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protocols::ligand_docking::LigandDockProtocol Member List

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

add_start_from(core::Real x, core::Real y, core::Real z)protocols::ligand_docking::LigandDockProtocol
append_ligand_docking_scores(core::pose::Pose const &before, core::pose::Pose const &after, core::scoring::ScoreFunctionCOP scorefxn, std::map< std::string, core::Real > &scores, protocols::toolbox::match_enzdes_util::EnzConstraintIOCOP constraint_io=nullptr) const protocols::ligand_docking::LigandDockProtocol
apply(core::pose::Pose &pose) overrideprotocols::ligand_docking::LigandDockProtocolvirtual
bb_interface_cutoff_protocols::ligand_docking::LigandBaseProtocolprotected
choose_desired_centroid(core::pose::Pose const &pose, core::Size jump_id, utility::vector1< core::Vector >)protocols::ligand_docking::LigandBaseProtocolprotected
classic_protocol(core::pose::Pose &pose, int jump_id, core::scoring::ScoreFunctionOP scorefxn, protocols::moves::MonteCarloOP monteCarlo, core::Size num_cycles, core::Size repack_every_Nth) const protocols::ligand_docking::LigandDockProtocolprivate
clear_info()protocols::moves::Moverinlinevirtual
clone() const protocols::moves::Movervirtual
create()protocols::moves::Movervirtual
find_interface_backbone(core::pose::Pose const &pose, int jump_id, core::Real cutoff_dist, utility::vector1< bool > &is_interface, utility::vector1< bool > &is_around_interface) const protocols::ligand_docking::LigandBaseProtocolprotected
find_interface_rsds(core::pose::Pose const &pose, int jump_id, core::Real padding, ObjexxFCL::FArray1D_bool &is_interface) const protocols::ligand_docking::LigandBaseProtocolprotected
fresh_instance() const protocols::moves::Movervirtual
get_additional_output()protocols::moves::Movervirtual
get_current_job() const protocols::moves::Mover
get_current_tag() const protocols::moves::Moverinline
get_input_pose() const protocols::moves::Mover
get_last_move_status() const protocols::moves::Mover
get_ligand_id(core::pose::Pose const &pose)protocols::ligand_docking::LigandBaseProtocolstatic
get_ligand_id(core::pose::Pose const &pose, core::Size jump_id)protocols::ligand_docking::LigandBaseProtocolstatic
get_ligand_jump_id(core::pose::Pose const &pose)protocols::ligand_docking::LigandBaseProtocolstatic
get_name() const overrideprotocols::ligand_docking::LigandDockProtocolvirtual
get_native_pose() const protocols::moves::Mover
get_non_bb_clashing_rotamers(core::pose::Pose const &pose, core::Size seqpos, core::scoring::ScoreFunctionCOP scofx, utility::vector1< core::conformation::ResidueCOP > &accepted_rotamers) const protocols::ligand_docking::LigandBaseProtocol
get_scorefxn()protocols::ligand_docking::LigandBaseProtocol
get_scorefxn() const protocols::ligand_docking::LigandBaseProtocol
get_self_ptr() const protocols::moves::Moverinline
get_self_ptr()protocols::moves::Moverinline
get_self_weak_ptr() const protocols::moves::Moverinline
get_self_weak_ptr()protocols::moves::Moverinline
get_type() const protocols::moves::Moverinline
hard_scorefxn_protocols::ligand_docking::LigandBaseProtocolprotected
info()protocols::moves::Moverinlinevirtual
info() const protocols::moves::Moverinlinevirtual
last_proposal_density_ratio()protocols::moves::Moverinlinevirtual
ligand_chi_stddev_deg_protocols::ligand_docking::LigandDockProtocolprivate
ligand_protonation_protocols::ligand_docking::LigandDockProtocolprivate
ligand_shear_moves_protocols::ligand_docking::LigandDockProtocolprivate
ligand_tether_stddev_Ang_protocols::ligand_docking::LigandDockProtocolprivate
ligand_torsion_restraints_protocols::ligand_docking::LigandDockProtocolprivate
LigandBaseProtocol()protocols::ligand_docking::LigandBaseProtocol
LigandDockProtocol()protocols::ligand_docking::LigandDockProtocol
LigandDockProtocol(std::string const &protocol, bool const minimize_ligand, bool const minimize_backbone, bool const tether_ligand, bool const mutate_same_name3, core::Real const ligand_chi_stddev_deg, core::Real const protein_CA_stddev_Ang, core::Real const ligand_tether_stddev_Ang_=-1, core::Size const ligand_shear_moves=0)protocols::ligand_docking::LigandDockProtocol
LigandDockProtocol(LigandDockProtocol const &)=deleteprotocols::ligand_docking::LigandDockProtocolprivate
make_dockmcm_mover(core::pose::Pose const &pose, int jump_id, protocols::moves::MoverOP repack_mover, protocols::moves::MoverOP rigbod_mover, core::kinematics::MoveMapOP movemap, core::scoring::ScoreFunctionOP scorefxn, protocols::moves::MonteCarloOP monteCarlo) const protocols::ligand_docking::LigandDockProtocolprivate
make_movemap(core::pose::Pose const &pose, core::Size jump_id, core::Real sc_padding, bool include_all_rsds, bool include_backbone, bool include_ligands, bool include_water) const protocols::ligand_docking::LigandBaseProtocolprotected
make_packer_task(core::pose::Pose const &pose, ObjexxFCL::FArray1D_bool const &allow_repack, bool ligand_protonation) const protocols::ligand_docking::LigandBaseProtocolprotected
make_packer_task(core::pose::Pose const &pose, int jump_id, core::Real sc_padding, bool include_all_rsds, bool ligand_protonation) const protocols::ligand_docking::LigandBaseProtocolprotected
make_packer_task_ligand_only(core::pose::Pose const &pose, int jump_id, bool ligand_protonation) const protocols::ligand_docking::LigandBaseProtocolprotected
make_tweaked_scorefxn(std::string const &weights_tag, bool estat_exclude_protein, bool estat_upweight, bool hbonds_downweight)protocols::ligand_docking::LigandBaseProtocolprotected
minimize_all_rsds_protocols::ligand_docking::LigandDockProtocolprivate
minimize_backbone_protocols::ligand_docking::LigandDockProtocolprivate
minimize_ligand_protocols::ligand_docking::LigandDockProtocolprivate
minimize_water_protocols::ligand_docking::LigandDockProtocolprivate
move_ligand_to_desired_centroid(core::pose::Pose &pose, core::Size jump_id, utility::vector1< core::Vector > start_from_pts)protocols::ligand_docking::LigandBaseProtocolprotected
move_ligand_to_desired_centroid(core::pose::Pose &pose, core::Size jump_id, core::Vector desired_centroid)protocols::ligand_docking::LigandBaseProtocolprotected
Mover()protocols::moves::Mover
Mover(std::string const &type_name)protocols::moves::Mover
name()protocols::moves::Moverinlinestatic
optimize_orientation3(core::pose::Pose &pose, int jump_id, core::Size lig_id)protocols::ligand_docking::LigandDockProtocolprivate
parse_my_tag(TagCOP tag, basic::datacache::DataMap &data)protocols::moves::Movervirtual
Pose typedefprotocols::moves::Mover
PoseCOP typedefprotocols::moves::Mover
protein_CA_stddev_Ang_protocols::ligand_docking::LigandDockProtocolprivate
protocol_protocols::ligand_docking::LigandDockProtocolprivate
provide_citation_info(basic::citation_manager::CitationCollectionList &) const protocols::moves::Movervirtual
random_conformer(core::pose::Pose &pose) const protocols::ligand_docking::LigandDockProtocolprivate
register_options()protocols::moves::Moverinlinestatic
reinitialize_for_each_job() const protocols::moves::Movervirtual
reinitialize_for_new_input() const protocols::moves::Movervirtual
reorder_foldtree_around_mobile_regions(core::pose::Pose &pose, core::Size const &jump_id, utility::vector1< bool > const &mobile_bb, core::Size const &lig_id) const protocols::ligand_docking::LigandBaseProtocol
repack_all_rsds_protocols::ligand_docking::LigandDockProtocolprivate
reset_status()protocols::moves::Mover
restrain_ligand_chis(core::pose::Pose &pose)protocols::ligand_docking::LigandDockProtocolprivate
restrain_ligand_nbr_atom(core::pose::Pose &pose, core::Size lig_id, core::Real stddev_Angstroms) const protocols::ligand_docking::LigandBaseProtocolprotected
restrain_protein_Calphas(core::pose::Pose &pose, utility::vector1< bool > const &is_restrained, core::scoring::func::FuncOP restr_func) const protocols::ligand_docking::LigandBaseProtocol
rottrials_all_rsds_protocols::ligand_docking::LigandDockProtocolprivate
sc_interface_padding_protocols::ligand_docking::LigandBaseProtocolprotected
scorefxn_protocols::ligand_docking::LigandBaseProtocolprotected
set_current_job(protocols::jobdist::BasicJobCOP job)protocols::moves::Mover
set_current_tag(std::string const &new_tag)protocols::moves::Moverinlinevirtual
set_input_pose(PoseCOP pose)protocols::moves::Movervirtual
set_last_move_status(MoverStatus status)protocols::moves::Moverprotected
set_native_pose(PoseCOP pose)protocols::moves::Movervirtual
set_type(std::string const &setting)protocols::moves::Moverinline
setup_bbmin_foldtree(core::pose::Pose &pose, core::Size const &jump_id, core::Real cutoff_dist, core::Real stddev_Angstroms)protocols::ligand_docking::LigandBaseProtocolprotected
shared_from_this()protocols::ligand_docking::LigandDockProtocolinline
shear_min_protocol(core::pose::Pose &pose, int jump_id, core::scoring::ScoreFunctionOP scorefxn, protocols::moves::MonteCarloOP monteCarlo, core::Size num_cycles) const protocols::ligand_docking::LigandDockProtocolprivate
show(std::ostream &output=std::cout) const protocols::moves::Movervirtual
soft_scorefxn_protocols::ligand_docking::LigandBaseProtocolprotected
start_from_pts_protocols::ligand_docking::LigandDockProtocolprivate
Strings typedefprotocols::moves::Mover
TagCOP typedefprotocols::moves::Mover
test_move(Pose &pose)protocols::moves::Moverinlinevirtual
tether_ligand_protocols::ligand_docking::LigandDockProtocolprivate
type(const std::string &type_in)protocols::moves::Moverinline
type() const protocols::moves::Moverinline
unboundrot_protocols::ligand_docking::LigandBaseProtocolprotected
use_soft_rep_protocols::ligand_docking::LigandBaseProtocolprotected
~LigandBaseProtocol() overrideprotocols::ligand_docking::LigandBaseProtocol
~LigandDockProtocol() overrideprotocols::ligand_docking::LigandDockProtocol