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protocols::ligand_docking::ga_ligand_dock::GAOptimizer Class Reference

Genetic Algorithm Optimizer called by GALigandDock. More...

#include <GAOptimizer.hh>

Public Member Functions

 GAOptimizer (GridScorerOP grid)
 
 ~GAOptimizer ()
 
void run (LigandConformers &genes)
 
void set_protocol (utility::vector1< GADockStageParams > const &protocol_in)
 
void set_native (LigandConformer const native)
 
void optimize_generation (LigandConformers &genes, utility::vector1< core::Real > const &ramping)
 optimize one generation More...
 
void show_status (LigandConformers &genes, std::string const &comment="", bool calculate_native_rmsd=true, bool verbose=false)
 
void set_max_rot_cumulative_prob (core::Real newval)
 
void set_rot_energy_cutoff (core::Real newval)
 
void set_favor_native (core::Real newval)
 
void set_align_reference_atom_ids (utility::vector1< core::id::AtomID > newval)
 

Private Member Functions

void initialize_rotamer_set_and_scores (LigandConformer lig)
 set up rotamer set More...
 
void update_tags (LigandConformers &genes) const
 reset tags for a generation More...
 
void next_generation (LigandConformers const &genes, LigandConformers &genes_new, core::Size, core::Real)
 generate putative next generation More...
 
void update_pool (LigandConformers &genes, LigandConformers &genes_new, core::Size, core::Real)
 update our pool More...
 

Private Attributes

LigandConformer nativegene_
 
GridScorerOP scorefxn_
 
utility::vector1< GADockStageParamsprotocol_
 
core::Real max_rot_cumulative_prob_
 
core::Real rot_energy_cutoff_
 
core::Real favor_native_
 
utility::vector1< PlaceableRotamersrotamer_data_
 
RotamerPairEnergies rotamer_energies_
 
utility::vector1< core::id::AtomIDalign_reference_atom_ids_
 

Detailed Description

Genetic Algorithm Optimizer called by GALigandDock.

Takes grid score & gene-representations of ligand (+flex sidechain) conformations returns multiple optimized gene-representations of ligand (+flex sidechain) conformations

Constructor & Destructor Documentation

◆ GAOptimizer()

protocols::ligand_docking::ga_ligand_dock::GAOptimizer::GAOptimizer ( GridScorerOP  grid)

References scorefxn_.

◆ ~GAOptimizer()

protocols::ligand_docking::ga_ligand_dock::GAOptimizer::~GAOptimizer ( )

Member Function Documentation

◆ initialize_rotamer_set_and_scores()

void protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores ( LigandConformer  lig)
private

set up rotamer set

HELPER FUNCTIONS

References core::conformation::Residue::aa(), protocols::cluster::calibur::aa, core::chemical::aa_cys, core::chemical::aa_ser, core::chemical::aa_thr, core::chemical::aa_tyr, protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies::add_residue(), protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy::bonus_wtd_, core::pack::dunbrack::DunbrackRotamerSampleData::chi_mean(), protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer::chis, protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies::clear(), protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies::energy1b(), protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies::energy2b(), core::chemical::element::F, core::chemical::FA_STANDARD, favor_native_, protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies::finalize(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_protein_chis(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_protein_restype(), core::chemical::element::I, protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer::lkbrinfo, core::conformation::Residue::mainchain_torsion(), protocols::mean_field::max(), max_rot_cumulative_prob_, protocols::ligand_docking::ga_ligand_dock::LigandConformer::moving_scs(), core::conformation::Residue::nchi(), core::pack::dunbrack::DunbrackRotamerSampleData::nchi(), protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer::prob, core::pack::dunbrack::DunbrackRotamerSampleData::probability(), protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy::reset(), protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer::resid, protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer::restype, rot_energy_cutoff_, rotamer_data_, rotamer_energies_, protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer::rotno, protocols::hybridization::score, protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer::score, scorefxn_, protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_pose(), core::id::to_string(), protocols::ligand_docking::ga_ligand_dock::TR(), and core::conformation::Residue::type().

Referenced by run().

◆ next_generation()

void protocols::ligand_docking::ga_ligand_dock::GAOptimizer::next_generation ( LigandConformers const &  genes,
LigandConformers genes_new,
core::Size  npoolout,
core::Real  pmut 
)
private

◆ optimize_generation()

void protocols::ligand_docking::ga_ligand_dock::GAOptimizer::optimize_generation ( LigandConformers genes,
utility::vector1< core::Real > const &  ramping 
)

◆ run()

void protocols::ligand_docking::ga_ligand_dock::GAOptimizer::run ( LigandConformers genes)

◆ set_align_reference_atom_ids()

void protocols::ligand_docking::ga_ligand_dock::GAOptimizer::set_align_reference_atom_ids ( utility::vector1< core::id::AtomID newval)
inline

◆ set_favor_native()

void protocols::ligand_docking::ga_ligand_dock::GAOptimizer::set_favor_native ( core::Real  newval)
inline

References favor_native_.

◆ set_max_rot_cumulative_prob()

void protocols::ligand_docking::ga_ligand_dock::GAOptimizer::set_max_rot_cumulative_prob ( core::Real  newval)
inline

◆ set_native()

void protocols::ligand_docking::ga_ligand_dock::GAOptimizer::set_native ( LigandConformer const  native)
inline

References nativegene_.

◆ set_protocol()

void protocols::ligand_docking::ga_ligand_dock::GAOptimizer::set_protocol ( utility::vector1< GADockStageParams > const &  protocol_in)
inline

References protocol_.

◆ set_rot_energy_cutoff()

void protocols::ligand_docking::ga_ligand_dock::GAOptimizer::set_rot_energy_cutoff ( core::Real  newval)
inline

References rot_energy_cutoff_.

◆ show_status()

void protocols::ligand_docking::ga_ligand_dock::GAOptimizer::show_status ( LigandConformers genes,
std::string const &  comment = "",
bool  calculate_native_rmsd = true,
bool  verbose = false 
)

◆ update_pool()

void protocols::ligand_docking::ga_ligand_dock::GAOptimizer::update_pool ( LigandConformers genes,
LigandConformers genes_new,
core::Size  npool,
core::Real  rmscut 
)
private

update our pool

References protocols::ligand_docking::ga_ligand_dock::distance_fast().

Referenced by run().

◆ update_tags()

void protocols::ligand_docking::ga_ligand_dock::GAOptimizer::update_tags ( LigandConformers genes) const
private

reset tags for a generation

References core::id::to_string().

Referenced by run().

Member Data Documentation

◆ align_reference_atom_ids_

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

◆ favor_native_

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

◆ max_rot_cumulative_prob_

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

◆ nativegene_

LigandConformer protocols::ligand_docking::ga_ligand_dock::GAOptimizer::nativegene_
private

Referenced by set_native(), and show_status().

◆ protocol_

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

Referenced by run(), and set_protocol().

◆ rot_energy_cutoff_

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

◆ rotamer_data_

utility::vector1< PlaceableRotamers > protocols::ligand_docking::ga_ligand_dock::GAOptimizer::rotamer_data_
private

◆ rotamer_energies_

RotamerPairEnergies protocols::ligand_docking::ga_ligand_dock::GAOptimizer::rotamer_energies_
private

◆ scorefxn_

GridScorerOP protocols::ligand_docking::ga_ligand_dock::GAOptimizer::scorefxn_
private

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