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protocols::ligand_docking::ga_ligand_dock::GridScorer Member List

This is the complete list of members for protocols::ligand_docking::ga_ligand_dock::GridScorer, including all inherited members.

bbox_padding_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
calculate_grid(core::pose::Pose const &pose, utility::vector1< core::Size > const &lig_resnos, utility::vector1< core::Size > const &movingSCs)protocols::ligand_docking::ga_ligand_dock::GridScorer
calculate_ligand_density_correlation(int resid, core::conformation::Residue const &rsd, core::pose::Pose const &pose)protocols::ligand_docking::ga_ligand_dock::GridScorer
calculate_pocket_density_correlation(core::pose::Pose const &pose)protocols::ligand_docking::ga_ligand_dock::GridScorer
calculate_pose_density_correlation(core::pose::Pose const &pose)protocols::ligand_docking::ga_ligand_dock::GridScorer
cartbonded_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
coeffs_faatr_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
coeffs_faelec_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
coeffs_farep_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
coeffs_fasol_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
coeffs_lkball_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
coeffs_lkbridge_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
coulomb_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
debug_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
debug_deriv(core::pose::Pose &pose, LigandConformer const &lig, core::optimization::MinimizerMap &min_map)protocols::ligand_docking::ga_ligand_dock::GridScorer
density_score(LigandConformer const &lig)protocols::ligand_docking::ga_ligand_dock::GridScorer
derivatives(core::pose::Pose &pose, LigandConformer const &lig, core::optimization::MinimizerMap &min_map)protocols::ligand_docking::ga_ligand_dock::GridScorer
dims_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
do_convolution_and_compute_coeffs(ObjexxFCL::FArray3D< float > const &rawdata, ObjexxFCL::FArray3D< float > &smoothed_coeffs, core::Real smoothing, bool inverted=false)protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
dof_derivative(core::pose::Pose &pose, core::optimization::MinimizerMap &min_map, core::id::DOF_ID const &dof_id, core::id::TorsionID const &torsion_id)protocols::ligand_docking::ga_ligand_dock::GridScorer
elec_scale_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
etable_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
exact_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
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)protocols::ligand_docking::ga_ligand_dock::GridScorerinlineprivate
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)protocols::ligand_docking::ga_ligand_dock::GridScorerinlineprivate
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)protocols::ligand_docking::ga_ligand_dock::GridScorerinlineprivate
force_exact_min_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
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)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)protocols::ligand_docking::ga_ligand_dock::GridScorer
get_debug()protocols::ligand_docking::ga_ligand_dock::GridScorerinline
get_elec_scale()protocols::ligand_docking::ga_ligand_dock::GridScorerinline
get_exact()protocols::ligand_docking::ga_ligand_dock::GridScorerinline
get_grid_all_atomtypes()protocols::ligand_docking::ga_ligand_dock::GridScorer
get_grid_atomtypes(utility::vector1< core::conformation::Residue > const &rsds, utility::vector1< bool > const &sconly)protocols::ligand_docking::ga_ligand_dock::GridScorer
get_hbond_map(core::pose::Pose pose, core::Size const lig_resno)protocols::ligand_docking::ga_ligand_dock::GridScorer
get_ligand_com()protocols::ligand_docking::ga_ligand_dock::GridScorerinline
get_maxiterminimize()protocols::ligand_docking::ga_ligand_dock::GridScorerinline
get_maxRad()protocols::ligand_docking::ga_ligand_dock::GridScorerinline
get_packer_cycles()protocols::ligand_docking::ga_ligand_dock::GridScorerinline
get_padding()protocols::ligand_docking::ga_ligand_dock::GridScorerinline
get_sfxn() constprotocols::ligand_docking::ga_ligand_dock::GridScorerinline
get_smoothing()protocols::ligand_docking::ga_ligand_dock::GridScorerinline
get_voxel_spacing()protocols::ligand_docking::ga_ligand_dock::GridScorerinline
get_w_rep()protocols::ligand_docking::ga_ligand_dock::GridScorerinline
GridScorer(core::scoring::ScoreFunctionOP sfxn)protocols::ligand_docking::ga_ligand_dock::GridScorer
has_atom_type(int atype)protocols::ligand_docking::ga_ligand_dock::GridScorerinline
has_cst_energies_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
hash_grid_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
hash_subgrid_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
hb_database_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
hbacceptors_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
hbdonors_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
is_point_in_grid(numeric::xyzVector< core::Real > x) constprotocols::ligand_docking::ga_ligand_dock::GridScorer
is_residue_in_grid(core::conformation::Residue const &res, core::Real angle_buffer, core::Real padding_buffer) constprotocols::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) constprotocols::ligand_docking::ga_ligand_dock::GridScorer
lig_com_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
ligids_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
LK_fade_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
LKBe_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
maxdis_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
maxiter_minimize_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
maxRad_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
min_time_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
minimizer_loop(LigandConformer &lig, core::optimization::MinimizerOptions const &minopt)protocols::ligand_docking::ga_ligand_dock::GridScorer
move_to_boundary(numeric::xyzVector< core::Real > &idxX) constprotocols::ligand_docking::ga_ligand_dock::GridScorerprivate
move_to_boundary(numeric::xyzVector< core::Real > &idxX, numeric::xyzVector< core::Real > &dpen)protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
optimize(LigandConformer &lig, utility::vector1< core::Real > ramp_schedule, utility::vector1< PlaceableRotamers > &placeable_rotdb, RotamerPairEnergies &rot_energies)protocols::ligand_docking::ga_ligand_dock::GridScorer
origin_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
out_of_bound_e_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
pack_time_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
packer_cycles_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
packer_loop(LigandConformer &lig, utility::vector1< PlaceableRotamers > &placeable_rotdb, RotamerPairEnergies &rotamer_energies)protocols::ligand_docking::ga_ligand_dock::GridScorer
point_clash_energy(numeric::xyzVector< core::Real > X, std::string atype_in="", bool soft=false)protocols::ligand_docking::ga_ligand_dock::GridScorer
point_energy(numeric::xyzVector< core::Real > X, std::string atype_in="", core::Real weightelec_in=0.0)protocols::ligand_docking::ga_ligand_dock::GridScorer
prepare_grid(core::pose::Pose const &pose, utility::vector1< core::Size > const &lig_resnos)protocols::ligand_docking::ga_ligand_dock::GridScorer
raw_faatr_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
raw_faelec_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
raw_farep_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
raw_fasol_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
raw_lkball_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
raw_lkbridge_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
ref_pose_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
report_and_reset_timers(std::chrono::duration< core::Real > &pack_time, std::chrono::duration< core::Real > &min_time)protocols::ligand_docking::ga_ligand_dock::GridScorerinline
score(LigandConformer const &lig, bool soft=false)protocols::ligand_docking::ga_ligand_dock::GridScorer
score(core::pose::Pose &pose, LigandConformer const &lig, bool soft=false)protocols::ligand_docking::ga_ligand_dock::GridScorer
score_init(LigandConformer const &lig, bool soft=false, core::Real init_dens_weight=100)protocols::ligand_docking::ga_ligand_dock::GridScorer
score_init(core::pose::Pose &pose, LigandConformer const &lig, bool soft, core::Real init_dens_weight=100)protocols::ligand_docking::ga_ligand_dock::GridScorer
set_bbox_padding(core::Real bbox_padding_in)protocols::ligand_docking::ga_ligand_dock::GridScorerinline
set_debug(bool debugin)protocols::ligand_docking::ga_ligand_dock::GridScorerinline
set_elec_scale(core::Real setting)protocols::ligand_docking::ga_ligand_dock::GridScorer
set_exact(bool exactin)protocols::ligand_docking::ga_ligand_dock::GridScorerinline
set_force_exact_min(bool setting)protocols::ligand_docking::ga_ligand_dock::GridScorerinline
set_grid_dim_with_maxRad(core::Real inval)protocols::ligand_docking::ga_ligand_dock::GridScorer
set_hash_gridding(core::Real hash_gridding_in)protocols::ligand_docking::ga_ligand_dock::GridScorerinline
set_hash_subgridding(core::Size hash_subgridding_in)protocols::ligand_docking::ga_ligand_dock::GridScorerinline
set_maxiter_minimize(core::Size setting)protocols::ligand_docking::ga_ligand_dock::GridScorerinline
set_out_of_bound_e(core::Real setting)protocols::ligand_docking::ga_ligand_dock::GridScorerinline
set_packer_cycles(core::Size setting)protocols::ligand_docking::ga_ligand_dock::GridScorerinline
set_smoothing(core::Real setting)protocols::ligand_docking::ga_ligand_dock::GridScorer
set_voxel_spacing(core::Real voxel_spacing_in)protocols::ligand_docking::ga_ligand_dock::GridScorerinline
set_w_rep(core::Real setting)protocols::ligand_docking::ga_ligand_dock::GridScorerinline
sfxn_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
sfxn_1b_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
sfxn_1b_clash_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
sfxn_1b_soft_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
sfxn_cart_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
sfxn_clash_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
sfxn_cst_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
sfxn_soft_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
smoothing_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
uniq_atoms_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
voxel_spacing_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
w_fa_elec_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
w_hbond_bb_sc_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
w_hbond_sc_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
w_rep_protocols::ligand_docking::ga_ligand_dock::GridScorerprivate
~GridScorer()protocols::ligand_docking::ga_ligand_dock::GridScorer