protocols::ligand_docking::ga_ligand_dock::GridScorer Class Reference

Grid representation of scorefunction. More...

#include <GridScorer.hh>

Public Member Functions
	GridScorer (core::scoring::ScoreFunctionOP sfxn)
	~GridScorer ()
void	prepare_grid (core::pose::Pose const &pose, utility::vector1< core::Size > const &lig_resnos)
	calulate the bounding box More...
void	get_grid_atomtypes (utility::vector1< core::conformation::Residue > const &rsds, utility::vector1< bool > const &sconly)
	pass list of residue (acutually rsdtypes) to construct grids for More...
void	get_grid_all_atomtypes ()
void	calculate_grid (core::pose::Pose const &pose, utility::vector1< core::Size > const &lig_resnos, utility::vector1< core::Size > const &movingSCs)
core::Real	score (LigandConformer const &lig, bool soft=false)
	calculate energies on the grid More...
core::Real	score_init (LigandConformer const &lig, bool soft=false, core::Real init_dens_weight=100)
	calculate energies on the grid for initial pool generation More...
core::Real	score_init (core::pose::Pose &pose, LigandConformer const &lig, bool soft, core::Real init_dens_weight=100)
core::Real	density_score (LigandConformer const &lig)
	calculate electron density on the grid More...
core::Real	calculate_ligand_density_correlation (int resid, core::conformation::Residue const &rsd, core::pose::Pose const &pose)
core::Real	calculate_pose_density_correlation (core::pose::Pose const &pose)
core::Real	calculate_pocket_density_correlation (core::pose::Pose const &pose)
core::Real	point_clash_energy (numeric::xyzVector< core::Real > X, std::string atype_in="", bool soft=false)
	gets the clash energy of a point More...
core::Real	point_energy (numeric::xyzVector< core::Real > X, std::string atype_in="", core::Real weightelec_in=0.0)
	gets the solvation energy of a point More...
ReweightableRepEnergy	get_1b_energy (core::conformation::Residue const &res_i, core::scoring::lkball::LKB_ResidueInfoOP lkbrinfo, bool include_bb, bool soft=false, bool has_density_map=false)
	get a residue:background energy More...
ReweightableRepEnergy	get_2b_energy (core::pose::Pose &pose, core::conformation::Residue const &res_i, core::scoring::lkball::LKB_ResidueInfoOP lkbrinfo_i, bool incl_bb_i, core::conformation::Residue const &res_j, core::scoring::lkball::LKB_ResidueInfoOP lkbrinfo_j, bool incl_bb_j, bool soft=false)
	get a residue:residue energy More...
std::map< std::pair< core::Size, core::Size >, std::vector< core::Size > >	get_hbond_map (core::pose::Pose pose, core::Size const lig_resno)
core::Real	score (core::pose::Pose &pose, LigandConformer const &lig, bool soft=false)
	calculate energies on the grid More...
void	derivatives (core::pose::Pose &pose, LigandConformer const &lig, core::optimization::MinimizerMap &min_map)
	calculate derivatives on the grid More...
core::Real	dof_derivative (core::pose::Pose &pose, core::optimization::MinimizerMap &min_map, core::id::DOF_ID const &dof_id, core::id::TorsionID const &torsion_id)
	(1b) dof derivatives More...
void	debug_deriv (core::pose::Pose &pose, LigandConformer const &lig, core::optimization::MinimizerMap &min_map)
core::Real	optimize (LigandConformer &lig, utility::vector1< core::Real > ramp_schedule, utility::vector1< PlaceableRotamers > &placeable_rotdb, RotamerPairEnergies &rot_energies)
	minimize a ligand conformer More...
core::Real	packer_loop (LigandConformer &lig, utility::vector1< PlaceableRotamers > &placeable_rotdb, RotamerPairEnergies &rotamer_energies)
	subroutine: run packing More...
core::Real	minimizer_loop (LigandConformer &lig, core::optimization::MinimizerOptions const &minopt)
	subroutine: min loop More...
bool	is_point_in_grid (numeric::xyzVector< core::Real > x) const
	check to see if a point falls w/i the grid boundaries More...
bool	is_residue_in_grid (core::conformation::Residue const &res, core::Real angle_buffer, core::Real padding_buffer) const
bool	is_residue_in_grid (core::conformation::Residue const &res, core::Real padding_buffer, numeric::xyzVector< core::Real > const &eigval, numeric::xyzMatrix< core::Real > const &eigvec) const
core::Real	get_padding ()
core::Real	get_voxel_spacing ()
void	set_voxel_spacing (core::Real voxel_spacing_in)
void	set_bbox_padding (core::Real bbox_padding_in)
void	set_hash_gridding (core::Real hash_gridding_in)
void	set_hash_subgridding (core::Size hash_subgridding_in)
void	set_exact (bool exactin)
bool	get_exact ()
void	set_debug (bool debugin)
bool	get_debug ()
void	set_grid_dim_with_maxRad (core::Real inval)
core::Real	get_maxRad ()
numeric::xyzVector< core::Real >	get_ligand_com ()
void	set_force_exact_min (bool setting)
void	set_maxiter_minimize (core::Size setting)
bool	get_maxiterminimize ()
void	set_packer_cycles (core::Size setting)
core::Size	get_packer_cycles ()
bool	set_smoothing (core::Real setting)
core::Real	get_smoothing ()
bool	set_elec_scale (core::Real setting)
core::Real	get_elec_scale ()
void	set_w_rep (core::Real setting)
core::Real	get_w_rep ()
void	set_out_of_bound_e (core::Real setting)
core::scoring::ScoreFunctionOP	get_sfxn () const
void	report_and_reset_timers (std::chrono::duration< core::Real > &pack_time, std::chrono::duration< core::Real > &min_time)
bool	has_atom_type (int atype)

Private Member Functions
void	do_convolution_and_compute_coeffs (ObjexxFCL::FArray3D< float > const &rawdata, ObjexxFCL::FArray3D< float > &smoothed_coeffs, core::Real smoothing, bool inverted=false)
	apply the convolution specified in "smoothing_" More...
core::Real	move_to_boundary (numeric::xyzVector< core::Real > &idxX) const
core::Real	move_to_boundary (numeric::xyzVector< core::Real > &idxX, numeric::xyzVector< core::Real > &dpen)
void	fast_eval_etable_split_fasol (core::scoring::etable::Etable const &etable, core::conformation::Atom const &atom1, core::conformation::Atom const &atom2, core::Real &lj_atrE, core::Real &lj_repE, core::Real &fa_solE1, core::Real &fa_solE2)
	fast etable energies More...
core::Real	fast_get_lk_fractional_contribution (numeric::xyzVector< core::Real > const &at2, core::Size const atom1_n_attached_waters, core::scoring::lkball::WaterCoords const &atom1_waters, core::Real ramp_width_A2, core::Real d2_low, core::Real multiwater_fade)
	fast lk_ball More...
core::Real	fast_get_lkbr_fractional_contribution (core::Size const atom1_n_attached_waters, core::Size const atom2_n_attached_waters, core::scoring::lkball::WaterCoords const &atom1_waters, core::scoring::lkball::WaterCoords const &atom2_waters, core::Real overlap_gap_A2, core::Real overlap_width_A2, core::Real multiwater_fade)
	fast lk_br More...

Private Attributes
core::scoring::ScoreFunctionOP	sfxn_
core::scoring::ScoreFunctionOP	sfxn_clash_
core::scoring::ScoreFunctionOP	sfxn_soft_
core::scoring::ScoreFunctionOP	sfxn_cart_
core::scoring::ScoreFunctionOP	sfxn_cst_
core::scoring::ScoreFunctionOP	sfxn_1b_
core::scoring::ScoreFunctionOP	sfxn_1b_clash_
core::scoring::ScoreFunctionOP	sfxn_1b_soft_
core::scoring::etable::Etable	etable_
core::pose::PoseOP	ref_pose_
bool	has_cst_energies_
core::scoring::lkball::LK_BallEnergyOP	LKBe_
core::scoring::etable::coulomb::CoulombOP	coulomb_
core::scoring::hbonds::HBondDatabaseCOP	hb_database_
core::energy_methods::CartesianBondedEnergyOP	cartbonded_
bool	exact_
bool	debug_
bool	force_exact_min_
std::chrono::duration< core::Real >	min_time_
std::chrono::duration< core::Real >	pack_time_
std::map< int, core::conformation::Atom >	uniq_atoms_
numeric::xyzVector< core::Real >	origin_
core::Real	bbox_padding_
core::Real	voxel_spacing_
core::Real	hash_grid_
core::Size	hash_subgrid_
numeric::xyzVector< core::Size >	dims_
std::map< int, ObjexxFCL::FArray3D< float > >	raw_faatr_
std::map< int, ObjexxFCL::FArray3D< float > >	raw_farep_
std::map< int, ObjexxFCL::FArray3D< float > >	raw_fasol_
std::map< int, ObjexxFCL::FArray3D< float > >	raw_lkball_
std::map< int, ObjexxFCL::FArray3D< float > >	raw_lkbridge_
ObjexxFCL::FArray3D< float >	raw_faelec_
std::map< int, ObjexxFCL::FArray3D< float > >	coeffs_faatr_
std::map< int, ObjexxFCL::FArray3D< float > >	coeffs_farep_
std::map< int, ObjexxFCL::FArray3D< float > >	coeffs_fasol_
std::map< int, ObjexxFCL::FArray3D< float > >	coeffs_lkball_
std::map< int, ObjexxFCL::FArray3D< float > >	coeffs_lkbridge_
ObjexxFCL::FArray3D< float >	coeffs_faelec_
GridHash3D< hbDon >	hbdonors_
GridHash3D< hbAcc >	hbacceptors_
core::Real	maxdis_
core::Real	out_of_bound_e_
core::Real	LK_fade_
core::Real	w_rep_
core::Real	w_fa_elec_
core::Real	w_hbond_sc_
core::Real	w_hbond_bb_sc_
core::Real	elec_scale_
core::Real	smoothing_
core::Size	packer_cycles_
core::Size	maxiter_minimize_
numeric::xyzVector< core::Real >	lig_com_
core::Real	maxRad_
utility::vector1< core::Size >	ligids_

Detailed Description

Grid representation of scorefunction.

Constructor & Destructor Documentation

GridScorer()

protocols::ligand_docking::ga_ligand_dock::GridScorer::GridScorer

(

core::scoring::ScoreFunctionOP

sfxn

)

References core::scoring::atom_pair_constraint, bbox_padding_, core::scoring::cart_bonded, core::scoring::cart_bonded_angle, core::scoring::cart_bonded_improper, core::scoring::cart_bonded_length, core::scoring::cart_bonded_ring, core::scoring::cart_bonded_torsion, cartbonded_, core::scoring::coordinate_constraint, coulomb_, core::scoring::ScoreFunctionFactory::create_score_function(), debug_, dims_, core::scoring::dslf_fa13, core::scoring::elec_dens_fast, exact_, core::scoring::fa_dun, core::scoring::fa_dun_dev, core::scoring::fa_dun_rot, core::scoring::fa_dun_semi, core::scoring::fa_elec, core::scoring::fa_intra_atr_xover4, core::scoring::fa_intra_elec, core::scoring::fa_intra_rep, core::scoring::fa_intra_rep_xover4, core::scoring::fa_intra_sol_xover4, core::scoring::fa_rep, force_exact_min_, core::scoring::gen_bonded, core::scoring::hbonds::HBondDatabase::get_database(), has_cst_energies_, hash_grid_, hash_subgrid_, hb_database_, core::scoring::hbond_bb_sc, core::scoring::methods::EnergyMethodOptions::hbond_options(), core::scoring::hbond_sc, lig_com_, LK_fade_, LKBe_, maxdis_, maxiter_minimize_, maxRad_, min_time_, out_of_bound_e_, pack_time_, packer_cycles_, core::scoring::hbonds::HBondOptions::params_database_tag(), core::scoring::ring_close, sfxn_, sfxn_1b_, sfxn_1b_clash_, sfxn_1b_soft_, sfxn_cart_, sfxn_clash_, sfxn_cst_, sfxn_soft_, smoothing_, voxel_spacing_, w_fa_elec_, w_hbond_bb_sc_, w_hbond_sc_, and w_rep_.

~GridScorer()

protocols::ligand_docking::ga_ligand_dock::GridScorer::~GridScorer

(

)

Member Function Documentation

calculate_grid()

void protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	lig_resnos,
		utility::vector1< core::Size > const &	movingSCs
	)

References protocols::ligand_docking::ga_ligand_dock::hbAcc::A, core::conformation::Residue::abase2(), core::conformation::Residue::accpt_pos(), protocols::ligand_docking::ga_ligand_dock::hbAcc::acctype, protocols::ligand_docking::ga_ligand_dock::GridHash3D< T >::add_point(), core::scoring::etable::Etable::analytic_lk_energy(), core::conformation::Residue::atom(), protocols::ligand_docking::ga_ligand_dock::atmInfo::atom, core::conformation::Residue::atom_base(), core::conformation::Residue::atomic_charge(), protocols::ligand_docking::ga_ligand_dock::atmInfo::atomicCharge, protocols::ligand_docking::ga_ligand_dock::atmInfo::atomWaters, protocols::ligand_docking::ga_ligand_dock::hbAcc::B, protocols::ligand_docking::ga_ligand_dock::hbAcc::B_0, coeffs_faatr_, coeffs_faelec_, coeffs_farep_, coeffs_fasol_, coeffs_lkball_, coeffs_lkbridge_, coulomb_, protocols::ligand_docking::ga_ligand_dock::hbDon::D, core::conformation::Residue::data_ptr(), dims_, do_convolution_and_compute_coeffs(), protocols::ligand_docking::ga_ligand_dock::hbDon::dontype, core::sequence::end, etable_, core::chemical::FA_STANDARD, fast_eval_etable_split_fasol(), fast_get_lk_fractional_contribution(), fast_get_lkbr_fractional_contribution(), core::conformation::Residue::first_sidechain_hydrogen(), core::scoring::lkball::LK_BallEnergy::get_d2_low(), get_grid_atomtypes(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), protocols::ligand_docking::ga_ligand_dock::GridHash3D< T >::get_neighbors(), core::scoring::lkball::LK_BallEnergy::get_overlap_gap2(), core::scoring::lkball::LK_BallEnergy::get_overlap_width_A2(), core::scoring::lkball::LK_BallEnergy::get_ramp_width_A2(), protocols::ligand_docking::ga_ligand_dock::hbDon::H, hash_grid_, hash_subgrid_, hbacceptors_, hbdonors_, core::conformation::Residue::Hpos_polar(), core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_donor(), core::chemical::AtomType::is_virtual(), core::conformation::Residue::last_backbone_atom(), core::scoring::lk_ball, core::scoring::lk_ball_bridge, core::scoring::lk_ball_bridge_uncpl, core::conformation::residue_datacache::LK_BALL_INFO, core::scoring::lk_ball_iso, core::scoring::lk_ball_wtd, core::scoring::lkball::LK_BallEnergy::lkb_max_dis(), protocols::mean_field::max(), core::scoring::etable::Etable::max_dis(), maxdis_, core::scoring::lkball::LKB_ResidueInfo::n_attached_waters(), core::conformation::Residue::natoms(), protocols::ligand_docking::ga_ligand_dock::atmInfo::nAtomWaters, core::conformation::Residue::nheavyatoms(), origin_, prepare_grid(), raw_faatr_, raw_faelec_, raw_farep_, raw_fasol_, raw_lkball_, raw_lkbridge_, core::pose::Pose::residue(), protocols::ligand_docking::ga_ligand_dock::GridHash3D< T >::set_resolution(), sfxn_, protocols::loops::start, core::pose::Pose::total_residue(), protocols::ligand_docking::ga_ligand_dock::TR(), core::conformation::Atom::type(), uniq_atoms_, voxel_spacing_, core::scoring::lkball::LKB_ResidueInfo::water_offset_for_atom(), core::scoring::lkball::LKB_ResidueInfo::waters(), protocols::ligand_docking::ga_ligand_dock::xform_atr(), protocols::ligand_docking::ga_ligand_dock::xform_rep(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

calculate_ligand_density_correlation()

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_ligand_density_correlation	(	int	resid,
		core::conformation::Residue const &	rsd,
		core::pose::Pose const &	pose
	)

References core::scoring::electron_density::getDensityMap(), and core::scoring::electron_density::ElectronDensity::matchRes().

calculate_pocket_density_correlation()

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_pocket_density_correlation

(

core::pose::Pose const &

pose

)

References core::scoring::electron_density::getDensityMap(), lig_com_, core::scoring::electron_density::ElectronDensity::matchPoseInPocket(), and maxRad_.

calculate_pose_density_correlation()

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_pose_density_correlation

(

core::pose::Pose const &

pose

)

References core::scoring::electron_density::getDensityMap(), and core::scoring::electron_density::ElectronDensity::matchPose().

debug_deriv()

void protocols::ligand_docking::ga_ligand_dock::GridScorer::debug_deriv	(	core::pose::Pose &	pose,
		LigandConformer const &	lig,
		core::optimization::MinimizerMap &	min_map
	)

References core::optimization::MinimizerMap::atom_derivatives(), derivatives(), core::conformation::Residue::first_sidechain_hydrogen(), core::conformation::Residue::last_backbone_atom(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_ids(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::moving_scs(), core::conformation::Residue::natoms(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), score(), core::pose::Pose::set_xyz(), and core::pose::Pose::xyz().

Referenced by protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dfunc().

density_score()

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::density_score

(

LigandConformer const &

lig

)

calculate electron density on the grid

References core::scoring::elec_dens_fast, core::scoring::electron_density::getDensityMap(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_ids(), core::scoring::electron_density::ElectronDensity::matchResFast(), ref_pose_, core::pose::Pose::residue(), core::conformation::Residue::seqpos(), sfxn_1b_soft_, and protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_pose().

derivatives()

void protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives	(	core::pose::Pose &	pose,
		LigandConformer const &	lig,
		core::optimization::MinimizerMap &	min_map
	)

calculate derivatives on the grid

References protocols::comparative_modeling::features::A, core::conformation::Residue::abase2(), core::scoring::hbonds::HBondDerivs::abase2_deriv, core::scoring::hbonds::HBondDerivs::abase_deriv, core::scoring::hbonds::HBondDerivs::acc_deriv, core::scoring::hbonds::HBEvalTuple::acc_type(), core::conformation::Residue::accpt_pos(), core::scoring::etable::Etable::analytic_etable_derivatives(), core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::optimization::MinimizerMap::atom_derivatives(), core::conformation::Residue::atom_index(), core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::atomic_charge(), core::chemical::ResidueConnection::atomno(), core::chemical::element::B, cartbonded_, coeffs_faatr_, coeffs_faelec_, coeffs_farep_, coeffs_fasol_, coeffs_lkball_, coeffs_lkbridge_, core::conformation::Residue::connect_map(), core::conformation::Residue::connected_residue_at_resconn(), core::pose::Pose::constraint_set(), coulomb_, core::id::D, core::chemical::DISULFIDE, core::scoring::hbonds::HBondDerivs::don_deriv, core::scoring::hbonds::HBEvalTuple::don_type(), core::scoring::dslf_fa13, protocols::ligand_docking::ga_ligand_dock::dxform_atr(), protocols::ligand_docking::ga_ligand_dock::dxform_rep(), protocols::buns::energy, etable_, core::scoring::eval_atom_derivatives_for_minnode(), core::scoring::hbonds::HBEvalTuple::eval_type(), core::scoring::DerivVectorPair::f2(), core::scoring::fa_atr, core::scoring::fa_elec, core::scoring::fa_rep, core::scoring::fa_sol, core::conformation::Residue::first_sidechain_hydrogen(), core::scoring::hbonds::HBondDatabase::get_database(), core::chemical::ResidueTypeBase::get_disulfide_atom_name(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::scoring::hbonds::get_hbond_weight_type(), core::scoring::MinimizationGraph::get_minimization_node(), core::chemical::element::H, core::scoring::hbonds::HBondDerivs::h_deriv, core::chemical::ResidueType::has(), has_cst_energies_, core::conformation::Residue::has_variant_type(), core::scoring::hbonds::hb_energy_deriv(), hbacceptors_, hbdonors_, core::scoring::hbond_bb_sc, core::scoring::methods::EnergyMethodOptions::hbond_options(), core::scoring::hbond_sc, core::scoring::hbonds::hbw_LR_BB_SC, core::scoring::hbonds::hbw_SC, core::scoring::hbonds::hbw_SR_BB_SC, core::conformation::Residue::Hpos_polar(), core::scoring::electron_density::interp_dspline(), core::scoring::electron_density::interp_spline(), core::conformation::Residue::is_ligand(), core::conformation::Residue::last_backbone_atom(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_ids(), core::scoring::lk_ball, core::scoring::lk_ball_bridge, core::scoring::lk_ball_bridge_uncpl, core::scoring::lk_ball_iso, LK_fade_, LKBe_, core::scoring::hbonds::HBondOptions::max_hb_energy(), core::scoring::hbonds::MAX_R2, move_to_boundary(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::moving_scs(), core::chemical::ResidueType::n_possible_residue_connections(), core::conformation::Residue::n_possible_residue_connections(), core::conformation::Residue::natoms(), core::conformation::Residue::nheavyatoms(), origin_, core::scoring::hbonds::HBondOptions::params_database_tag(), core::chemical::ResConnID::resid(), core::pose::Pose::residue(), core::chemical::ResidueType::residue_connection(), core::conformation::Residue::residue_connection_partner(), core::pose::Pose::residue_data(), core::pose::Pose::residue_type(), sfxn_, sfxn_1b_, sfxn_cart_, sfxn_cst_, core::conformation::Residue::type(), core::conformation::Atom::type(), voxel_spacing_, w_rep_, and core::conformation::Residue::xyz().

Referenced by debug_deriv(), and protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dfunc().

do_convolution_and_compute_coeffs()

void protocols::ligand_docking::ga_ligand_dock::GridScorer::do_convolution_and_compute_coeffs ( ObjexxFCL::FArray3D< float > const &  rawdata, ObjexxFCL::FArray3D< float > &  smoothed_coeffs, core::Real  smoothing, bool  inverted = false  )

private

apply the convolution specified in "smoothing_"

References protocols::mean_field::max(), protocols::mean_field::min(), core::chemical::element::N, core::scoring::electron_density::spline_coeffs(), voxel_spacing_, and protocols::comparative_modeling::features::X.

Referenced by calculate_grid(), and set_smoothing().

dof_derivative()

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::dof_derivative	(	core::pose::Pose &	pose,
		core::optimization::MinimizerMap &	min_map,
		core::id::DOF_ID const &	dof_id,
		core::id::TorsionID const &	torsion_id
	)

(1b) dof derivatives

References core::optimization::MinimizerMap::atom_derivatives(), core::id::DOF_ID::atom_id(), core::scoring::eval_atom_derivatives_for_minnode(), core::scoring::eval_dof_deriv_for_minnode(), core::scoring::MinimizationGraph::get_minimization_node(), core::pose::Pose::residue(), core::pose::Pose::residue_data(), core::id::AtomID::rsd(), core::id::TorsionID::rsd(), sfxn_1b_, and core::id::TorsionID::valid().

Referenced by protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dfunc().

fast_eval_etable_split_fasol()

void protocols::ligand_docking::ga_ligand_dock::GridScorer::fast_eval_etable_split_fasol ( core::scoring::etable::Etable const &  etable, core::conformation::Atom const &  atom1, core::conformation::Atom const &  atom2, core::Real &  lj_atrE, core::Real &  lj_repE, core::Real &  fa_solE1, core::Real &  fa_solE2  )

inlineprivate

fast etable energies

References core::scoring::etable::Etable::analytic_params_for_pair(), core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly1_close, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly1_close_flat, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly1_far, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly2_close, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly2_close_flat, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly2_far, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly_close_end, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly_close_start, core::scoring::etable::Etable::fasol_cubic_poly_far_xhi(), core::scoring::etable::Etable::fasol_cubic_poly_far_xlo(), core::scoring::etable::EtableParamsOnePair::fasol_final_weight, core::scoring::etable::EtableParamsOnePair::lj_minimum, core::scoring::etable::EtableParamsOnePair::lj_r12_coeff, core::scoring::etable::EtableParamsOnePair::lj_r6_coeff, core::scoring::etable::Etable::lj_radius(), core::scoring::etable::EtableParamsOnePair::lj_switch_intercept, core::scoring::etable::EtableParamsOnePair::lj_switch_slope, core::scoring::etable::EtableParamsOnePair::lj_val_at_minimum, core::scoring::etable::EtableParamsOnePair::ljatr_cubic_poly_parameters, core::scoring::etable::EtableParamsOnePair::ljatr_cubic_poly_xhi, core::scoring::etable::EtableParamsOnePair::ljatr_cubic_poly_xlo, core::scoring::etable::EtableParamsOnePair::ljatr_final_weight, core::scoring::etable::EtableParamsOnePair::ljrep_linear_ramp_d2_cutoff, core::scoring::etable::EtableParamsOnePair::lk_coeff1, core::scoring::etable::EtableParamsOnePair::lk_coeff2, core::scoring::etable::Etable::lk_inv_lambda2(), core::scoring::etable::Etable::max_dis2(), core::scoring::etable::EtableParamsOnePair::maxd2, core::scoring::etable::Etable::min_dis2(), core::conformation::Atom::type(), and core::conformation::Atom::xyz().

Referenced by calculate_grid(), and get_2b_energy().

fast_get_lk_fractional_contribution()

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::fast_get_lk_fractional_contribution ( numeric::xyzVector< core::Real > const &  at2, core::Size const  atom1_n_attached_waters, core::scoring::lkball::WaterCoords const &  atom1_waters, core::Real  ramp_width_A2, core::Real  d2_low, core::Real  multiwater_fade  )

inlineprivate

fast lk_ball

References protocols::mean_field::min().

Referenced by calculate_grid().

fast_get_lkbr_fractional_contribution()

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::fast_get_lkbr_fractional_contribution ( core::Size const  atom1_n_attached_waters, core::Size const  atom2_n_attached_waters, core::scoring::lkball::WaterCoords const &  atom1_waters, core::scoring::lkball::WaterCoords const &  atom2_waters, core::Real  overlap_gap_A2, core::Real  overlap_width_A2, core::Real  multiwater_fade  )

inlineprivate

fast lk_br

References protocols::mean_field::min().

Referenced by calculate_grid().

get_1b_energy()

ReweightableRepEnergy protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy	(	core::conformation::Residue const &	res_i,
		core::scoring::lkball::LKB_ResidueInfoOP	lkbrinfo,
		bool	include_bb,
		bool	soft = false,
		bool	has_density_map = false
	)

get a residue:background energy

References protocols::comparative_modeling::features::A, core::conformation::Residue::abase2(), core::scoring::hbonds::HBEvalTuple::acc_type(), core::conformation::Residue::accpt_pos(), core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_name(), core::conformation::Residue::atomic_charge(), core::chemical::element::B, cartbonded_, coeffs_faatr_, coeffs_faelec_, coeffs_farep_, coeffs_fasol_, coeffs_lkball_, coeffs_lkbridge_, core::id::D, core::scoring::hbonds::HBEvalTuple::don_type(), core::scoring::EMapVector::dot(), core::scoring::elec_dens_fast, protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy::elec_dens_wtd_, core::scoring::fa_atr, protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy::fa_atr_wtd_, core::scoring::fa_elec, protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy::fa_elec_wtd_, core::scoring::fa_rep, protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy::fa_rep_, core::scoring::fa_sol, protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy::fa_sol_wtd_, core::conformation::Residue::first_sidechain_hydrogen(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), protocols::ligand_docking::ga_ligand_dock::get_hbond_score_weighted(), core::scoring::electron_density::getDensityMap(), core::chemical::element::H, hb_database_, hbacceptors_, hbdonors_, protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy::hbond_wtd_, core::conformation::Residue::Hpos_polar(), core::scoring::electron_density::interp_spline(), core::conformation::Residue::is_ligand(), protocols::ligand_docking::ga_ligand_dock::ixform_atr(), protocols::ligand_docking::ga_ligand_dock::ixform_rep(), core::conformation::Residue::last_backbone_atom(), core::scoring::lk_ball, core::scoring::lk_ball_bridge, core::scoring::lk_ball_bridge_uncpl, core::scoring::lk_ball_iso, protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy::lk_ball_wtd_, LK_fade_, core::scoring::electron_density::ElectronDensity::matchResFast(), core::scoring::hbonds::MAX_R2, move_to_boundary(), core::conformation::Residue::natoms(), core::conformation::Residue::nheavyatoms(), protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy::oneb_wtd_, origin_, protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy::penalty_wtd_, core::conformation::Residue::seqpos(), sfxn_, sfxn_1b_, sfxn_1b_soft_, sfxn_cart_, sfxn_soft_, protocols::ligand_docking::ga_ligand_dock::TR(), core::conformation::Atom::type(), voxel_spacing_, and core::conformation::Residue::xyz().

Referenced by packer_loop(), and score().

get_2b_energy()

ReweightableRepEnergy protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy	(	core::pose::Pose &	pose,
		core::conformation::Residue const &	res_i,
		core::scoring::lkball::LKB_ResidueInfoOP	lkbrinfo_i,
		bool	incl_bb_i,
		core::conformation::Residue const &	res_j,
		core::scoring::lkball::LKB_ResidueInfoOP	lkbrinfo_j,
		bool	incl_bb_j,
		bool	soft = false
	)

get a residue:residue energy

References protocols::comparative_modeling::features::A, core::conformation::Residue::abase2(), core::scoring::hbonds::HBEvalTuple::acc_type(), core::conformation::Residue::accpt_pos(), core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::atomic_charge(), core::chemical::element::B, core::pose::Pose::constraint_set(), coulomb_, protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy::cst_wtd_, core::id::D, core::scoring::hbonds::HBEvalTuple::don_type(), core::scoring::EMapVector::dot(), etable_, core::scoring::fa_atr, protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy::fa_atr_wtd_, core::scoring::fa_elec, protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy::fa_elec_wtd_, core::scoring::fa_rep, protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy::fa_rep_, core::scoring::fa_sol, protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy::fa_sol_wtd_, fast_eval_etable_split_fasol(), core::conformation::Residue::first_sidechain_hydrogen(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), protocols::ligand_docking::ga_ligand_dock::get_hbond_score_weighted(), core::chemical::element::H, has_cst_energies_, hb_database_, protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy::hbond_wtd_, core::conformation::Residue::Hpos_polar(), core::conformation::Residue::last_backbone_atom(), core::scoring::lk_ball, core::scoring::lk_ball_bridge, core::scoring::lk_ball_bridge_uncpl, core::scoring::lk_ball_iso, protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy::lk_ball_wtd_, LKBe_, core::scoring::hbonds::MAX_R2, core::conformation::Residue::natoms(), core::conformation::Residue::nheavyatoms(), sfxn_, sfxn_cst_, sfxn_soft_, core::conformation::Atom::type(), and core::conformation::Residue::xyz().

Referenced by packer_loop(), and score().

get_debug()

bool protocols::ligand_docking::ga_ligand_dock::GridScorer::get_debug ( )

inline

References debug_.

get_elec_scale()

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::get_elec_scale ( )

inline

References elec_scale_.

get_exact()

bool protocols::ligand_docking::ga_ligand_dock::GridScorer::get_exact ( )

inline

References exact_.

get_grid_all_atomtypes()

void protocols::ligand_docking::ga_ligand_dock::GridScorer::get_grid_all_atomtypes

(

)

References protocols::ligand_docking::ga_ligand_dock::TR(), core::conformation::Atom::type(), and uniq_atoms_.

get_grid_atomtypes()

void protocols::ligand_docking::ga_ligand_dock::GridScorer::get_grid_atomtypes	(	utility::vector1< core::conformation::Residue > const &	rsds,
		utility::vector1< bool > const &	sconly
	)

pass list of residue (acutually rsdtypes) to construct grids for

References core::conformation::Residue::atom(), core::conformation::Residue::first_sidechain_hydrogen(), core::conformation::Residue::last_backbone_atom(), core::conformation::Residue::natoms(), core::conformation::Residue::nheavyatoms(), protocols::ligand_docking::ga_ligand_dock::TR(), core::conformation::Atom::type(), and uniq_atoms_.

Referenced by calculate_grid().

get_hbond_map()

std::map< std::pair< core::Size, core::Size >, std::vector< core::Size > > protocols::ligand_docking::ga_ligand_dock::GridScorer::get_hbond_map	(	core::pose::Pose	pose,
		core::Size const	lig_resno
	)

References protocols::comparative_modeling::features::A, core::conformation::Residue::abase2(), core::scoring::hbonds::HBEvalTuple::acc_type(), core::conformation::Residue::accpt_pos(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_name(), core::chemical::element::B, core::id::D, core::scoring::hbonds::HBEvalTuple::don_type(), core::conformation::Residue::first_sidechain_hydrogen(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::chemical::element::H, core::conformation::Residue::Hpos_polar(), core::conformation::Residue::last_backbone_atom(), core::scoring::hbonds::MAX_R2, core::conformation::Residue::name(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::conformation::Residue::seqpos(), core::pose::Pose::total_residue(), protocols::ligand_docking::ga_ligand_dock::TR(), and core::conformation::Residue::xyz().

get_ligand_com()

numeric::xyzVector< core::Real > protocols::ligand_docking::ga_ligand_dock::GridScorer::get_ligand_com ( )

inline

References lig_com_.

get_maxiterminimize()

bool protocols::ligand_docking::ga_ligand_dock::GridScorer::get_maxiterminimize ( )

inline

References maxiter_minimize_.

get_maxRad()

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::get_maxRad ( )

inline

References maxRad_.

get_packer_cycles()

core::Size protocols::ligand_docking::ga_ligand_dock::GridScorer::get_packer_cycles ( )

inline

References packer_cycles_.

get_padding()

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::get_padding ( )

inline

References bbox_padding_.

get_sfxn()

core::scoring::ScoreFunctionOP protocols::ligand_docking::ga_ligand_dock::GridScorer::get_sfxn ( ) const

inline

References sfxn_.

get_smoothing()

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::get_smoothing ( )

inline

References smoothing_.

get_voxel_spacing()

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::get_voxel_spacing ( )

inline

References voxel_spacing_.

get_w_rep()

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::get_w_rep ( )

inline

References w_rep_.

Referenced by optimize().

has_atom_type()

bool protocols::ligand_docking::ga_ligand_dock::GridScorer::has_atom_type ( int  atype )

inline

References raw_faatr_.

is_point_in_grid()

bool protocols::ligand_docking::ga_ligand_dock::GridScorer::is_point_in_grid

(

numeric::xyzVector< core::Real >

x

)

const

check to see if a point falls w/i the grid boundaries

References move_to_boundary(), origin_, and voxel_spacing_.

is_residue_in_grid() [1/2]

bool protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid	(	core::conformation::Residue const &	res,
		core::Real	angle_buffer,
		core::Real	padding_buffer
	)		const

@detail check to see if sidechain lies within the grid "angle buffer" makes sure residues near the edge point toward middle (higer values == stricter, 0 = no filter) "padding buffer" adds a region on the outside where residues may not move

References core::conformation::Residue::atom_name(), bbox_padding_, dims_, core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::first_sidechain_hydrogen(), protocols::mean_field::max(), protocols::mean_field::min(), core::conformation::Residue::natoms(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::nheavyatoms(), origin_, core::conformation::Residue::seqpos(), protocols::ligand_docking::ga_ligand_dock::TR(), voxel_spacing_, and core::conformation::Residue::xyz().

is_residue_in_grid() [2/2]

bool protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid	(	core::conformation::Residue const &	res,
		core::Real	padding_buffer,
		numeric::xyzVector< core::Real > const &	eigval,
		numeric::xyzMatrix< core::Real > const &	eigvec
	)		const

@detail check to see if sidechain lies within the grid (ALTERNATE version) similar to the above, but pass in eigenvalues/vectors that define pocket shape

References dims_, core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::first_sidechain_hydrogen(), core::conformation::Residue::natoms(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_radius(), core::conformation::Residue::nheavyatoms(), origin_, voxel_spacing_, and core::conformation::Residue::xyz().

minimizer_loop()

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::minimizer_loop	(	LigandConformer &	lig,
		core::optimization::MinimizerOptions const &	minopt
	)

subroutine: min loop

References core::optimization::MinimizerMap::copy_dofs_from_pose(), core::optimization::MinimizerMap::copy_dofs_to_pose(), exact_, protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_jumpid(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::is_ligand_bb_frozen(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::is_ligand_frozen(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_ids(), maxiter_minimize_, protocols::ligand_docking::ga_ligand_dock::LigandConformer::moving_scs(), core::optimization::MinimizerMap::nangles(), core::optimization::MinimizerMap::reset_jump_rb_deltas(), core::optimization::Minimizer::run(), core::optimization::AtomTreeMinimizer::run(), score(), core::optimization::MinimizerMap::setup(), sfxn_, protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_minipose(), and protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf_from_minipose().

Referenced by optimize().

move_to_boundary() [1/2]

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::move_to_boundary ( numeric::xyzVector< core::Real > &  idxX ) const

private

References dims_, out_of_bound_e_, and voxel_spacing_.

Referenced by derivatives(), get_1b_energy(), is_point_in_grid(), point_clash_energy(), and point_energy().

move_to_boundary() [2/2]

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::move_to_boundary ( numeric::xyzVector< core::Real > &  idxX, numeric::xyzVector< core::Real > &  dpen  )

private

References dims_, out_of_bound_e_, and voxel_spacing_.

optimize()

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::optimize	(	LigandConformer &	lig,
		utility::vector1< core::Real >	ramp_schedule,
		utility::vector1< PlaceableRotamers > &	placeable_rotdb,
		RotamerPairEnergies &	rot_energies
	)

minimize a ligand conformer

References debug_, exact_, force_exact_min_, get_w_rep(), core::optimization::MinimizerOptions::max_iter(), maxiter_minimize_, min_time_, minimizer_loop(), pack_time_, packer_loop(), score(), set_w_rep(), and protocols::ligand_docking::ga_ligand_dock::TR().

packer_loop()

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_loop	(	LigandConformer &	lig,
		utility::vector1< PlaceableRotamers > &	placeable_rotdb,
		RotamerPairEnergies &	rotamer_energies
	)

subroutine: run packing

References protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies::energy1b(), protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies::energy2b(), protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies::energyBG(), get_1b_energy(), get_2b_energy(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_protein_chis(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_protein_restype(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_ref_pose(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_ids(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_typename(), ligids_, protocols::mean_field::max(), protocols::mean_field::min(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::moving_scs(), packer_cycles_, ref_pose_, core::scoring::rg, protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy::score(), score(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_protein_chis(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_protein_restype(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_pose(), and w_rep_.

Referenced by optimize().

point_clash_energy()

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::point_clash_energy	(	numeric::xyzVector< core::Real >	X,
		std::string	atype_in = "",
		bool	soft = false
	)

gets the clash energy of a point

References coeffs_farep_, core::scoring::fa_rep, core::scoring::electron_density::interp_spline(), protocols::ligand_docking::ga_ligand_dock::ixform_rep(), move_to_boundary(), origin_, sfxn_, sfxn_1b_, sfxn_1b_soft_, sfxn_soft_, voxel_spacing_, and protocols::comparative_modeling::features::X.

point_energy()

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::point_energy	(	numeric::xyzVector< core::Real >	X,
		std::string	atype_in = "",
		core::Real	weightelec_in = 0.0
	)

gets the solvation energy of a point

References coeffs_faatr_, coeffs_faelec_, coeffs_farep_, coeffs_fasol_, core::scoring::fa_atr, core::scoring::fa_elec, core::scoring::fa_rep, core::scoring::fa_sol, core::scoring::electron_density::interp_spline(), protocols::ligand_docking::ga_ligand_dock::ixform_atr(), protocols::ligand_docking::ga_ligand_dock::ixform_rep(), move_to_boundary(), origin_, raw_faatr_, sfxn_, sfxn_soft_, voxel_spacing_, and protocols::comparative_modeling::features::X.

prepare_grid()

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

calulate the bounding box

References bbox_padding_, dims_, lig_com_, ligids_, protocols::mean_field::max(), maxRad_, core::conformation::Residue::natoms(), origin_, ref_pose_, core::pose::Pose::residue(), protocols::ligand_docking::ga_ligand_dock::TR(), voxel_spacing_, and core::conformation::Residue::xyz().

Referenced by calculate_grid().

report_and_reset_timers()

void protocols::ligand_docking::ga_ligand_dock::GridScorer::report_and_reset_timers ( std::chrono::duration< core::Real > &  pack_time, std::chrono::duration< core::Real > &  min_time  )

inline

References min_time_, and pack_time_.

score() [1/2]

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::score	(	core::pose::Pose &	pose,
		LigandConformer const &	lig,
		bool	soft = false
	)

calculate energies on the grid

References core::conformation::Residue::atom_index(), core::chemical::ResidueConnection::atomno(), cartbonded_, core::conformation::Residue::connect_map(), core::conformation::Residue::connected_residue_at_resconn(), debug_, core::chemical::DISULFIDE, core::scoring::EMapVector::dot(), core::scoring::dslf_fa13, exact_, core::chemical::element::F, get_1b_energy(), get_2b_energy(), core::chemical::ResidueTypeBase::get_disulfide_atom_name(), core::chemical::ResidueType::has(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::has_density_map(), core::conformation::Residue::has_variant_type(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_ids(), core::scoring::lk_ball, core::scoring::lk_ball_bridge, core::scoring::lk_ball_bridge_uncpl, core::scoring::lk_ball_iso, protocols::ligand_docking::ga_ligand_dock::LigandConformer::moving_scs(), core::chemical::ResidueType::n_possible_residue_connections(), core::conformation::Residue::n_possible_residue_connections(), core::chemical::ResConnID::resid(), core::pose::Pose::residue(), core::chemical::ResidueType::residue_connection(), core::conformation::Residue::residue_connection_partner(), core::pose::Pose::residue_type(), protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy::score(), core::scoring::disulfides::FullatomDisulfidePotential::score_this_disulfide(), sfxn_, sfxn_cart_, sfxn_soft_, protocols::ligand_docking::ga_ligand_dock::TR(), core::conformation::Residue::type(), and w_rep_.

score() [2/2]

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::score	(	LigandConformer const &	lig,
		bool	soft = false
	)

calculate energies on the grid

References protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_ref_pose(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_ids(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_typename(), ligids_, ref_pose_, and protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_pose().

Referenced by debug_deriv(), minimizer_loop(), protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::operator()(), optimize(), packer_loop(), and score_init().

score_init() [1/2]

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::score_init	(	core::pose::Pose &	pose,
		LigandConformer const &	lig,
		bool	soft,
		core::Real	init_dens_weight = 100
	)

References core::scoring::elec_dens_fast, score(), sfxn_, sfxn_1b_, and sfxn_1b_soft_.

score_init() [2/2]

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::score_init	(	LigandConformer const &	lig,
		bool	soft = false,
		core::Real	init_dens_weight = 100
	)

calculate energies on the grid for initial pool generation

References core::scoring::elec_dens_fast, ref_pose_, score(), sfxn_, sfxn_1b_, sfxn_1b_soft_, and protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_pose().

set_bbox_padding()

void protocols::ligand_docking::ga_ligand_dock::GridScorer::set_bbox_padding ( core::Real  bbox_padding_in )

inline

References bbox_padding_.

set_debug()

void protocols::ligand_docking::ga_ligand_dock::GridScorer::set_debug ( bool  debugin )

inline

References debug_.

set_elec_scale()

bool protocols::ligand_docking::ga_ligand_dock::GridScorer::set_elec_scale

(

core::Real

setting

)

References core::scoring::fa_elec, core::scoring::hbond_bb_sc, core::scoring::hbond_sc, sfxn_, w_fa_elec_, w_hbond_bb_sc_, and w_hbond_sc_.

set_exact()

void protocols::ligand_docking::ga_ligand_dock::GridScorer::set_exact ( bool  exactin )

inline

References exact_.

set_force_exact_min()

void protocols::ligand_docking::ga_ligand_dock::GridScorer::set_force_exact_min ( bool  setting )

inline

References force_exact_min_.

set_grid_dim_with_maxRad()

void protocols::ligand_docking::ga_ligand_dock::GridScorer::set_grid_dim_with_maxRad

(

core::Real

inval

)

References bbox_padding_, dims_, lig_com_, maxRad_, origin_, protocols::ligand_docking::ga_ligand_dock::TR(), and voxel_spacing_.

set_hash_gridding()

void protocols::ligand_docking::ga_ligand_dock::GridScorer::set_hash_gridding ( core::Real  hash_gridding_in )

inline

References hash_grid_.

set_hash_subgridding()

void protocols::ligand_docking::ga_ligand_dock::GridScorer::set_hash_subgridding ( core::Size  hash_subgridding_in )

inline

References hash_subgrid_.

set_maxiter_minimize()

void protocols::ligand_docking::ga_ligand_dock::GridScorer::set_maxiter_minimize ( core::Size  setting )

inline

References maxiter_minimize_.

set_out_of_bound_e()

void protocols::ligand_docking::ga_ligand_dock::GridScorer::set_out_of_bound_e ( core::Real  setting )

inline

References out_of_bound_e_.

set_packer_cycles()

void protocols::ligand_docking::ga_ligand_dock::GridScorer::set_packer_cycles ( core::Size  setting )

inline

References packer_cycles_.

set_smoothing()

bool protocols::ligand_docking::ga_ligand_dock::GridScorer::set_smoothing

(

core::Real

setting

)

References coeffs_farep_, do_convolution_and_compute_coeffs(), raw_farep_, smoothing_, and protocols::ligand_docking::ga_ligand_dock::TR().

set_voxel_spacing()

void protocols::ligand_docking::ga_ligand_dock::GridScorer::set_voxel_spacing ( core::Real  voxel_spacing_in )

inline

References voxel_spacing_.

set_w_rep()

void protocols::ligand_docking::ga_ligand_dock::GridScorer::set_w_rep ( core::Real  setting )

inline

References w_rep_.

Referenced by optimize().

Member Data Documentation

bbox_padding_

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::bbox_padding_

private

Referenced by get_padding(), GridScorer(), is_residue_in_grid(), prepare_grid(), set_bbox_padding(), and set_grid_dim_with_maxRad().

cartbonded_

core::energy_methods::CartesianBondedEnergyOP protocols::ligand_docking::ga_ligand_dock::GridScorer::cartbonded_

private

Referenced by derivatives(), get_1b_energy(), GridScorer(), and score().

coeffs_faatr_

std::map< int, ObjexxFCL::FArray3D< float > > protocols::ligand_docking::ga_ligand_dock::GridScorer::coeffs_faatr_

private

Referenced by calculate_grid(), derivatives(), get_1b_energy(), and point_energy().

coeffs_faelec_

ObjexxFCL::FArray3D< float > protocols::ligand_docking::ga_ligand_dock::GridScorer::coeffs_faelec_

private

Referenced by calculate_grid(), derivatives(), get_1b_energy(), and point_energy().

coeffs_farep_

std::map< int, ObjexxFCL::FArray3D< float > > protocols::ligand_docking::ga_ligand_dock::GridScorer::coeffs_farep_

private

Referenced by calculate_grid(), derivatives(), get_1b_energy(), point_clash_energy(), point_energy(), and set_smoothing().

coeffs_fasol_

std::map< int, ObjexxFCL::FArray3D< float > > protocols::ligand_docking::ga_ligand_dock::GridScorer::coeffs_fasol_

private

Referenced by calculate_grid(), derivatives(), get_1b_energy(), and point_energy().

coeffs_lkball_

std::map< int, ObjexxFCL::FArray3D< float > > protocols::ligand_docking::ga_ligand_dock::GridScorer::coeffs_lkball_

private

Referenced by calculate_grid(), derivatives(), and get_1b_energy().

coeffs_lkbridge_

std::map< int, ObjexxFCL::FArray3D< float > > protocols::ligand_docking::ga_ligand_dock::GridScorer::coeffs_lkbridge_

private

Referenced by calculate_grid(), derivatives(), and get_1b_energy().

coulomb_

core::scoring::etable::coulomb::CoulombOP protocols::ligand_docking::ga_ligand_dock::GridScorer::coulomb_

private

Referenced by calculate_grid(), derivatives(), get_2b_energy(), and GridScorer().

debug_

bool protocols::ligand_docking::ga_ligand_dock::GridScorer::debug_

private

Referenced by get_debug(), GridScorer(), optimize(), score(), and set_debug().

dims_

numeric::xyzVector< core::Size > protocols::ligand_docking::ga_ligand_dock::GridScorer::dims_

private

Referenced by calculate_grid(), GridScorer(), is_residue_in_grid(), move_to_boundary(), prepare_grid(), and set_grid_dim_with_maxRad().

elec_scale_

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::elec_scale_

private

Referenced by get_elec_scale().

etable_

core::scoring::etable::Etable protocols::ligand_docking::ga_ligand_dock::GridScorer::etable_

private

Referenced by calculate_grid(), derivatives(), and get_2b_energy().

exact_

bool protocols::ligand_docking::ga_ligand_dock::GridScorer::exact_

private

Referenced by get_exact(), GridScorer(), minimizer_loop(), optimize(), score(), and set_exact().

force_exact_min_

bool protocols::ligand_docking::ga_ligand_dock::GridScorer::force_exact_min_

private

Referenced by GridScorer(), optimize(), and set_force_exact_min().

has_cst_energies_

bool protocols::ligand_docking::ga_ligand_dock::GridScorer::has_cst_energies_

private

Referenced by derivatives(), get_2b_energy(), and GridScorer().

hash_grid_

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::hash_grid_

private

Referenced by calculate_grid(), GridScorer(), and set_hash_gridding().

hash_subgrid_

core::Size protocols::ligand_docking::ga_ligand_dock::GridScorer::hash_subgrid_

private

Referenced by calculate_grid(), GridScorer(), and set_hash_subgridding().

hb_database_

core::scoring::hbonds::HBondDatabaseCOP protocols::ligand_docking::ga_ligand_dock::GridScorer::hb_database_

private

Referenced by get_1b_energy(), get_2b_energy(), and GridScorer().

hbacceptors_

GridHash3D<hbAcc> protocols::ligand_docking::ga_ligand_dock::GridScorer::hbacceptors_

private

Referenced by calculate_grid(), derivatives(), and get_1b_energy().

hbdonors_

GridHash3D<hbDon> protocols::ligand_docking::ga_ligand_dock::GridScorer::hbdonors_

private

Referenced by calculate_grid(), derivatives(), and get_1b_energy().

lig_com_

numeric::xyzVector< core::Real > protocols::ligand_docking::ga_ligand_dock::GridScorer::lig_com_

private

Referenced by calculate_pocket_density_correlation(), get_ligand_com(), GridScorer(), prepare_grid(), and set_grid_dim_with_maxRad().

ligids_

utility::vector1< core::Size > protocols::ligand_docking::ga_ligand_dock::GridScorer::ligids_

private

Referenced by packer_loop(), prepare_grid(), and score().

LK_fade_

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::LK_fade_

private

Referenced by derivatives(), get_1b_energy(), and GridScorer().

LKBe_

core::scoring::lkball::LK_BallEnergyOP protocols::ligand_docking::ga_ligand_dock::GridScorer::LKBe_

private

Referenced by derivatives(), get_2b_energy(), and GridScorer().

maxdis_

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::maxdis_

private

Referenced by calculate_grid(), and GridScorer().

maxiter_minimize_

core::Size protocols::ligand_docking::ga_ligand_dock::GridScorer::maxiter_minimize_

private

Referenced by get_maxiterminimize(), GridScorer(), minimizer_loop(), optimize(), and set_maxiter_minimize().

maxRad_

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::maxRad_

private

Referenced by calculate_pocket_density_correlation(), get_maxRad(), GridScorer(), prepare_grid(), and set_grid_dim_with_maxRad().

min_time_

std::chrono::duration<core::Real> protocols::ligand_docking::ga_ligand_dock::GridScorer::min_time_

private

Referenced by GridScorer(), optimize(), and report_and_reset_timers().

origin_

numeric::xyzVector< core::Real > protocols::ligand_docking::ga_ligand_dock::GridScorer::origin_

private

Referenced by calculate_grid(), derivatives(), get_1b_energy(), is_point_in_grid(), is_residue_in_grid(), point_clash_energy(), point_energy(), prepare_grid(), and set_grid_dim_with_maxRad().

out_of_bound_e_

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::out_of_bound_e_

private

Referenced by GridScorer(), move_to_boundary(), and set_out_of_bound_e().

pack_time_

std::chrono::duration<core::Real> protocols::ligand_docking::ga_ligand_dock::GridScorer::pack_time_

private

Referenced by GridScorer(), optimize(), and report_and_reset_timers().

packer_cycles_

core::Size protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_cycles_

private

Referenced by get_packer_cycles(), GridScorer(), packer_loop(), and set_packer_cycles().

raw_faatr_

std::map< int, ObjexxFCL::FArray3D< float > > protocols::ligand_docking::ga_ligand_dock::GridScorer::raw_faatr_

private

Referenced by calculate_grid(), has_atom_type(), and point_energy().

raw_faelec_

ObjexxFCL::FArray3D< float > protocols::ligand_docking::ga_ligand_dock::GridScorer::raw_faelec_

private

Referenced by calculate_grid().

raw_farep_

std::map< int, ObjexxFCL::FArray3D< float > > protocols::ligand_docking::ga_ligand_dock::GridScorer::raw_farep_

private

Referenced by calculate_grid(), and set_smoothing().

raw_fasol_

std::map< int, ObjexxFCL::FArray3D< float > > protocols::ligand_docking::ga_ligand_dock::GridScorer::raw_fasol_

private

Referenced by calculate_grid().

raw_lkball_

std::map< int, ObjexxFCL::FArray3D< float > > protocols::ligand_docking::ga_ligand_dock::GridScorer::raw_lkball_

private

Referenced by calculate_grid().

raw_lkbridge_

std::map< int, ObjexxFCL::FArray3D< float > > protocols::ligand_docking::ga_ligand_dock::GridScorer::raw_lkbridge_

private

Referenced by calculate_grid().

ref_pose_

core::pose::PoseOP protocols::ligand_docking::ga_ligand_dock::GridScorer::ref_pose_

private

Referenced by density_score(), packer_loop(), prepare_grid(), score(), and score_init().

sfxn_

core::scoring::ScoreFunctionOP protocols::ligand_docking::ga_ligand_dock::GridScorer::sfxn_

private

Referenced by calculate_grid(), derivatives(), get_1b_energy(), get_2b_energy(), get_sfxn(), GridScorer(), minimizer_loop(), point_clash_energy(), point_energy(), score(), score_init(), and set_elec_scale().

sfxn_1b_

core::scoring::ScoreFunctionOP protocols::ligand_docking::ga_ligand_dock::GridScorer::sfxn_1b_

private

Referenced by derivatives(), dof_derivative(), get_1b_energy(), GridScorer(), point_clash_energy(), and score_init().

sfxn_1b_clash_

core::scoring::ScoreFunctionOP protocols::ligand_docking::ga_ligand_dock::GridScorer::sfxn_1b_clash_

private

Referenced by GridScorer().

sfxn_1b_soft_

core::scoring::ScoreFunctionOP protocols::ligand_docking::ga_ligand_dock::GridScorer::sfxn_1b_soft_

private

Referenced by density_score(), get_1b_energy(), GridScorer(), point_clash_energy(), and score_init().

sfxn_cart_

core::scoring::ScoreFunctionOP protocols::ligand_docking::ga_ligand_dock::GridScorer::sfxn_cart_

private

Referenced by derivatives(), get_1b_energy(), GridScorer(), and score().

sfxn_clash_

core::scoring::ScoreFunctionOP protocols::ligand_docking::ga_ligand_dock::GridScorer::sfxn_clash_

private

Referenced by GridScorer().

sfxn_cst_

core::scoring::ScoreFunctionOP protocols::ligand_docking::ga_ligand_dock::GridScorer::sfxn_cst_

private

Referenced by derivatives(), get_2b_energy(), and GridScorer().

sfxn_soft_

core::scoring::ScoreFunctionOP protocols::ligand_docking::ga_ligand_dock::GridScorer::sfxn_soft_

private

Referenced by get_1b_energy(), get_2b_energy(), GridScorer(), point_clash_energy(), point_energy(), and score().

smoothing_

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::smoothing_

private

Referenced by get_smoothing(), GridScorer(), and set_smoothing().

uniq_atoms_

std::map< int, core::conformation::Atom > protocols::ligand_docking::ga_ligand_dock::GridScorer::uniq_atoms_

private

Referenced by calculate_grid(), get_grid_all_atomtypes(), and get_grid_atomtypes().

voxel_spacing_

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::voxel_spacing_

private

Referenced by calculate_grid(), derivatives(), do_convolution_and_compute_coeffs(), get_1b_energy(), get_voxel_spacing(), GridScorer(), is_point_in_grid(), is_residue_in_grid(), move_to_boundary(), point_clash_energy(), point_energy(), prepare_grid(), set_grid_dim_with_maxRad(), and set_voxel_spacing().

w_fa_elec_

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::w_fa_elec_

private

Referenced by GridScorer(), and set_elec_scale().

w_hbond_bb_sc_

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::w_hbond_bb_sc_

private

Referenced by GridScorer(), and set_elec_scale().

w_hbond_sc_

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::w_hbond_sc_

private

Referenced by GridScorer(), and set_elec_scale().

w_rep_

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::w_rep_

private

Referenced by derivatives(), get_w_rep(), GridScorer(), packer_loop(), score(), and set_w_rep().

---

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

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