- a -

• A : protocols::comparative_modeling::features , protocols::features
• A3B_HBS_POST : core::chemical
• A3B_HBS_PRE : core::chemical
• A_MINOR : core::scoring::rna
• AA : core::enzymes
• aa_ala : core::chemical
• aa_arg : core::chemical
• aa_asn : core::chemical
• aa_asp : core::chemical
• aa_b3a : core::chemical
• aa_b3c : core::chemical
• aa_b3cisACHC : core::chemical
• aa_b3cisACPC : core::chemical
• aa_b3d : core::chemical
• aa_b3e : core::chemical
• aa_b3f : core::chemical
• aa_b3g : core::chemical
• aa_b3h : core::chemical
• aa_b3i : core::chemical
• aa_b3k : core::chemical
• aa_b3l : core::chemical
• aa_b3m : core::chemical
• aa_b3n : core::chemical
• aa_b3p : core::chemical
• aa_b3q : core::chemical
• aa_b3r : core::chemical
• aa_b3s : core::chemical
• aa_b3t : core::chemical
• aa_b3transACPC : core::chemical
• aa_b3v : core::chemical
• aa_b3w : core::chemical
• aa_b3y : core::chemical
• aa_cmp : core::scoring
• aa_composition : core::scoring
• aa_cys : core::chemical
• aa_dal : core::chemical
• aa_dan : core::chemical
• aa_dar : core::chemical
• aa_das : core::chemical
• aa_dcs : core::chemical
• aa_dgn : core::chemical
• aa_dgu : core::chemical
• aa_dhi : core::chemical
• aa_dil : core::chemical
• aa_dle : core::chemical
• aa_dly : core::chemical
• aa_dme : core::chemical
• aa_dph : core::chemical
• aa_dpr : core::chemical
• aa_dse : core::chemical
• aa_dth : core::chemical
• aa_dtr : core::chemical
• aa_dty : core::chemical
• aa_dva : core::chemical
• aa_gln : core::chemical
• aa_glu : core::chemical
• aa_gly : core::chemical
• aa_h2o : core::chemical
• aa_his : core::chemical
• aa_ile : core::chemical
• aa_leu : core::chemical
• aa_lys : core::chemical
• aa_met : core::chemical
• aa_none : core::chemical
• aa_phe : core::chemical
• aa_pro : core::chemical
• aa_repeat : core::scoring
• aa_ser : core::chemical
• aa_thr : core::chemical
• aa_trp : core::chemical
• aa_tyr : core::chemical
• aa_unk : core::chemical
• aa_unp : core::chemical
• aa_val : core::chemical
• aa_vrt : core::chemical
• abego : core::scoring
• ABEGO_index_A : core::scoring
• ABEGO_index_B : core::scoring
• ABEGO_index_COUNT : core::scoring
• ABEGO_index_E : core::scoring
• ABEGO_index_G : core::scoring
• ABEGO_index_INVALID : core::scoring
• ABEGO_index_O : core::scoring
• ABEGO_index_START : core::scoring
• ABOVE : core::chemical::rna
• above : core::sequence
• ABS : protocols::calc_taskop_filters
• Ac : core::chemical::element
• accept : protocols::hotspot_hashing
• accept_reject : protocols::moves
• ACCEPTED : protocols::monte_carlo
• ACETYL_SUGAR : core::chemical
• ACETYLAMINO_SUGAR : core::chemical
• ACETYLATED_NTERMINUS : core::chemical
• ACETYLATED_NTERMINUS_VARIANT : core::chemical
• ACETYLATION : core::chemical
• ACHIRAL_BACKBONE : core::chemical
• ACHIRAL_SIDECHAIN : core::chemical
• ADD : protocols::stepwise::monte_carlo::mover
• add_daemon : protocols::pack_daemon
• ADD_EDGE : protocols::legacy_sewing
• ADD_LOOP_RES : protocols::stepwise::monte_carlo::mover
• ADD_NEW : protocols::enzdes
• ADD_PREGENERATED : protocols::enzdes
• ADD_SUBMOTIF : protocols::stepwise::monte_carlo::mover
• ADDED_STRUCTURE_AS_INTENDED : protocols::optimize_weights
• ADDED_STRUCTURE_OPPOSITE_AS_INTENDED : protocols::optimize_weights
• ADDUCT : core::chemical
• ADDUCT_VARIANT : core::chemical
• Ag : core::chemical::element
• AHO_Scheme : protocols::antibody
• Al : core::chemical::element
• ALDONIC_ACID : core::chemical
• ALDONIC_ACID_VARIANT : core::chemical
• ALDOSE : core::chemical
• ALIGN_RMSD : protocols::stepwise::screener
• alignment : core::scoring
• ALIGNMENT_ANCHOR_RES : core::pose::full_model_info
• ALIPHATIC : core::chemical , core::chemical::rings
• all_chunks : protocols::hybridization
• ALL_DNA_TYPES_ON : core::pack::palette
• ALL_SASA : core::scoring::sasa
• ALL_STAGES : protocols::abinitio
• all_stats : protocols::moves
• AllBB : protocols::canonical_sampling
• AllChi : protocols::canonical_sampling
• ALLOW_ALTERNATE_BACKBONE_MATCHING : core::pack::palette
• ALPHA : core::chemical::rna , core::scoring::dna
• ALPHA6_LINKS : core::scoring::carbohydrates
• ALPHA_AA : core::chemical
• alpha_aa_rama_check : protocols::generalized_kinematic_closure::filter
• ALPHA_ATOM : core::chemical
• ALPHA_LINKS : core::scoring::carbohydrates
• ALPHA_SUGAR : core::chemical
• ALREADY_SYMMETRIZED : core::pack::task
• ALTERNATIVE_PROTONATION : core::chemical
• ALWAYS_CLEAR : protocols::forge::components::VLB_VallMemoryUsage
• Am : core::chemical::element
• AMINO_SUGAR : core::chemical
• anc_grandparent : core::chemical
• anc_greatgrandparent : core::chemical
• anc_parent : core::chemical
• ANCHOR_SUGAR : protocols::stepwise::screener
• AND : protocols::filters , protocols::task_operations
• and_logic : core::select::residue_selector
• ANDNOT : protocols::filters , protocols::task_operations
• angle_constraint : core::scoring
• angleA : protocols::jumping
• angleB : protocols::jumping
• ANISOU : core::io::pdb
• ANTI : core::chemical::rna , core::fragment::rna , core::scoring::carbohydrates
• AntibodyNumberingSchemeEnum_start : protocols::antibody
• AntibodyNumberingSchemeEnum_total : protocols::antibody
• AntibodyRegionEnum_start : protocols::antibody
• AntibodyRegionEnum_total : protocols::antibody
• antigen_region : protocols::antibody
• ANTIPARALLEL : core::chemical::rna
• ANY : core::fragment::rna , protocols::toolbox
• ANY_BASE_DOUBLET_ORIENTATION : core::chemical::rna
• ANY_BASE_EDGE : core::chemical::rna
• ANY_BASE_STACK_SIDE : core::chemical::rna
• ANY_CHI : core::chemical::rna
• ANY_LW_BASE_DOUBLET_ORIENTATION : core::chemical::rna
• ANY_PUCKER : core::chemical::rna
• ANY_TORSION : core::chemical::rna
• approximate_buried_unsat_penalty : core::scoring
• Ar : core::chemical::element
• ARAMID : core::chemical
• arg_cation_pi : core::scoring
• AROMATIC : core::chemical , core::chemical::rings
• AROMATIC_CARBON_WITH_FREE_VALENCE : core::chemical
• AROMATIC_HYDROGEN : core::chemical
• aromatic_restraint : core::scoring
• AromaticBond : core::chemical
• Aroop : protocols::antibody
• As : core::chemical::element
• aspartimide_penalty : core::scoring
• aspartimide_penalty_lr : core::scoring::methods
• At : core::chemical::element
• ATOM : core::io::pdb
• atom_pair_constraint : core::scoring
• atom_pair_distance : protocols::generalized_kinematic_closure::filter
• ATOM_TREE_FILE : protocols::jd2::JobInputterInputSource
• ATR_REP : protocols::stepwise::screener
• ATTEN_2 : core::scoring::sc
• ATTEN_6 : core::scoring::sc
• ATTEN_BLOCKER : core::scoring::sc
• ATTEN_BURIED_FLAGGED : core::scoring::sc
• Au : core::chemical::element
• AUTHOR : core::io::pdb
• AUTOMATIC : core::conformation
• AXIAL : core::chemical::rings