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Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
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
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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 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...
 
void eval_docked_pose_helper (core::pose::Pose &pose, utility::vector1< core::Size > const &lig_ids, utility::vector1< core::Size > &movable_scs)
 
void eval_docked_pose (core::pose::Pose &pose, utility::vector1< core::Size > const &lig_ids)
 
utility::vector1< core::Sizeget_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, utility::vector1< core::conformation::Residue > const &rsds_to_build_grids, utility::vector1< bool > const &use_sc_only_in_grid) 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_template_pool (LigandConformer const &gene_initial, LigandConformers &genes_sel, core::Size nsel, utility::vector1< ConstraintInfo > &template_cst_infos) 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
 
std::pair< core::Real, core::Realcompare_hbonds_to_native (HbondMap const &native_hbond_map, HbondMap const &lig_hbond_map) 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, core::pack::task::PackerTaskOP task)
 final optimization cycle More...
 
void final_exact_scmin (LigandConformer const &gene, core::pose::Pose &pose, core::pack::task::PackerTaskOP task)
 alternate final optimization cycle More...
 
void final_exact_ligmin_helper (LigandConformer const &gene, core::pose::Pose &pose, core::kinematics::MoveMapOP movemap, core::scoring::ScoreFunctionOP scfxn_local, core::Real const &fa_rep_weight, core::Real const &coordinate_cst_weight, core::Real const &torlerance, core::Size const &maxiter)
 
void final_exact_ligmin (LigandConformer const &gene, core::pose::Pose &pose, core::pack::task::PackerTaskOP task)
 
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...
 
void final_optH (core::Size const &optH_mode, LigandConformer const &gene, core::pose::Pose &pose, core::pack::task::PackerTaskOP task, utility::vector1< core::Size > &contact_scs)
 
void get_ligand_resids (core::pose::Pose const &pose, utility::vector1< core::Size > &lig_resids) const
 get ligand residue ids from pose More...
 
core::pose::PoseOP replace_ligand (core::pose::Pose pose_complex, core::pose::Pose &pose_ligand, bool align=true) const
 
void add_macrocycle_constraints (core::pose::Pose &pose, utility::vector1< core::Size > const &ligids) const
 
core::Size auto_determine_optH_mode (core::pose::Pose const &pose, utility::vector1< core::Size > const &movable_scs) const
 

Private Attributes

core::scoring::ScoreFunctionOP scfxn_
 
core::scoring::ScoreFunctionOP scfxn_relax_
 
std::string runmode_
 
std::string top_pose_metric_
 
core::pose::PoseOP pose_native_
 
core::Real grid_
 
core::Real padding_
 
core::Real hashsize_
 
core::Real grid_radius_
 
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 aligner_fastmode_
 
core::Real max_rot_cumulative_prob_
 
core::Real rot_energy_cutoff_
 
core::Real random_oversample_
 
core::Real reference_oversample_
 
core::Real reference_frac_
 
core::Real init_dens_weight_
 
bool reference_frac_auto_
 
std::string initial_pool_
 
std::string reference_pool_
 
std::string template_pool_
 
core::Size n_template_
 
bool premin_ligand_
 
bool sample_ring_conformers_
 
core::Real torsion_sampler_percentage_
 
TorsionSamplerCOP torsion_sampler_
 
core::Real contact_distance_
 
bool freeze_ligand_backbone_
 
bool freeze_ligand_
 
bool macrocycle_ligand_
 
core::Size shuffle_ligands_
 
core::Real skeleton_threshold_const_
 
core::Size neighborhood_size_
 
bool print_initial_pool_
 
core::Real rtmutationRate_
 
core::Real rotmutWidth_
 
core::Real transmutWidth_
 
bool calculate_native_density_
 
std::string final_exact_minimize_
 
bool cartmin_lig_
 
bool min_neighbor_
 
bool final_solvate_
 
bool turnon_flexscs_at_relax_
 
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 pre_optH_relax_
 
bool auto_final_optH_
 
core::Size final_optH_mode_
 
bool full_repack_before_finalmin_
 
core::Size nrelax_
 
core::Size nreport_
 
bool estimate_dG_
 
std::string entropy_method_
 
bool estimate_buns_
 
utility::vector1< core::Sizehb_resids_
 
bool hb_resids_include_bb_
 
std::string hb_resids_metric_
 
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< GADockStageParamsprotocol_
 
utility::vector1< std::string > multiple_ligands_
 
utility::vector1< std::string > ligand_file_list_
 
utility::vector1< core::id::AtomIDalign_reference_atom_ids_
 
OutputStructureStore remaining_outputs_
 
bool is_virtual_root_
 
core::kinematics::FoldTree input_fold_tree_
 
bool has_density_map_
 
bool output_ligand_only_
 

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

◆ GALigandDock()

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

Member Function Documentation

◆ add_macrocycle_constraints()

void protocols::ligand_docking::ga_ligand_dock::GALigandDock::add_macrocycle_constraints ( core::pose::Pose pose,
utility::vector1< core::Size > const &  ligids 
) const
private

◆ apply()

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

main apply of GA ligand docking

Implements protocols::moves::Mover.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::io::silent::SilentFileData::begin(), protocols::membrane::com(), core::conformation::Residue::connected_residue_at_resconn(), core::io::silent::SilentFileData::end(), core::sequence::end, core::pose::Pose::fold_tree(), core::pose::get_center_of_mass(), protocols::ligand_docking::ga_ligand_dock::get_ligand_resids(), core::conformation::get_residue_from_name(), core::pose::get_resnum_list_ordered(), core::scoring::electron_density::getDensityMap(), core::pose::getPoseExtraScore(), core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), core::pose::initialize_disulfide_bonds(), core::conformation::Residue::is_polymer(), 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::conformation::Residue::name(), core::pose::parse_resnum(), core::import_pose::PDB_file, core::pose::Pose::pdb_info(), core::import_pose::pose_from_file(), core::io::silent::SilentFileData::read_file(), core::pose::Pose::residue(), core::scoring::rms, core::kinematics::FoldTree::root(), protocols::hybridization::score, protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_has_density_map(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_sample_ring_conformers(), protocols::loops::start, core::id::to_string(), core::pose::Pose::total_residue(), protocols::ligand_docking::ga_ligand_dock::TR(), core::conformation::Residue::type(), and core::chemical::ResidueType::upper_connect_id().

◆ apply_coord_cst_to_sctip()

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

◆ auto_determine_optH_mode()

core::Size protocols::ligand_docking::ga_ligand_dock::GALigandDock::auto_determine_optH_mode ( core::pose::Pose const &  pose,
utility::vector1< core::Size > const &  movable_scs 
) const
private

◆ calculate_free_ligand_score()

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

◆ calculate_free_receptor_score()

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

◆ clone()

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.

◆ compare_hbonds_to_native()

std::pair< core::Real, core::Real > protocols::ligand_docking::ga_ligand_dock::GALigandDock::compare_hbonds_to_native ( HbondMap const &  native_hbond_map,
HbondMap const &  lig_hbond_map 
) const
private

◆ eval_docked_pose()

void protocols::ligand_docking::ga_ligand_dock::GALigandDock::eval_docked_pose ( core::pose::Pose pose,
utility::vector1< core::Size > const &  lig_ids 
)
private

◆ eval_docked_pose_helper()

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

◆ final_cartligmin()

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

◆ final_exact_cartmin()

void protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin ( core::Size  nneigh,
LigandConformer gene,
core::pose::Pose pose,
core::pack::task::PackerTaskOP  task 
)
private

final optimization cycle

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::pose::Pose::add_constraint(), core::pose::addVirtualResAsRoot(), core::scoring::angle_constraint, core::conformation::Residue::atom_index(), core::scoring::atom_pair_constraint, core::scoring::cart_bonded, core::scoring::coordinate_constraint, core::pose::Pose::delete_residue_slow(), core::scoring::dihedral_constraint, core::pose::Pose::fold_tree(), protocols::ligand_docking::ga_ligand_dock::get_atomic_contacting_sidechains(), 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_polymer(), core::conformation::Residue::is_protein(), core::kinematics::FoldTree::is_root(), 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(), protocols::ligand_docking::ga_ligand_dock::OPTH_NONE, core::scoring::pro_close, protocols::antibody::design::relax, core::pose::Pose::remove_constraints(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::root(), core::pose::Pose::size(), core::pose::Pose::total_residue(), protocols::ligand_docking::ga_ligand_dock::TR(), core::pose::Pose::xyz(), protocols::kinmatch::xyz(), and core::conformation::Residue::xyz().

◆ final_exact_ligmin()

void protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_ligmin ( LigandConformer const &  gene,
core::pose::Pose pose,
core::pack::task::PackerTaskOP  task 
)
private

◆ final_exact_ligmin_helper()

void protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_ligmin_helper ( LigandConformer const &  gene,
core::pose::Pose pose,
core::kinematics::MoveMapOP  movemap,
core::scoring::ScoreFunctionOP  scfxn_local,
core::Real const &  fa_rep_weight,
core::Real const &  coordinate_cst_weight,
core::Real const &  torlerance,
core::Size const &  maxiter 
)
private

◆ final_exact_scmin()

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

◆ final_optH()

void protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_optH ( core::Size const &  optH_mode,
LigandConformer const &  gene,
core::pose::Pose pose,
core::pack::task::PackerTaskOP  task,
utility::vector1< core::Size > &  contact_scs 
)
private

◆ final_solvate()

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

◆ fresh_instance()

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.

◆ generate_perturbed_structures()

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

◆ get_additional_output()

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.

◆ get_ligand_resids()

void protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_ligand_resids ( core::pose::Pose const &  pose,
utility::vector1< core::Size > &  lig_resids 
) const
private

◆ get_movable_scs()

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

◆ get_name()

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.

◆ get_optimizer()

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

◆ idealize_and_repack_pose()

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

◆ load_initial_pool()

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

◆ load_reference_pool()

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

◆ load_template_pool()

void protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_template_pool ( LigandConformer const &  gene_initial,
LigandConformers genes_sel,
core::Size  nsel,
utility::vector1< ConstraintInfo > &  template_cst_infos 
) const
private

◆ make_starting_pose_for_virtual_screening()

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

◆ mover_name()

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

◆ parse_my_tag()

void protocols::ligand_docking::ga_ligand_dock::GALigandDock::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data 
)
overridevirtual

◆ premin_ligand()

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

◆ provide_xml_schema()

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

◆ replace_ligand()

core::pose::PoseOP protocols::ligand_docking::ga_ligand_dock::GALigandDock::replace_ligand ( core::pose::Pose  pose_complex,
core::pose::Pose pose_ligand,
bool  align = true 
) const
private

◆ run_docking()

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(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::apply(), core::scoring::automorphic_rmsd(), core::scoring::Energies::clear(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::ligand_docking::ga_ligand_dock::compute_nhbonds(), core::pack::task::TaskFactory::create_packer_task(), core::pose::Pose::data(), protocols::ligand_docking::ga_ligand_dock::OutputStructureStore::dens_pop(), protocols::ligand_docking::ga_ligand_dock::OutputStructureStore::dens_push(), core::pose::Pose::energies(), core::pose::getPoseExtraScore(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_ids(), protocols::ligand_docking::ga_ligand_dock::make_ligand_only_pose(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::moving_scs(), core::chemical::element::N, protocols::ligand_docking::ga_ligand_dock::OPTH_REDEFINE_SIDECHAINS, protocols::ligand_docking::ga_ligand_dock::OutputStructureStore::pop(), protocols::ligand_docking::ga_ligand_dock::OutputStructureStore::push(), core::pose::Pose::residue(), core::scoring::rms, protocols::hybridization::score, protocols::simple_filters::BuriedUnsatHbondFilter::set_atomic_depth_apo_surface(), protocols::simple_filters::BuriedUnsatHbondFilter::set_dalphaball_sasa(), protocols::simple_filters::BuriedUnsatHbondFilter::set_is_ligand_residue(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::set_niter(), protocols::simple_filters::BuriedUnsatHbondFilter::set_probe_radius(), protocols::simple_filters::BuriedUnsatHbondFilter::set_report_all_heavy_atom_unsats(), protocols::simple_filters::BuriedUnsatHbondFilter::set_use_ddG_style(), core::pose::setPoseExtraScore(), core::id::to_string(), and protocols::ligand_docking::ga_ligand_dock::TR().

◆ setup_ligand_aligner()

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,
utility::vector1< core::conformation::Residue > const &  rsds_to_build_grids,
utility::vector1< bool > const &  use_sc_only_in_grid 
) const
private

◆ setup_params_for_runmode()

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

Member Data Documentation

◆ align_reference_atom_ids_

utility::vector1< core::id::AtomID > protocols::ligand_docking::ga_ligand_dock::GALigandDock::align_reference_atom_ids_
private

◆ aligner_fastmode_

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::aligner_fastmode_
private

◆ auto_final_optH_

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::auto_final_optH_
private

◆ calculate_native_density_

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::calculate_native_density_
private

◆ cartmin_lig_

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

◆ contact_distance_

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::contact_distance_
private

◆ debug_

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

◆ entropy_method_

std::string protocols::ligand_docking::ga_ligand_dock::GALigandDock::entropy_method_
private

◆ estimate_buns_

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::estimate_buns_
private

◆ estimate_dG_

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

◆ exact_

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

◆ fa_rep_grid_

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

◆ fast_relax_lines_

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

◆ fast_relax_script_file_

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

◆ favor_native_

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

◆ final_exact_minimize_

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

◆ final_optH_mode_

core::Size protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_optH_mode_
private

◆ final_solvate_

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

◆ freeze_ligand_

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::freeze_ligand_
private

◆ freeze_ligand_backbone_

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::freeze_ligand_backbone_
private

◆ frozen_residues_

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

◆ full_repack_before_finalmin_

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

◆ grid_

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

◆ grid_bound_penalty_

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

◆ grid_radius_

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::grid_radius_
private

◆ has_density_map_

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::has_density_map_
private

◆ hashsize_

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

◆ hb_resids_

utility::vector1< core::Size > protocols::ligand_docking::ga_ligand_dock::GALigandDock::hb_resids_
private

◆ hb_resids_include_bb_

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::hb_resids_include_bb_
private

◆ hb_resids_metric_

std::string protocols::ligand_docking::ga_ligand_dock::GALigandDock::hb_resids_metric_
private

◆ init_dens_weight_

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::init_dens_weight_
private

◆ initial_pool_

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

◆ input_fold_tree_

core::kinematics::FoldTree protocols::ligand_docking::ga_ligand_dock::GALigandDock::input_fold_tree_
private

◆ is_virtual_root_

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::is_virtual_root_
private

◆ ligand_file_list_

utility::vector1< std::string > protocols::ligand_docking::ga_ligand_dock::GALigandDock::ligand_file_list_
private

◆ ligid_

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

◆ macrocycle_ligand_

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::macrocycle_ligand_
private

◆ max_rot_cumulative_prob_

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

◆ maxiter_

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

◆ min_neighbor_

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

◆ move_water_

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

◆ multi_ligands_maxRad_

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

◆ multiple_ligands_

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

◆ n_template_

core::Size protocols::ligand_docking::ga_ligand_dock::GALigandDock::n_template_
private

◆ neighborhood_size_

core::Size protocols::ligand_docking::ga_ligand_dock::GALigandDock::neighborhood_size_
private

◆ ngen_

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

◆ npool_

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

◆ nrelax_

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

◆ nreport_

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

◆ optimize_input_H_

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

◆ output_ligand_only_

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::output_ligand_only_
private

◆ packer_cycles_

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

◆ padding_

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

◆ pmut_

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

◆ pose_native_

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

◆ pre_optH_relax_

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::pre_optH_relax_
private

◆ premin_ligand_

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

◆ print_initial_pool_

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::print_initial_pool_
private

◆ protocol_

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

◆ ramp_schedule_

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

◆ random_oversample_

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

◆ redefine_flexscs_at_relax_

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

◆ reference_frac_

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

◆ reference_frac_auto_

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

◆ reference_oversample_

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

◆ reference_pool_

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

◆ remaining_outputs_

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

◆ rmsdthreshold_

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

◆ rot_energy_cutoff_

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

◆ rotmutWidth_

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::rotmutWidth_
private

◆ rtmutationRate_

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::rtmutationRate_
private

◆ runmode_

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

◆ sample_ring_conformers_

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

◆ sc_edge_buffer_

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

◆ scfxn_

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

◆ scfxn_relax_

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

◆ shuffle_ligands_

core::Size protocols::ligand_docking::ga_ligand_dock::GALigandDock::shuffle_ligands_
private

◆ sidechains_

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

◆ skeleton_threshold_const_

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::skeleton_threshold_const_
private

◆ smoothing_

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

◆ stdev_multiplier_

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

◆ subhash_

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

◆ template_pool_

std::string protocols::ligand_docking::ga_ligand_dock::GALigandDock::template_pool_
private

◆ top_pose_metric_

std::string protocols::ligand_docking::ga_ligand_dock::GALigandDock::top_pose_metric_
private

◆ torsion_sampler_

TorsionSamplerCOP protocols::ligand_docking::ga_ligand_dock::GALigandDock::torsion_sampler_
private

◆ torsion_sampler_percentage_

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

◆ transmutWidth_

core::Real protocols::ligand_docking::ga_ligand_dock::GALigandDock::transmutWidth_
private

◆ turnon_flexscs_at_relax_

bool protocols::ligand_docking::ga_ligand_dock::GALigandDock::turnon_flexscs_at_relax_
private

◆ use_mean_maxRad_

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

◆ use_pharmacophore_

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

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