| apply(LigandConformer &lig) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | |
| chi_step_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| estimate_nstruct_sample(core::pose::Pose const &pose, utility::vector1< core::Size > const &ligids, core::Size const ntotal) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | |
| faster_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| istruct_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| LigandAligner() | protocols::ligand_docking::ga_ligand_dock::LigandAligner | |
| LigandAligner(bool use_pharmacophore, utility::vector1< core::Size > const &movable_scs, bool faster) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | |
| movable_scs_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| perturb_lig(core::pose::Pose &pose, utility::vector1< core::Size > ligid) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| randomize_lig(core::pose::Pose &pose, utility::vector1< core::Size > ligid, numeric::xyzVector< core::Real > const &T) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| refine_input(bool setting) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | inline |
| refine_input_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| rot_step_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| set_chi_step(core::Size chi_step_in) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | inline |
| set_constraints(core::pose::Pose &pose, utility::vector1< core::Size > ligids, utility::vector1< std::pair< core::Size, core::Size > > &marked_pairs, core::Real const w_prior=1.0, utility::vector1< core::Size > const &SrcPriorIDs=utility::vector1< core::Size >(), utility::vector1< core::Size > const &TgtPriorIDs=utility::vector1< core::Size >()) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| set_hard_constraint_on_marked(core::pose::Pose &pose, utility::vector1< core::Size > ligid, utility::vector1< std::pair< core::Size, core::Size > > const &marked_pairs) const | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| set_pharmacophore_reference(core::pose::Pose const &pose) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | |
| set_rot_step(core::Size rot_step_in) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | inline |
| set_sf(GridScorerOP sf_in) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | inline |
| set_target(ConstraintInfo const &tgt_in) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | inline |
| set_trans_step(core::Size trans_step_in) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | inline |
| set_use_pharmacophore(bool setting) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | inline |
| sf_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| target_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| trans_step_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| use_pharmacophore() const | protocols::ligand_docking::ga_ligand_dock::LigandAligner | inline |
| use_pharmacophore_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| weighted_score_ij_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
1.8.7