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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, core::Size const lig_resid)
 calulate the bounding box More...
 
void get_grid_atomtypes (utility::vector1< core::conformation::Residue > const &rsds)
 pass list of residue (acutually rsdtypes) to construct grids for More...
 
void get_grid_all_atomtypes ()
 
void calculate_grid (core::pose::Pose const &pose, core::Size const lig_resid, utility::vector1< core::Size > const &movingSCs)
 
core::Real score (LigandConformer const &lig, bool soft=false)
 calculate energies on the grid More...
 
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 soft=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, core::conformation::Residue const &res_j, core::scoring::lkball::LKB_ResidueInfoOP lkbrinfo_j, bool soft=false)
 get a residue:residue energy More...
 
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 clash_score (LigandConformer const &lig)
 
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 ()
 
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::Realget_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::scoring::methods::CartesianBondedEnergyOP cartbonded_
 
bool exact_
 
bool debug_
 
bool force_exact_min_
 
std::chrono::duration< core::Realmin_time_
 
std::chrono::duration< core::Realpack_time_
 
std::map< int,
core::conformation::Atom
uniq_atoms_
 
numeric::xyzVector< core::Realorigin_
 
core::Real bbox_padding_
 
core::Real voxel_spacing_
 
core::Real hash_grid_
 
core::Size hash_subgrid_
 
numeric::xyzVector< core::Sizedims_
 
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< hbDonhbdonors_
 
GridHash3D< hbAcchbacceptors_
 
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::Reallig_com_
 
core::Real maxRad_
 
core::Size ligid_
 

Detailed Description

Grid representation of scorefunction.

Constructor & Destructor Documentation

protocols::ligand_docking::ga_ligand_dock::GridScorer::GridScorer ( core::scoring::ScoreFunctionOP  sfxn)
protocols::ligand_docking::ga_ligand_dock::GridScorer::~GridScorer ( )

Member Function Documentation

void protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid ( core::pose::Pose const &  pose,
core::Size const  lig_resid,
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(), protocols::ligand_docking::ga_ligand_dock::atmInfo::atom, core::conformation::Residue::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(), 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(), 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, 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().

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::clash_score ( LigandConformer const &  lig)
void protocols::ligand_docking::ga_ligand_dock::GridScorer::debug_deriv ( core::pose::Pose pose,
LigandConformer const &  lig,
core::optimization::MinimizerMap min_map 
)
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_is_hydrogen(), core::conformation::Residue::atomic_charge(), core::chemical::element::B, cartbonded_, coeffs_faatr_, coeffs_faelec_, coeffs_farep_, coeffs_fasol_, coeffs_lkball_, coeffs_lkbridge_, core::pose::Pose::constraint_set(), coulomb_, core::id::D, core::scoring::hbonds::HBondDerivs::don_deriv, core::scoring::hbonds::HBEvalTuple::don_type(), protocols::ligand_docking::ga_ligand_dock::dxform_atr(), protocols::ligand_docking::ga_ligand_dock::dxform_rep(), 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::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, has_cst_energies_, 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_id(), 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::conformation::Residue::natoms(), core::conformation::Residue::nheavyatoms(), origin_, core::scoring::hbonds::HBondOptions::params_database_tag(), core::pose::Pose::residue(), core::pose::Pose::residue_data(), sfxn_, sfxn_1b_, sfxn_cart_, sfxn_cst_, 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().

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
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 
)
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().

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().

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().

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

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,
core::conformation::Residue const &  res_j,
core::scoring::lkball::LKB_ResidueInfoOP  lkbrinfo_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().

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

References debug_.

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

References elec_scale_.

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

References exact_.

void protocols::ligand_docking::ga_ligand_dock::GridScorer::get_grid_all_atomtypes ( )
void protocols::ligand_docking::ga_ligand_dock::GridScorer::get_grid_atomtypes ( utility::vector1< core::conformation::Residue > const &  rsds)
numeric::xyzVector< core::Real > protocols::ligand_docking::ga_ligand_dock::GridScorer::get_ligand_com ( )
inline

References lig_com_.

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

References maxiter_minimize_.

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

References maxRad_.

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

References packer_cycles_.

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

References bbox_padding_.

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

References sfxn_.

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

References smoothing_.

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

References w_rep_.

Referenced by optimize().

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

References raw_faatr_.

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_.

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
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
core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::minimizer_loop ( LigandConformer lig,
core::optimization::MinimizerOptions const &  minopt 
)
core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::move_to_boundary ( numeric::xyzVector< core::Real > &  idxX) const
private
core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::move_to_boundary ( numeric::xyzVector< core::Real > &  idxX,
numeric::xyzVector< core::Real > &  dpen 
)
private
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 
)
core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_loop ( LigandConformer lig,
utility::vector1< PlaceableRotamers > &  placeable_rotdb,
RotamerPairEnergies rotamer_energies 
)
core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::point_clash_energy ( numeric::xyzVector< core::Real X,
std::string  atype_in = "",
bool  soft = false 
)
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 
)
void protocols::ligand_docking::ga_ligand_dock::GridScorer::prepare_grid ( core::pose::Pose const &  pose,
core::Size const  lig_resid 
)
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_.

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

References bbox_padding_.

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

References debug_.

bool protocols::ligand_docking::ga_ligand_dock::GridScorer::set_elec_scale ( core::Real  setting)
void protocols::ligand_docking::ga_ligand_dock::GridScorer::set_exact ( bool  exactin)
inline

References exact_.

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

References force_exact_min_.

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

References hash_grid_.

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

References hash_subgrid_.

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

References maxiter_minimize_.

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

References out_of_bound_e_.

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

References packer_cycles_.

bool protocols::ligand_docking::ga_ligand_dock::GridScorer::set_smoothing ( core::Real  setting)
void protocols::ligand_docking::ga_ligand_dock::GridScorer::set_voxel_spacing ( core::Real  voxel_spacing_in)
inline

References voxel_spacing_.

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

References w_rep_.

Referenced by optimize().

Member Data Documentation

core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::bbox_padding_
private
core::scoring::methods::CartesianBondedEnergyOP protocols::ligand_docking::ga_ligand_dock::GridScorer::cartbonded_
private
std::map< int, ObjexxFCL::FArray3D< float > > protocols::ligand_docking::ga_ligand_dock::GridScorer::coeffs_faatr_
private
ObjexxFCL::FArray3D< float > protocols::ligand_docking::ga_ligand_dock::GridScorer::coeffs_faelec_
private
std::map< int, ObjexxFCL::FArray3D< float > > protocols::ligand_docking::ga_ligand_dock::GridScorer::coeffs_farep_
private
std::map< int, ObjexxFCL::FArray3D< float > > protocols::ligand_docking::ga_ligand_dock::GridScorer::coeffs_fasol_
private
std::map< int, ObjexxFCL::FArray3D< float > > protocols::ligand_docking::ga_ligand_dock::GridScorer::coeffs_lkball_
private
std::map< int, ObjexxFCL::FArray3D< float > > protocols::ligand_docking::ga_ligand_dock::GridScorer::coeffs_lkbridge_
private
core::scoring::etable::coulomb::CoulombOP protocols::ligand_docking::ga_ligand_dock::GridScorer::coulomb_
private
bool protocols::ligand_docking::ga_ligand_dock::GridScorer::debug_
private
numeric::xyzVector< core::Size > protocols::ligand_docking::ga_ligand_dock::GridScorer::dims_
private
core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::elec_scale_
private

Referenced by get_elec_scale().

core::scoring::etable::Etable protocols::ligand_docking::ga_ligand_dock::GridScorer::etable_
private
bool protocols::ligand_docking::ga_ligand_dock::GridScorer::exact_
private
bool protocols::ligand_docking::ga_ligand_dock::GridScorer::force_exact_min_
private
bool protocols::ligand_docking::ga_ligand_dock::GridScorer::has_cst_energies_
private
core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::hash_grid_
private
core::Size protocols::ligand_docking::ga_ligand_dock::GridScorer::hash_subgrid_
private
core::scoring::hbonds::HBondDatabaseCOP protocols::ligand_docking::ga_ligand_dock::GridScorer::hb_database_
private
GridHash3D<hbAcc> protocols::ligand_docking::ga_ligand_dock::GridScorer::hbacceptors_
private
GridHash3D<hbDon> protocols::ligand_docking::ga_ligand_dock::GridScorer::hbdonors_
private
numeric::xyzVector< core::Real > protocols::ligand_docking::ga_ligand_dock::GridScorer::lig_com_
private
core::Size protocols::ligand_docking::ga_ligand_dock::GridScorer::ligid_
private
core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::LK_fade_
private
core::scoring::lkball::LK_BallEnergyOP protocols::ligand_docking::ga_ligand_dock::GridScorer::LKBe_
private
core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::maxdis_
private

Referenced by calculate_grid(), and GridScorer().

core::Size protocols::ligand_docking::ga_ligand_dock::GridScorer::maxiter_minimize_
private
core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::maxRad_
private
std::chrono::duration<core::Real> protocols::ligand_docking::ga_ligand_dock::GridScorer::min_time_
private
numeric::xyzVector< core::Real > protocols::ligand_docking::ga_ligand_dock::GridScorer::origin_
private
core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::out_of_bound_e_
private
std::chrono::duration<core::Real> protocols::ligand_docking::ga_ligand_dock::GridScorer::pack_time_
private
core::Size protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_cycles_
private
std::map< int, ObjexxFCL::FArray3D< float > > protocols::ligand_docking::ga_ligand_dock::GridScorer::raw_faatr_
private
ObjexxFCL::FArray3D< float > protocols::ligand_docking::ga_ligand_dock::GridScorer::raw_faelec_
private

Referenced by calculate_grid().

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

Referenced by calculate_grid(), and set_smoothing().

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

Referenced by calculate_grid().

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

Referenced by calculate_grid().

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

Referenced by calculate_grid().

core::pose::PoseOP protocols::ligand_docking::ga_ligand_dock::GridScorer::ref_pose_
private
core::scoring::ScoreFunctionOP protocols::ligand_docking::ga_ligand_dock::GridScorer::sfxn_
private
core::scoring::ScoreFunctionOP protocols::ligand_docking::ga_ligand_dock::GridScorer::sfxn_1b_
private
core::scoring::ScoreFunctionOP protocols::ligand_docking::ga_ligand_dock::GridScorer::sfxn_1b_clash_
private

Referenced by clash_score(), and GridScorer().

core::scoring::ScoreFunctionOP protocols::ligand_docking::ga_ligand_dock::GridScorer::sfxn_1b_soft_
private
core::scoring::ScoreFunctionOP protocols::ligand_docking::ga_ligand_dock::GridScorer::sfxn_cart_
private
core::scoring::ScoreFunctionOP protocols::ligand_docking::ga_ligand_dock::GridScorer::sfxn_clash_
private

Referenced by GridScorer().

core::scoring::ScoreFunctionOP protocols::ligand_docking::ga_ligand_dock::GridScorer::sfxn_cst_
private
core::scoring::ScoreFunctionOP protocols::ligand_docking::ga_ligand_dock::GridScorer::sfxn_soft_
private
core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::smoothing_
private
std::map< int, core::conformation::Atom > protocols::ligand_docking::ga_ligand_dock::GridScorer::uniq_atoms_
private
core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::voxel_spacing_
private
core::Real protocols::ligand_docking::ga_ligand_dock::GridScorer::w_fa_elec_
private

Referenced by GridScorer(), and set_elec_scale().

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

Referenced by GridScorer().

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

Referenced by GridScorer().

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

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