Rosetta Protocols  2014.35
protocols::motif_grafting::movers::MotifGraftMover Member List

This is the complete list of members for protocols::motif_grafting::movers::MotifGraftMover, including all inherited members.

apply(Pose &)protocols::motif_grafting::movers::MotifGraftMovervirtual
protocols::moves::Mover::apply(core::io::serialization::PipeMap &pmap)protocols::moves::Movervirtual
clear_info()protocols::moves::Moverinlinevirtual
clone() const protocols::motif_grafting::movers::MotifGraftMovervirtual
count_clashes_between_two_poses(core::pose::Pose const &p_A, core::pose::Pose const &p_B, core::Size clash_cutoff)protocols::motif_grafting::movers::MotifGraftMover
create()protocols::moves::Movervirtual
Filters_map typedefprotocols::moves::Mover
fragments_permutation_test_by_CA_distances(core::pose::Pose const &p_scaffold, core::pose::PoseOP const &p_motif_, utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > const &vv_scaffold_fragments_indexes, utility::vector1< std::pair< core::Size, core::Size > > const &v_motif_fragments_indexes, core::Real const &RMSD_tol, core::Size const &start_motif_num, utility::vector1< std::pair< core::Size, core::Size > > &buff_combVec, utility::vector1< motif2scaffold_data > &v_m2s_data)protocols::motif_grafting::movers::MotifGraftMover
fresh_instance() const protocols::moves::Movervirtual
generate_combinations_of_motif_fragments_by_delta_variation(core::pose::PoseOP const &p_motif_, utility::vector1< std::pair< long int, long int > > const &combinatory_fragment_size_delta, utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > &vv_resulting_permutations)protocols::motif_grafting::movers::MotifGraftMover
generate_match_pose(core::pose::Pose &target_pose, core::pose::Pose const &contextStructure, bool b_revert_graft_to_native_sequence, MotifMatch motif_match)protocols::motif_grafting::movers::MotifGraftMover
generate_scaffold_matches(core::pose::Pose &target_scaffold, core::pose::PoseOP &target_motif_, core::pose::PoseOP &target_contextStructure_)protocols::motif_grafting::movers::MotifGraftMover
get_additional_output()protocols::motif_grafting::movers::MotifGraftMovervirtual
get_bb_alignment_and_transformation(core::pose::Pose const &poseA, utility::vector1< core::Size > const &positions_to_alignA, core::pose::Pose const &poseB, utility::vector1< core::Size > const &positions_to_alignB, numeric::xyzMatrix< core::Real > &RotM, numeric::xyzVector< core::Real > &TvecA, numeric::xyzVector< core::Real > &TvecB)protocols::motif_grafting::movers::MotifGraftMover
get_bb_alignment_and_transformation_wTipsExtraInfo(utility::vector1< bool > const &v_isNorC, core::pose::Pose const &poseA, utility::vector1< core::Size > const &positions_to_alignA, core::pose::Pose const &poseB, utility::vector1< core::Size > const &positions_to_alignB, numeric::xyzMatrix< core::Real > &RotM, numeric::xyzVector< core::Real > &TvecA, numeric::xyzVector< core::Real > &TvecB, utility::vector1< core::Real > &RMSD_tip_elements)protocols::motif_grafting::movers::MotifGraftMover
get_bb_distance(core::pose::Pose const &poseA, utility::vector1< core::Size > const &positions_to_alignA, core::pose::Pose const &poseB, utility::vector1< core::Size > const &positions_to_alignB)protocols::motif_grafting::movers::MotifGraftMover
get_clash_score_from_pose(core::pose::Pose &p_input, core::scoring::ScoreFunctionOP const &scorefxn_)protocols::motif_grafting::movers::MotifGraftMover
get_current_job() const protocols::moves::Mover
get_current_tag() const protocols::moves::Moverinline
get_fragments_by_CA_distances_and_NCpoints_restrains(core::pose::Pose const &p_scaffold, core::pose::PoseOP const &p_motif_, utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > &vv_scaffold_fragments_indexes, utility::vector1< std::pair< core::Size, core::Size > > &v_motif_fragments_indexes, core::Real const &RMSD_tol, utility::vector1< std::pair< long int, long int > > const &max_fragment_replacement_size_delta, utility::vector1< std::pair< core::Size, core::Size > > const &v_motif_fragments_permutation, bool const &b_only_allow_if_N_point_match_aa_identity, bool const &b_only_allow_if_C_point_match_aa_identity, bool const &b_N_point_can_replace_proline, bool const &b_C_point_can_replace_proline)protocols::motif_grafting::movers::MotifGraftMover
get_input_pose() const protocols::moves::Mover
get_last_move_status() const protocols::moves::Mover
get_matching_fragments(core::pose::Pose const &target_scaffold, core::pose::PoseOP const &target_motif_, core::pose::PoseOP const &target_contextStructure_, core::Real const &RMSD_tol, core::Real const &NC_points_RMSD_tol, core::Size const &clash_cutoff, std::string const &clash_test_residue, utility::vector1< std::pair< long int, long int > > const &max_fragment_replacement_size_delta_, utility::vector1< std::pair< core::Size, core::Size > > const &combinatory_fragment_size_delta, utility::vector1< utility::vector1< core::Size > > const &vvr_hotspots, bool const &b_full_motif_bb_alignment, bool const &b_allow_independent_alignment_per_fragment, bool const &b_graft_only_hotspots_by_sidechain_replacement, bool const &b_only_allow_if_N_point_match_aa_identity, bool const &b_only_allow_if_C_point_match_aa_identity, std::priority_queue< MotifMatch > &pq)protocols::motif_grafting::movers::MotifGraftMover
get_mono_aa_pose_copy(core::pose::Pose const &p_input, std::string const &aminoacid_code)protocols::motif_grafting::movers::MotifGraftMover
get_motif_scaffold_superposition_and_RMSD(core::pose::Pose const &p_scaffold, core::pose::PoseOP const &p_motif_, core::Real const &RMSD_tol, core::Real const &tip_RMSD_tol, utility::vector1< utility::vector1< core::Size > > const &vvr_hotspots, bool const &b_full_motif_bb_alignment, bool const &b_allow_independent_alignment_per_fragment, bool const &b_graft_only_hotspots_by_sidechain_replacement, utility::vector1< motif2scaffold_data > &v_m2s_data)protocols::motif_grafting::movers::MotifGraftMover
get_name() const protocols::motif_grafting::movers::MotifGraftMoverinlinevirtual
get_native_pose() const protocols::moves::Mover
get_rotated_and_translated_pose(core::pose::Pose const &p_scaffold, numeric::xyzMatrix< core::Real > const &RotM, numeric::xyzVector< core::Real > const &TvecA, numeric::xyzVector< core::Real > const &TvecB)protocols::motif_grafting::movers::MotifGraftMover
get_type() const protocols::moves::Moverinline
gp_b_allow_independent_alignment_per_fragment_protocols::motif_grafting::movers::MotifGraftMoverprotected
gp_b_allow_repeat_same_graft_output_protocols::motif_grafting::movers::MotifGraftMoverprotected
gp_b_full_motif_bb_alignment_protocols::motif_grafting::movers::MotifGraftMoverprotected
gp_b_graft_only_hotspots_by_sidechain_replacement_protocols::motif_grafting::movers::MotifGraftMoverprotected
gp_b_is_first_run_protocols::motif_grafting::movers::MotifGraftMoverprotected
gp_b_only_allow_if_C_point_match_aa_identity_protocols::motif_grafting::movers::MotifGraftMoverprotected
gp_b_only_allow_if_N_point_match_aa_identity_protocols::motif_grafting::movers::MotifGraftMoverprotected
gp_b_revert_graft_to_native_sequence_protocols::motif_grafting::movers::MotifGraftMoverprotected
gp_i_clash_score_cutoff_protocols::motif_grafting::movers::MotifGraftMoverprotected
gp_p_contextStructure_protocols::motif_grafting::movers::MotifGraftMoverprotected
gp_p_motif_protocols::motif_grafting::movers::MotifGraftMoverprotected
gp_p_target_pose_protocols::motif_grafting::movers::MotifGraftMoverprotected
gp_r_NC_points_RMSD_tolerance_protocols::motif_grafting::movers::MotifGraftMoverprotected
gp_r_RMSD_tolerance_protocols::motif_grafting::movers::MotifGraftMoverprotected
gp_s_clash_test_residue_protocols::motif_grafting::movers::MotifGraftMoverprotected
gp_vp_combinatory_fragment_size_delta_protocols::motif_grafting::movers::MotifGraftMoverprotected
gp_vp_max_fragment_replacement_size_delta_protocols::motif_grafting::movers::MotifGraftMoverprotected
gp_vvr_hotspots_protocols::motif_grafting::movers::MotifGraftMoverprotected
info()protocols::moves::Moverinlinevirtual
info() const protocols::moves::Moverinlinevirtual
init_parameters(std::string const &s_contextStructure, std::string const &s_motif, core::Real const &r_RMSD_tolerance, core::Real const &r_NC_points_RMSD_tolerance, core::Size const &i_clash_score_cutoff, std::string const &s_combinatory_fragment_size_delta, std::string const &s_max_fragment_replacement_size_delta, std::string const &s_clash_test_residue, std::string const &s_hotspots, bool &b_full_motif_bb_alignment, bool const &b_allow_independent_alignment_per_fragment, bool const &b_graft_only_hotspots_by_sidechain_replacement, bool const &b_only_allow_if_N_point_match_aa_identity, bool const &b_only_allow_if_C_point_match_aa_identity, bool const &b_revert_graft_to_native_sequence, bool const &b_allow_repeat_same_graft_output)protocols::motif_grafting::movers::MotifGraftMover
join_two_poses_by_jump(core::pose::Pose const &p_A, core::pose::Pose const &p_B)protocols::motif_grafting::movers::MotifGraftMover
last_proposal_density_ratio()protocols::moves::Moverinlinevirtual
motif_match_results_protocols::motif_grafting::movers::MotifGraftMoverprotected
MotifGraftMover()protocols::motif_grafting::movers::MotifGraftMover
Mover()protocols::moves::Mover
Mover(std::string const &type_name)protocols::moves::Mover
Mover(Mover const &other)protocols::moves::Mover
name()protocols::moves::Moverinlinestatic
operator=(Mover const &other)protocols::moves::Mover
parse_def(utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)protocols::moves::Movervirtual
parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables(std::string const &s_contextStructure, std::string const &s_motif, core::Real const &r_RMSD_tolerance, core::Real const &r_NC_points_RMSD_tolerance, core::Size const &i_clash_score_cutoff, std::string const &s_combinatory_fragment_size_delta, std::string const &s_max_fragment_replacement_size_delta, std::string const &s_clash_test_residue, std::string const &s_hotspots, bool &b_full_motif_bb_alignment, bool const &b_allow_independent_alignment_per_fragment, bool const &b_graft_only_hotspots_by_sidechain_replacement, bool const &b_only_allow_if_N_point_match_aa_identity, bool const &b_only_allow_if_C_point_match_aa_identity, bool const &b_revert_graft_to_native_sequence, bool const &b_allow_repeat_same_graft_output)protocols::motif_grafting::movers::MotifGraftMover
parse_my_tag(utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)protocols::motif_grafting::movers::MotifGraftMovervirtual
parse_state(SerializableState const &state)protocols::moves::Movervirtual
permutate_n_vv_of_pairs(utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > const &vv_of_pairs, utility::vector1< std::pair< core::Size, core::Size > > &buff_combVec, core::Size start_index, utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > &vv_resulting_permutations)protocols::motif_grafting::movers::MotifGraftMover
Pose typedefprotocols::moves::Mover
PoseCOP typedefprotocols::moves::Mover
register_options()protocols::moves::Moverinlinestatic
reinitialize_for_each_job() const protocols::moves::Movervirtual
reinitialize_for_new_input() const protocols::moves::Movervirtual
reset_status()protocols::moves::Mover
save_state(SerializableState &state)protocols::moves::Movervirtual
set_current_job(protocols::jobdist::BasicJobCOP job)protocols::moves::Mover
set_current_tag(std::string const &new_tag)protocols::moves::Moverinline
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
show(std::ostream &output=std::cout) const protocols::moves::Movervirtual
stich_motif_in_scaffold_by_indexes_rotation_and_translation(core::pose::Pose const &p_scaffold, core::pose::Pose const &p_motif_, motif2scaffold_data &m2s_dat, bool const &skip_motif_extremes)protocols::motif_grafting::movers::MotifGraftMover
Strings typedefprotocols::moves::Mover
superposition_transform(core::Size natoms, ObjexxFCL::FArray1_double const &weights, ObjexxFCL::FArray2_double &ref_coords, ObjexxFCL::FArray2_double &coords, numeric::xyzMatrix< core::Real > &RotM, numeric::xyzVector< core::Real > &TvecA, numeric::xyzVector< core::Real > &TvecB)protocols::motif_grafting::movers::MotifGraftMover
TagCOP typedefprotocols::moves::Mover
test_epigraft_and_contextStructure_clashes(core::pose::Pose const &p_scaffold, core::pose::Pose const &p_motif_, core::pose::Pose const &p_contextStructure_, core::Size const &clash_cutoff, utility::vector1< motif2scaffold_data > &v_m2s_data)protocols::motif_grafting::movers::MotifGraftMover
test_move(Pose &pose)protocols::moves::Moverinlinevirtual
type() const protocols::moves::Moverinline
type(const std::string &type_in)protocols::moves::Moverinline
~MotifGraftMover()protocols::motif_grafting::movers::MotifGraftMover
~Mover()protocols::moves::Movervirtual