utility::vector1< core::Size > const &	moving_scs,
		bool	simple = `true`
	)		const

private

References core::conformation::Residue::aa(), core::chemical::aa_his, protocols::relax::FastRelax::apply(), core::scoring::Energies::clear(), core::pack::task::TaskFactory::create_packer_task(), core::pose::Pose::data(), core::pose::Pose::delete_residue_slow(), core::pose::Pose::energies(), protocols::antibody::design::relax, core::pose::Pose::residue(), protocols::relax::RelaxProtocolBase::set_movemap(), protocols::relax::FastRelax::set_movemap_disables_packing_of_fixed_chi_positions(), protocols::relax::RelaxProtocolBase::set_scorefxn(), protocols::relax::FastRelax::set_script_from_lines(), protocols::relax::RelaxProtocolBase::set_task_factory(), core::pose::Pose::size(), and protocols::ligand_docking::ga_ligand_dock::TR().

protocols::moves::MoverOP protocols::ligand_docking::ga_ligand_dock::GALigandDock::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.

void protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_cartligmin	(	LigandConformer const &	gene,
		core::pose::Pose &	pose
	)

private

alternate final optimization cycle

References core::scoring::cart_bonded, core::scoring::cart_bonded_ring, protocols::ligand_docking::ga_ligand_dock::get_atomic_contacting_sidechains(), core::select::get_residue_set_from_subset(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_ids(), core::optimization::MinimizerOptions::max_iter(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::moving_scs(), core::scoring::pro_close, core::optimization::CartesianMinimizer::run(), core::pose::Pose::size(), and protocols::ligand_docking::ga_ligand_dock::TR().

void protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin	(	core::Size	nneigh,
		LigandConformer &	gene,
		core::pose::Pose &	pose
	)

private

final optimization cycle

References core::pose::Pose::add_constraint(), protocols::relax::FastRelax::apply(), core::conformation::Residue::atom_index(), core::scoring::atom_pair_constraint, core::scoring::cart_bonded, core::scoring::coordinate_constraint, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_jump_that_builds_residue(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_jumpid(), core::select::get_residue_set_from_subset(), core::conformation::Residue::is_protein(), core::chemical::ResidueType::is_water(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_ids(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::moving_scs(), core::chemical::ResidueType::nheavyatoms(), core::scoring::pro_close, protocols::antibody::design::relax, core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::relax::RelaxProtocolBase::set_movemap(), protocols::relax::FastRelax::set_movemap_disables_packing_of_fixed_chi_positions(), protocols::relax::RelaxProtocolBase::set_scorefxn(), protocols::relax::FastRelax::set_script_from_lines(), core::pose::Pose::size(), core::pose::Pose::total_residue(), protocols::ligand_docking::ga_ligand_dock::TR(), protocols::kinmatch::xyz(), core::conformation::Residue::xyz(), and core::pose::Pose::xyz().

void protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_scmin	(	LigandConformer const &	gene,
		core::pose::Pose &	pose
	)

private

alternate final optimization cycle

References protocols::relax::FastRelax::apply(), core::pack::task::TaskFactory::create_packer_task(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_jumpid(), core::select::get_residue_set_from_subset(), core::chemical::ResidueType::is_water(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_ids(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::moving_scs(), core::pack::pack_rotamers(), protocols::antibody::design::relax, core::pose::Pose::residue_type(), protocols::relax::RelaxProtocolBase::set_movemap(), protocols::relax::FastRelax::set_movemap_disables_packing_of_fixed_chi_positions(), protocols::relax::RelaxProtocolBase::set_scorefxn(), protocols::relax::FastRelax::set_script_from_lines(), core::pose::Pose::size(), core::pose::Pose::total_residue(), and protocols::ligand_docking::ga_ligand_dock::TR().

void protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_solvate	(	LigandConformer &	gene,
		core::pose::Pose &	pose
	)

private

solvate pose before final relax

References protocols::simple_moves::ExplicitWaterMover::apply(), core::pack::task::TaskFactory::create_packer_task(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_ids(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::moving_scs(), core::scoring::pointwater, protocols::simple_moves::ExplicitWaterMover::set_taskop(), and core::pose::Pose::total_residue().

protocols::moves::MoverOP protocols::ligand_docking::ga_ligand_dock::GALigandDock::fresh_instance ( ) const

overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. 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. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

LigandConformers protocols::ligand_docking::ga_ligand_dock::GALigandDock::generate_perturbed_structures	(	LigandConformer const &	gene_initial,
		GridScorerOP	gridscorer,
		core::Size	npool,
		LigandAligner	aligner
	)		const

private

generate an initial set of perturbed structures

core::pose::PoseOP protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_additional_output ( )

overridevirtual

as this is a one->many mover, use this function to return multiple outputs from a single call to apply

Reimplemented from protocols::moves::Mover.

utility::vector1< core::Size > protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_movable_scs	(	core::pose::Pose const &	pose,
		GridScorerCOP	gridscore,
		utility::vector1< core::Size > const &	lig_resnos
	)		const

private

References core::conformation::Residue::aa(), core::chemical::aa_ala, core::chemical::aa_gly, core::chemical::DISULFIDE, core::select::get_residue_set_from_subset(), core::pose::get_resnum_list(), core::chemical::ResidueTypeBase::has_variant_type(), core::conformation::Residue::is_protein(), protocols::mean_field::max(), core::simple_metrics::metrics::mean, core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), protocols::ligand_docking::ga_ligand_dock::TR(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

std::string protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

GAOptimizerOP protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_optimizer	(	LigandConformer const &	gene_initial,
		GridScorerOP	gridscorer
	)		const

private

create and initialize the grid optimizer

References protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_ids(), and protocols::ligand_docking::ga_ligand_dock::LigandConformer::moving_scs().

void protocols::ligand_docking::ga_ligand_dock::GALigandDock::idealize_and_repack_pose	(	core::pose::Pose &	pose,
		utility::vector1< core::Size > const &	movable_scs,
		utility::vector1< core::Size > const &	lig_resnos
	)		const

private

References core::conformation::Residue::chi(), core::pack::task::TaskFactory::create_packer_task(), core::optimization::MinimizerOptions::max_iter(), core::conformation::Residue::natoms(), core::pack::pack_rotamers(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::optimization::AtomTreeMinimizer::run(), core::pose::Pose::set_chi(), core::pose::Pose::set_xyz(), protocols::ligand_docking::ga_ligand_dock::TR(), and core::conformation::Residue::xyz().

void protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_initial_pool	(	LigandConformer const &	gene_initial,
		LigandConformers &	genes_sel
	)		const

private

load the initial pool

References core::io::silent::SilentFileData::begin(), core::sequence::end, core::io::silent::SilentFileData::end(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), core::io::silent::SilentFileData::read_file(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::score(), and protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf().

void protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_reference_pool	(	LigandConformer const &	gene_initial,
		utility::vector1< ConstraintInfo > &	ref_ligs
	)		const

private

References core::io::silent::SilentFileData::begin(), core::sequence::end, core::io::silent::SilentFileData::end(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_ids(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), core::io::silent::SilentFileData::read_file(), and protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_pose().

core::pose::PoseOP protocols::ligand_docking::ga_ligand_dock::GALigandDock::make_starting_pose_for_virtual_screening	(	core::pose::Pose const &	pose_apo,
		core::Size const &	lig_resno,
		std::string const	ligand_name
	)		const

private

replace ligand to a new ideal res named by ligand_name

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_jump_that_builds_residue(), core::conformation::get_residue_from_name(), core::kinematics::Jump::get_translation(), core::pose::Pose::jump(), protocols::sewing::data_storage::ligand, and core::kinematics::Jump::set_translation().

std::string protocols::ligand_docking::ga_ligand_dock::GALigandDock::mover_name ( )

static

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDockCreator::keyname().

void protocols::ligand_docking::ga_ligand_dock::GALigandDock::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.

void protocols::ligand_docking::ga_ligand_dock::GALigandDock::premin_ligand	(	core::pose::Pose &	pose,
		utility::vector1< core::Size > const &	lig_resnos
	)		const

private

pre cart-min ligand before docking

References core::scoring::cart_bonded, core::scoring::fa_atr, core::scoring::fa_rep, core::optimization::MinimizerOptions::max_iter(), core::scoring::pro_close, and core::optimization::CartesianMinimizer::run().

void protocols::ligand_docking::ga_ligand_dock::GALigandDock::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::ligand_docking::ga_ligand_dock::gadock_subelement_ct_name(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDockCreator::provide_xml_schema().

core::pose::Pose protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking	(	LigandConformer const &	gene_initial,
		GridScorerOP	gridscore,
		LigandAligner &	aligner,
		OutputStructureStore &	outputs
	)

private

main function running on single ligand type

References core::scoring::all_atom_rmsd_nosuper(), core::scoring::automorphic_rmsd(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_ids(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_typename(), core::chemical::element::N, protocols::ligand_docking::ga_ligand_dock::OutputStructureStore::pop(), protocols::ligand_docking::ga_ligand_dock::OutputStructureStore::push(), core::scoring::rms, protocols::hybridization::score, core::conformation::Residue::set_chi(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::set_niter(), core::pose::setPoseExtraScore(), core::id::to_string(), and protocols::ligand_docking::ga_ligand_dock::TR().

LigandAligner protocols::ligand_docking::ga_ligand_dock::GALigandDock::setup_ligand_aligner	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	lig_resnos,
		utility::vector1< core::Size >	movable_scs_in_ref
	)		const

private

generate object containing binding-motif search results

References core::conformation::get_residue_from_name(), protocols::sewing::data_storage::ligand, protocols::ligand_docking::ga_ligand_dock::LigandAligner::refine_input(), core::pose::Pose::residue(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_pharmacophore_reference(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_sf(), and protocols::ligand_docking::ga_ligand_dock::TR().

void protocols::ligand_docking::ga_ligand_dock::GALigandDock::setup_params_for_runmode ( std::string runmode )

parse options based on umbrella runmode option

References protocols::ligand_docking::ga_ligand_dock::GADockStageParams::elec_scale, and protocols::ligand_docking::ga_ligand_dock::GADockStageParams::maxiter.

Member Data Documentation

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::cartmin_lig_

private

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::debug_

private

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::estimate_dG_

private

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::exact_

private

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::fa_rep_grid_

private

std::vector< std::string > protocols::ligand_docking::ga_ligand_dock::GALigandDock::fast_relax_lines_

private

std::string protocols::ligand_docking::ga_ligand_dock::GALigandDock::fast_relax_script_file_

private

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::favor_native_

private

std::string protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_minimize_

private

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_solvate_

private

core::select::residue_selector::ResidueSelectorCOP protocols::ligand_docking::ga_ligand_dock::GALigandDock::frozen_residues_

private

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::full_repack_before_finalmin_

private

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::grid_

private

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::grid_bound_penalty_

private

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::hashsize_

private

std::string protocols::ligand_docking::ga_ligand_dock::GALigandDock::initial_pool_

private

std::string protocols::ligand_docking::ga_ligand_dock::GALigandDock::ligid_

private

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::max_rot_cumulative_prob_

private

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::maxiter_

private

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::min_neighbor_

private

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::move_water_

private

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::multi_ligands_maxRad_

private

utility::vector1< std::string > protocols::ligand_docking::ga_ligand_dock::GALigandDock::multiple_ligands_

private

core::Size protocols::ligand_docking::ga_ligand_dock::GALigandDock::ngen_

private

core::Size protocols::ligand_docking::ga_ligand_dock::GALigandDock::npool_

private

core::Size protocols::ligand_docking::ga_ligand_dock::GALigandDock::nrelax_

private

core::Size protocols::ligand_docking::ga_ligand_dock::GALigandDock::nreport_

private

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::optimize_input_H_

private

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::packer_cycles_

private

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::padding_

private

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::pmut_

private

core::pose::PoseOP protocols::ligand_docking::ga_ligand_dock::GALigandDock::pose_native_

private

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::premin_ligand_

private

utility::vector1< GADockStageParams > protocols::ligand_docking::ga_ligand_dock::GALigandDock::protocol_

private

utility::vector1<core::Real> protocols::ligand_docking::ga_ligand_dock::GALigandDock::ramp_schedule_

private

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::random_oversample_

private

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::redefine_flexscs_at_relax_

private

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::reference_frac_

private

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::reference_frac_auto_

private

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::reference_oversample_

private

std::string protocols::ligand_docking::ga_ligand_dock::GALigandDock::reference_pool_

private

OutputStructureStore protocols::ligand_docking::ga_ligand_dock::GALigandDock::remaining_outputs_

private

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::rmsdthreshold_

private

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::rot_energy_cutoff_

private

std::string protocols::ligand_docking::ga_ligand_dock::GALigandDock::runmode_

private

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::sample_ring_conformers_

private

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::sc_edge_buffer_

private

core::scoring::ScoreFunctionOP protocols::ligand_docking::ga_ligand_dock::GALigandDock::scfxn_

private

core::scoring::ScoreFunctionOP protocols::ligand_docking::ga_ligand_dock::GALigandDock::scfxn_relax_

private

std::string protocols::ligand_docking::ga_ligand_dock::GALigandDock::sidechains_

private

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::smoothing_

private

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::stdev_multiplier_

private

core::Size protocols::ligand_docking::ga_ligand_dock::GALigandDock::subhash_

private

TorsionSampler protocols::ligand_docking::ga_ligand_dock::GALigandDock::torsion_sampler_

private

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::torsion_sampler_percentage_

private

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::use_mean_maxRad_

private

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::use_pharmacophore_

private

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

src/protocols/ligand_docking/GALigandDock/GALigandDock.hh
src/protocols/ligand_docking/GALigandDock/GALigandDock.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation