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protocols::enzdes::SecondaryMatchProtocol Member List

This is the complete list of members for protocols::enzdes::SecondaryMatchProtocol, including all inherited members.

add_enz_cst_interaction_to_pose(core::pose::Pose &pose, toolbox::match_enzdes_util::EnzConstraintParametersCOP params, toolbox::match_enzdes_util::EnzCstTemplateResCOP missing_template, toolbox::match_enzdes_util::EnzCstTemplateResCOP present_template, toolbox::match_enzdes_util::EnzConstraintIOCOP cstio)protocols::enzdes::SecondaryMatchProtocolprotected
add_pregenerated_enzdes_constraints(core::pose::Pose &pose) constprotocols::enzdes::EnzdesBaseProtocol
apply(core::pose::Pose &start_pose) overrideprotocols::enzdes::SecondaryMatchProtocolvirtual
atoms_to_superimpose_on_protocols::enzdes::EnzdesBaseProtocolprivate
bb_backrub_protocols::enzdes::EnzdesBaseProtocolprivate
bb_interface_cutoff() constprotocols::ligand_docking::LigandBaseProtocolinlineprotected
bb_interface_cutoff_protocols::ligand_docking::LigandBaseProtocolprivate
bb_min_protocols::enzdes::EnzdesBaseProtocolprivate
bb_min_allowed_dev_protocols::enzdes::EnzdesBaseProtocolprivate
catalytic_res(core::pose::Pose const &pose) constprotocols::enzdes::EnzdesBaseProtocol
chi_min_protocols::enzdes::EnzdesBaseProtocolprivate
choose_desired_centroid(core::pose::Pose const &pose, core::Size jump_id, utility::vector1< core::Vector >)protocols::ligand_docking::LigandBaseProtocolprotected
clear_info()protocols::moves::Moverinlinevirtual
clone() constprotocols::moves::Movervirtual
constraint_weights_protocols::enzdes::EnzdesBaseProtocolprivate
create()protocols::moves::Movervirtual
create_enzdes_movemap(core::pose::Pose &pose, core::pack::task::PackerTaskCOP task, bool min_all_jumps=false)protocols::enzdes::EnzdesBaseProtocol
create_enzdes_pack_task(core::pose::Pose &pose, bool design=true)protocols::enzdes::EnzdesBaseProtocol
cst_minimize(core::pose::Pose &pose, core::pack::task::PackerTaskCOP task, bool cst_opt=false)protocols::enzdes::EnzdesBaseProtocol
current_job_protocols::moves::Moverprivate
current_tag_protocols::moves::Moverprivate
cut1_protocols::enzdes::SecondaryMatchProtocolprivate
cut2_protocols::enzdes::SecondaryMatchProtocolprivate
cut3_protocols::enzdes::SecondaryMatchProtocolprivate
cut4_protocols::enzdes::SecondaryMatchProtocolprivate
design_targets(core::pose::Pose const &pose) constprotocols::enzdes::EnzdesBaseProtocol
design_targets_protocols::enzdes::EnzdesBaseProtocolmutableprotected
design_targets_score(core::pose::Pose const &pose) constprotocols::enzdes::EnzdesBaseProtocol
determine_found_residues_compatibility(core::pose::PoseCOP ref_poseCOP)protocols::enzdes::SecondaryMatchProtocolprotected
disable_constraint_scoreterms()protocols::enzdes::EnzdesBaseProtocolprotected
do_matching(core::pose::Pose &start_pose)protocols::enzdes::SecondaryMatchProtocol
enable_constraint_scoreterms()protocols::enzdes::EnzdesBaseProtocolprotected
enzdes_pack(core::pose::Pose &pose, core::pack::task::PackerTaskCOP, core::scoring::ScoreFunctionCOP scorefxn, core::Size cycles, bool minimize_after_packing, bool pack_unconstrained, bool favor_native)protocols::enzdes::EnzdesBaseProtocol
EnzdesBaseProtocol()protocols::enzdes::EnzdesBaseProtocol
exchange_ligands_in_pose(core::pose::Pose &pose, bool check_bb_clashes, core::scoring::ScoreFunctionCOP scofx)protocols::enzdes::EnzdesBaseProtocolprotected
exclude_protein_protein_fa_elec_protocols::enzdes::EnzdesBaseProtocolprivate
find_all_allowed_positions(core::pose::Pose const &pose)protocols::enzdes::SecondaryMatchProtocolprotected
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) constprotocols::ligand_docking::LigandBaseProtocolprotected
find_interface_rsds(core::pose::Pose const &pose, int jump_id, core::Real padding, ObjexxFCL::FArray1D_bool &is_interface) constprotocols::ligand_docking::LigandBaseProtocolprotected
fix_catalytic_aa_protocols::enzdes::EnzdesBaseProtocolprivate
found_res_compatibility_protocols::enzdes::SecondaryMatchProtocolprivate
found_res_compatibility_determined_protocols::enzdes::SecondaryMatchProtocolprivate
found_resis_protocols::enzdes::SecondaryMatchProtocolprivate
fresh_instance() constprotocols::moves::Movervirtual
generate_and_dump_pose_found_residues_combinations(core::pose::PoseCOP ref_poseCOP)protocols::enzdes::SecondaryMatchProtocolprotected
generate_explicit_ligand_rotamer_poses(core::pose::Pose const &orig_pose, utility::vector1< core::pose::PoseOP > &ligrot_poses, core::scoring::ScoreFunctionCOP scofx)protocols::enzdes::EnzdesBaseProtocol
get_additional_output()protocols::moves::Movervirtual
get_current_job() constprotocols::moves::Mover
get_current_tag() constprotocols::moves::Moverinline
get_input_pose() constprotocols::moves::Mover
get_last_move_status() constprotocols::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::enzdes::SecondaryMatchProtocolvirtual
get_native_pose() constprotocols::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) constprotocols::ligand_docking::LigandBaseProtocol
get_scorefxn()protocols::ligand_docking::LigandBaseProtocol
get_scorefxn() constprotocols::ligand_docking::LigandBaseProtocol
get_self_ptr() constprotocols::moves::Moverinline
get_self_ptr()protocols::moves::Moverinline
get_self_weak_ptr() constprotocols::moves::Moverinline
get_self_weak_ptr()protocols::moves::Moverinline
get_type() constprotocols::moves::Moverinline
hard_scorefxn()protocols::ligand_docking::LigandBaseProtocolprotected
hard_scorefxn_protocols::ligand_docking::LigandBaseProtocolprivate
include_all_design_targets_in_design_interface_protocols::enzdes::EnzdesBaseProtocolprotected
info()protocols::moves::Moverinlinevirtual
info() constprotocols::moves::Moverinlinevirtual
info_protocols::moves::Moverprivate
initialize_scorefxns()protocols::ligand_docking::LigandBaseProtocolprivate
input_pose_protocols::moves::Moverprivate
is_catalytic_position(core::pose::Pose const &pose, core::Size const seqpos) constprotocols::enzdes::EnzdesBaseProtocol
last_proposal_density_ratio()protocols::moves::Moverinlinevirtual
last_status_protocols::moves::Moverprivate
lig_min_stddev_protocols::enzdes::EnzdesBaseProtocolprivate
lig_superposition_file_read_protocols::enzdes::EnzdesBaseProtocolprivate
LigandBaseProtocol()protocols::ligand_docking::LigandBaseProtocol
loop_bb_min_allowed_dev_protocols::enzdes::EnzdesBaseProtocolprivate
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) constprotocols::ligand_docking::LigandBaseProtocolprotected
make_packer_task(core::pose::Pose const &pose, ObjexxFCL::FArray1D_bool const &allow_repack, bool ligand_protonation) constprotocols::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) constprotocols::ligand_docking::LigandBaseProtocolprotected
make_packer_task_ligand_only(core::pose::Pose const &pose, int jump_id, bool ligand_protonation) constprotocols::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
match_params_protocols::enzdes::SecondaryMatchProtocolprivate
min_all_jumps_protocols::enzdes::EnzdesBaseProtocolprivate
minimize_all_ligand_torsions_protocols::enzdes::EnzdesBaseProtocolprivate
minimize_ligand_torsions_protocols::enzdes::EnzdesBaseProtocolprivate
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
native_needs_load() constprotocols::enzdes::EnzdesBaseProtocolprotected
native_needs_load_protocols::enzdes::EnzdesBaseProtocolprivate
native_pose_protocols::moves::Moverprivate
parse_my_tag(TagCOP tag, basic::datacache::DataMap &data)protocols::moves::Movervirtual
Pose typedefprotocols::moves::Mover
PoseCOP typedefprotocols::moves::Mover
provide_citation_info(basic::citation_manager::CitationCollectionList &) constprotocols::moves::Movervirtual
rb_min_protocols::enzdes::EnzdesBaseProtocolprivate
rb_min_jumps() constprotocols::enzdes::EnzdesBaseProtocol
rb_min_jumps(utility::vector1< core::Size > const)protocols::enzdes::EnzdesBaseProtocol
rb_min_jumps_protocols::enzdes::EnzdesBaseProtocolprivate
read_ligand_superposition_file(std::string filename)protocols::enzdes::EnzdesBaseProtocolprivate
reduced_scofx_protocols::enzdes::SecondaryMatchProtocolprivate
reduced_scorefxn() constprotocols::enzdes::EnzdesBaseProtocol
reduced_scorefxn()protocols::enzdes::EnzdesBaseProtocol
reduced_sfxn_protocols::enzdes::EnzdesBaseProtocolprotected
register_options()protocols::enzdes::EnzdesBaseProtocolstatic
reinitialize_for_each_job() constprotocols::moves::Movervirtual
reinitialize_for_new_input() constprotocols::moves::Movervirtual
remap_resid(core::pose::Pose const &pose, core::id::SequenceMapping const &smap)protocols::enzdes::EnzdesBaseProtocolvirtual
remove_enzdes_constraints(core::pose::Pose &pose, bool keep_covalent) constprotocols::enzdes::EnzdesBaseProtocol
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) constprotocols::ligand_docking::LigandBaseProtocol
res_to_superimpose_protocols::enzdes::EnzdesBaseProtocolprivate
reset_status()protocols::moves::Mover
residues_compatible(core::conformation::ResidueCOP res1, core::conformation::ResidueCOP res2) constprotocols::enzdes::SecondaryMatchProtocol
restrain_ligand_nbr_atom(core::pose::Pose &pose, core::Size lig_id, core::Real stddev_Angstroms) constprotocols::ligand_docking::LigandBaseProtocolprotected
restrain_protein_Calphas(core::pose::Pose &pose, utility::vector1< bool > const &is_restrained, core::scoring::func::FuncOP restr_func)protocols::ligand_docking::LigandBaseProtocol
restype_possible_at_position(core::pose::Pose const &pose, core::chemical::ResidueTypeCOP restype, core::conformation::ResidueCOP target_residue, core::Size const trial_pos)protocols::enzdes::SecondaryMatchProtocolprotected
restype_set() constprotocols::enzdes::EnzdesBaseProtocolinline
restype_set_protocols::enzdes::EnzdesBaseProtocolprivate
rosetta_electrostatics_protocols::ligand_docking::LigandBaseProtocolprivate
sc_interface_padding() constprotocols::ligand_docking::LigandBaseProtocolinlineprotected
sc_interface_padding_protocols::ligand_docking::LigandBaseProtocolprivate
scorefxn()protocols::ligand_docking::LigandBaseProtocolprotected
scorefxn_protocols::ligand_docking::LigandBaseProtocolprivate
scorefxns_initialized_protocols::ligand_docking::LigandBaseProtocolprivate
SecondaryMatchProtocol()protocols::enzdes::SecondaryMatchProtocol
set_all_jumps_minimizable(bool const &setting)protocols::enzdes::EnzdesBaseProtocolinline
set_bb_interface_cutoff(core::Real const setting)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_fix_cataa(bool const &setting)protocols::enzdes::EnzdesBaseProtocolinline
set_input_pose(PoseCOP pose)protocols::moves::Movervirtual
set_last_move_status(MoverStatus status)protocols::moves::Moverprotected
set_minimize_options(bool const &min_sc, bool const &min_bb, bool const &min_rb, bool const &min_lig, bool backrub=false)protocols::enzdes::EnzdesBaseProtocolinline
set_native_needs_load(bool const setting)protocols::enzdes::EnzdesBaseProtocolprotected
set_native_pose(PoseCOP pose)protocols::moves::Movervirtual
set_sc_interface_padding(core::Real const setting)protocols::ligand_docking::LigandBaseProtocolprotected
set_scorefxn(core::scoring::ScoreFunctionCOP scorefxn)protocols::enzdes::EnzdesBaseProtocol
protocols::ligand_docking::LigandBaseProtocol::set_scorefxn(core::scoring::ScoreFunctionCOP const &sfxn_in)protocols::ligand_docking::LigandBaseProtocolprotected
set_trial_positions(utility::vector1< core::Size > const &trial_pos)protocols::enzdes::SecondaryMatchProtocolinline
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
setup_bbmin_ft_and_csts(core::pose::Pose &pose, utility::vector1< bool > allow_move_bb, core::Size jump_id)protocols::enzdes::EnzdesBaseProtocol
setup_enzdes_constraints(core::pose::Pose &pose, bool allow_missing_remark_blocks) constprotocols::enzdes::EnzdesBaseProtocolprotected
setup_sequence_recovery_cache(core::pose::Pose &pose, core::pack::task::PackerTask const &task) constprotocols::enzdes::EnzdesBaseProtocol
shared_from_this()protocols::ligand_docking::LigandBaseProtocolinline
show(std::ostream &output=std::cout) constprotocols::moves::Movervirtual
soft_scorefxn()protocols::ligand_docking::LigandBaseProtocolprotected
soft_scorefxn_protocols::ligand_docking::LigandBaseProtocolprivate
Strings typedefprotocols::moves::Mover
TagCOP typedefprotocols::moves::Mover
test_move(Pose &pose)protocols::moves::Moverinlinevirtual
trial_positions_protocols::enzdes::SecondaryMatchProtocolprivate
type(const std::string &type_in)protocols::moves::Moverinline
type() constprotocols::moves::Moverinline
type_protocols::moves::Moverprivate
unboundrot()protocols::ligand_docking::LigandBaseProtocolprotected
unboundrot_protocols::ligand_docking::LigandBaseProtocolprivate
use_soft_rep() constprotocols::ligand_docking::LigandBaseProtocolinlineprotected
use_soft_rep_protocols::ligand_docking::LigandBaseProtocolprivate
~LigandBaseProtocol() overrideprotocols::ligand_docking::LigandBaseProtocol
~SecondaryMatchProtocol() overrideprotocols::enzdes::SecondaryMatchProtocol