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protocols::ligand_docking::ga_ligand_dock::GALigandDock Class Reference

Ligand Docking protocol using Genetic Algorithm. More...

#include <GALigandDock.hh>

Inheritance diagram for protocols::ligand_docking::ga_ligand_dock::GALigandDock:
Inheritance graph
[legend]

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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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::Sizeget_movable_scs (core::pose::Pose const &pose, GridScorerCOP gridscore, core::Size const lig_resno) const
 
void idealize_and_repack_pose (core::pose::Pose &pose, utility::vector1< core::Size > const &movable_scs, core::Size const lig_resno) const
 
LigandAligner setup_ligand_aligner (core::pose::Pose const &pose, core::Size const lig_resno, 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, core::Size const lig_resno, utility::vector1< core::Size > const &moving_scs, bool simple=true) const
 
core::Real calculate_free_ligand_score (core::conformation::Residue const ligand) 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, core::Size const lig_resno) 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_
 
bool altcrossover_
 
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_
 
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::Realramp_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 ( )

Member Function Documentation

void protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply ( pose::Pose pose)
overridevirtual
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::conformation::Residue const  ligand) const
private
Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::calculate_free_receptor_score ( core::pose::Pose  pose,
core::Size const  lig_resno,
utility::vector1< core::Size > const &  moving_scs,
bool  simple = true 
) const
private
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
void protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin ( core::Size  nneigh,
LigandConformer gene,
core::pose::Pose pose 
)
private
void protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_scmin ( LigandConformer const &  gene,
core::pose::Pose pose 
)
private
void protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_solvate ( LigandConformer gene,
core::pose::Pose pose 
)
private
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
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,
core::Size const  lig_resno 
) const
private
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
void protocols::ligand_docking::ga_ligand_dock::GALigandDock::idealize_and_repack_pose ( core::pose::Pose pose,
utility::vector1< core::Size > const &  movable_scs,
core::Size const  lig_resno 
) const
private
void protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_initial_pool ( LigandConformer const &  gene_initial,
LigandConformers genes_sel 
) const
private
void protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_reference_pool ( LigandConformer const &  gene_initial,
utility::vector1< ConstraintInfo > &  ref_ligs 
) const
private
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
std::string protocols::ligand_docking::ga_ligand_dock::GALigandDock::mover_name ( )
static
void protocols::ligand_docking::ga_ligand_dock::GALigandDock::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::ligand_docking::ga_ligand_dock::GALigandDock::premin_ligand ( core::pose::Pose pose,
core::Size const  lig_resno 
) const
private
void protocols::ligand_docking::ga_ligand_dock::GALigandDock::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
core::pose::Pose protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking ( LigandConformer const &  gene_initial,
GridScorerOP  gridscore,
LigandAligner aligner,
OutputStructureStore outputs 
)
private
LigandAligner protocols::ligand_docking::ga_ligand_dock::GALigandDock::setup_ligand_aligner ( core::pose::Pose const &  pose,
core::Size const  lig_resno,
utility::vector1< core::Size movable_scs_in_ref 
) const
private
void protocols::ligand_docking::ga_ligand_dock::GALigandDock::setup_params_for_runmode ( std::string  runmode)

Member Data Documentation

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::altcrossover_
private
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
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: