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protocols::ligand_docking::ga_ligand_dock::LigandAligner Member List

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

apply(LigandConformer &lig)protocols::ligand_docking::ga_ligand_dock::LigandAligner
assign_neighbors(numeric::xyzVector< core::Real > point, core::Size neighborhood_size=27)protocols::ligand_docking::ga_ligand_dock::LigandAlignerprivate
check_voxel_distance_to_receptor(numeric::xyzVector< core::Real > voxel, core::pose::Pose const &pose, core::Size const ligid)protocols::ligand_docking::ga_ligand_dock::LigandAlignerprivate
chi_step_protocols::ligand_docking::ga_ligand_dock::LigandAlignerprivate
erode_points(utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > selected_points, core::Size neighborhood_size=27)protocols::ligand_docking::ga_ligand_dock::LigandAlignerprivate
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::LigandAlignerprivate
find_biggest_skeleton(utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > eroded_points)protocols::ligand_docking::ga_ligand_dock::LigandAlignerprivate
find_network(numeric::xyzVector< core::Real > start_point, utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > network, utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > eroded_points)protocols::ligand_docking::ga_ligand_dock::LigandAlignerprivate
gridStep_protocols::ligand_docking::ga_ligand_dock::LigandAlignerprivate
is_point_in_network(numeric::xyzVector< core::Real > point, utility::vector1< utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > > networks)protocols::ligand_docking::ga_ligand_dock::LigandAlignerprivate
is_point_in_search_group(utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > selected_points, numeric::xyzVector< core::Real > point_to_compare)protocols::ligand_docking::ga_ligand_dock::LigandAlignerprivate
istruct_protocols::ligand_docking::ga_ligand_dock::LigandAlignerprivate
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::LigandAlignerprivate
perturb_lig(core::pose::Pose &pose, utility::vector1< core::Size > ligid)protocols::ligand_docking::ga_ligand_dock::LigandAlignerprivate
points_to_search() constprotocols::ligand_docking::ga_ligand_dock::LigandAlignerinline
points_to_search_protocols::ligand_docking::ga_ligand_dock::LigandAlignerprivate
prealigned_input(bool setting)protocols::ligand_docking::ga_ligand_dock::LigandAlignerinline
prealigned_input() constprotocols::ligand_docking::ga_ligand_dock::LigandAlignerinline
prealigned_input_protocols::ligand_docking::ga_ligand_dock::LigandAlignerprivate
randomize_lig(core::pose::Pose &pose, utility::vector1< core::Size > ligid, numeric::xyzVector< core::Real > const &T)protocols::ligand_docking::ga_ligand_dock::LigandAlignerprivate
refine_input(bool setting)protocols::ligand_docking::ga_ligand_dock::LigandAlignerinline
refine_input_protocols::ligand_docking::ga_ligand_dock::LigandAlignerprivate
rot_step_protocols::ligand_docking::ga_ligand_dock::LigandAlignerprivate
sample_ring_conformers() constprotocols::ligand_docking::ga_ligand_dock::LigandAlignerinline
sample_ring_conformers_protocols::ligand_docking::ga_ligand_dock::LigandAlignerprivate
select_points(core::pose::Pose const &pose, core::Size const ligid, core::Real skeleton_threshold_const=2.5, core::Size neighborhood_size=27)protocols::ligand_docking::ga_ligand_dock::LigandAligner
set_chi_step(core::Size chi_step_in)protocols::ligand_docking::ga_ligand_dock::LigandAlignerinline
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::LigandAlignerprivate
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) constprotocols::ligand_docking::ga_ligand_dock::LigandAlignerprivate
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::LigandAlignerinline
set_sample_ring_conformers(bool const setting)protocols::ligand_docking::ga_ligand_dock::LigandAlignerinline
set_sf(GridScorerOP sf_in)protocols::ligand_docking::ga_ligand_dock::LigandAlignerinline
set_target(ConstraintInfo const &tgt_in)protocols::ligand_docking::ga_ligand_dock::LigandAlignerinline
set_trans_step(core::Size trans_step_in)protocols::ligand_docking::ga_ligand_dock::LigandAlignerinline
set_use_pharmacophore(bool setting)protocols::ligand_docking::ga_ligand_dock::LigandAlignerinline
sf_protocols::ligand_docking::ga_ligand_dock::LigandAlignerprivate
target_protocols::ligand_docking::ga_ligand_dock::LigandAlignerprivate
trans_step_protocols::ligand_docking::ga_ligand_dock::LigandAlignerprivate
use_pharmacophore() constprotocols::ligand_docking::ga_ligand_dock::LigandAlignerinline
use_pharmacophore_protocols::ligand_docking::ga_ligand_dock::LigandAlignerprivate
weighted_score_ij_protocols::ligand_docking::ga_ligand_dock::LigandAlignerprivate