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 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)

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 < GADockStageParams >	protocol_
core::Real	max_rot_cumulative_prob_
core::Real	rot_energy_cutoff_
core::Real	favor_native_
utility::vector1 < PlaceableRotamers >	rotamer_data_
RotamerPairEnergies	rotamer_energies_

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

protocols::ligand_docking::ga_ligand_dock::GAOptimizer::GAOptimizer

(

GridScorerOP

grid

)

References scorefxn_.

protocols::ligand_docking::ga_ligand_dock::GAOptimizer::~GAOptimizer

(

)

Member Function Documentation

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

private

set up rotamer set

HELPER FUNCTIONS

References protocols::cluster::calibur::aa, core::conformation::Residue::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::pack::dunbrack::DunbrackRotamerSampleData::nchi(), core::conformation::Residue::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::ligand_docking::ga_ligand_dock::PlaceableRotamer::score, protocols::hybridization::score, scorefxn_, core::conformation::Residue::set_chi(), 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().

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

private

generate putative next generation

References protocols::ligand_docking::ga_ligand_dock::crossover(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::generation_tag(), protocols::ligand_docking::ga_ligand_dock::mutate(), core::scoring::rg, protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_generation_tag(), core::id::to_string(), and protocols::ligand_docking::ga_ligand_dock::TR().

Referenced by run().

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

optimize one generation

References rotamer_data_, rotamer_energies_, protocols::hybridization::score, scorefxn_, and protocols::ligand_docking::ga_ligand_dock::TR().

Referenced by run().

void protocols::ligand_docking::ga_ligand_dock::GAOptimizer::run

(

LigandConformers &

genes

)

References protocols::ligand_docking::ga_ligand_dock::GADockStageParams::elec_scale, initialize_rotamer_set_and_scores(), max_rot_cumulative_prob_, protocols::ligand_docking::ga_ligand_dock::GADockStageParams::maxiter, next_generation(), optimize_generation(), protocols::ligand_docking::ga_ligand_dock::GADockStageParams::packcycles, protocols::ligand_docking::ga_ligand_dock::GADockStageParams::pmut, protocols::ligand_docking::ga_ligand_dock::GADockStageParams::pool, protocol_, protocols::ligand_docking::ga_ligand_dock::GADockStageParams::ramp_schedule, protocols::ligand_docking::ga_ligand_dock::GADockStageParams::repeats, protocols::ligand_docking::ga_ligand_dock::GADockStageParams::rmsthreshold, rot_energy_cutoff_, scorefxn_, show_status(), protocols::ligand_docking::ga_ligand_dock::GADockStageParams::smoothing, core::id::to_string(), protocols::ligand_docking::ga_ligand_dock::TR(), update_pool(), and update_tags().

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

inline

References favor_native_.

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

inline

References max_rot_cumulative_prob_.

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

inline

References nativegene_.

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

inline

References protocol_.

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

inline

References rot_energy_cutoff_.

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

References protocols::ligand_docking::ga_ligand_dock::LigandConformer::defined(), protocols::ligand_docking::ga_ligand_dock::distance_internal(), protocols::ligand_docking::ga_ligand_dock::distance_slow(), core::chemical::element::F, core::chemical::element::I, nativegene_, core::scoring::rms, protocols::hybridization::score, protocols::ligand_docking::ga_ligand_dock::LigandConformer::score(), scorefxn_, and protocols::ligand_docking::ga_ligand_dock::TR().

Referenced by run().

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(), and protocols::ligand_docking::ga_ligand_dock::LigandConformer::score().

Referenced by run().

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

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

private

Referenced by initialize_rotamer_set_and_scores(), and set_favor_native().

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

private

Referenced by initialize_rotamer_set_and_scores(), run(), and set_max_rot_cumulative_prob().

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

private

Referenced by set_native(), and show_status().

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

private

Referenced by run(), and set_protocol().

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

private

Referenced by initialize_rotamer_set_and_scores(), run(), and set_rot_energy_cutoff().

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

private

Referenced by initialize_rotamer_set_and_scores(), and optimize_generation().

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

private

Referenced by initialize_rotamer_set_and_scores(), and optimize_generation().

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

private

Referenced by GAOptimizer(), initialize_rotamer_set_and_scores(), optimize_generation(), run(), and show_status().

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

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