Index A | B | C | D | E | I | J | L | M | N | O | P | R | S | T | V A add() (Job method) alignment (Protein attribute) (RNA attribute) Atom (class in alphafold3_input) B Bond (class in alphafold3_input) bonds (Job attribute) C ccd (Job attribute) ccd() (in module alphafold3_input) component() (in module alphafold3_input) copies (DNA attribute) (Ligand attribute) (Protein attribute) (RNA attribute) D definition (Ligand attribute) DEL (Operation attribute) description (DNA attribute) (Ligand attribute) (Protein attribute) (RNA attribute) Dialect (class in alphafold3_input) dialect (Job attribute) DNA (class in alphafold3_input) (Entity attribute) E entities (Job attribute) entity (Atom attribute) Entity (class in alphafold3_input) export() (Job method) I I (Version attribute) id (DNA attribute) (Ligand attribute) (Protein attribute) (RNA attribute) II (Version attribute) III (Version attribute) indexes (Template attribute) INS (Operation attribute) IV (Version attribute) J Job (class in alphafold3_input) L Ligand (class in alphafold3_input) LIGAND (Entity attribute) load() (Job class method) LOCAL (Dialect attribute) M Modification (class in alphafold3_input) modifications (DNA attribute) (Protein attribute) (RNA attribute) modify() (DNA method) (Protein method) (RNA method) N name (Atom attribute) (Job attribute) O Operation (class in alphafold3_input) P position (Modification attribute) Protein (class in alphafold3_input) PROTEIN (Entity attribute) R realign() (in module alphafold3_input) REF (Operation attribute) reindex() (in module alphafold3_input) residue (Atom attribute) RNA (class in alphafold3_input) (Entity attribute) S save() (Job method) scope (Modification attribute) seeds (Job attribute) sequence (DNA attribute) (Protein attribute) (RNA attribute) SERVER (Dialect attribute) source (Bond attribute) structure (Template attribute) SUB (Operation attribute) T target (Bond attribute) Template (class in alphafold3_input) templates (Protein attribute) trace() (in module alphafold3_input) type (Modification attribute) V Version (class in alphafold3_input) version (Job attribute)