Index A | B | C | D | E | F | G | I | L | M | N | O | P | R | S | T | U | V | W A acidic (openff.pablo.ccd.CcdCache.with_varied_protonation parameter), [1] (openff.pablo.residue.ResidueDefinition.vary_protonation parameter), [1] (openff.pablo.ResidueDefinition.vary_protonation parameter), [1] ACIDIC_PROTONS (in module openff.pablo.ccd.patches) add_dephosphorylated_5p_terminus() (in module openff.pablo.ccd.patches) add_disulfide_crosslink() (in module openff.pablo.ccd.patches) add_nh2_leaving_atom() (in module openff.pablo.ccd.patches) add_protonation_variants() (in module openff.pablo.ccd.patches) add_synonyms() (in module openff.pablo.ccd.patches) additional_definitions (openff.pablo.topology_from_pdb parameter), [1] anon_from_molecule() (openff.pablo.residue.ResidueDefinition class method) (openff.pablo.ResidueDefinition class method) anon_from_sdf() (openff.pablo.residue.ResidueDefinition class method) (openff.pablo.ResidueDefinition class method) anon_from_smiles() (openff.pablo.residue.ResidueDefinition class method) (openff.pablo.ResidueDefinition class method) anon_from_smiles_marked_leaving() (openff.pablo.residue.ResidueDefinition class method) (openff.pablo.ResidueDefinition class method) aromatic (openff.pablo.residue.AtomDefinition attribute) (openff.pablo.residue.BondDefinition attribute) atom1 (openff.pablo.residue.BondDefinition attribute) atom2 (openff.pablo.residue.BondDefinition attribute) ATOM_NAME_SYNONYMS (in module openff.pablo.ccd.patches) atom_names (openff.pablo.residue.ResidueDefinition.from_smiles parameter), [1] (openff.pablo.ResidueDefinition.from_smiles parameter), [1] AtomDefinition (class in openff.pablo.residue) atoms (openff.pablo.residue.ResidueDefinition attribute) (openff.pablo.ResidueDefinition attribute) atoms_bonded_to() (openff.pablo.residue.ResidueDefinition method) (openff.pablo.ResidueDefinition method) B basic (openff.pablo.ccd.CcdCache.with_varied_protonation parameter), [1] (openff.pablo.residue.ResidueDefinition.vary_protonation parameter), [1] (openff.pablo.ResidueDefinition.vary_protonation parameter), [1] BASIC_ATOMS (in module openff.pablo.ccd.patches) BondDefinition (class in openff.pablo.residue) bonds (openff.pablo.residue.ResidueDefinition attribute) (openff.pablo.ResidueDefinition attribute) bonds_to() (openff.pablo.residue.ResidueDefinition method) (openff.pablo.ResidueDefinition method) C cache_path (openff.pablo.ccd.CcdCache parameter), [1] canonical_name_to_atom (openff.pablo.residue.ResidueDefinition property) (openff.pablo.ResidueDefinition property) CcdCache (class in openff.pablo.ccd) charge (openff.pablo.residue.AtomDefinition attribute) chemical graph complete chemical graph complete molecular graph connected connectivity graph crosslink (openff.pablo.residue.ResidueDefinition attribute) (openff.pablo.residue.ResidueDefinition.from_capped_molecule parameter), [1] (openff.pablo.residue.ResidueDefinition.from_molecule parameter), [1] (openff.pablo.residue.ResidueDefinition.from_smiles parameter), [1] (openff.pablo.ResidueDefinition attribute) (openff.pablo.ResidueDefinition.from_capped_molecule parameter), [1] (openff.pablo.ResidueDefinition.from_molecule parameter), [1] (openff.pablo.ResidueDefinition.from_smiles parameter), [1] D delete_doubly_deprotonated_arginine() (in module openff.pablo.ccd.patches) deprotonated_at() (openff.pablo.residue.ResidueDefinition method) (openff.pablo.ResidueDefinition method) description (openff.pablo.residue.ResidueDefinition attribute) (openff.pablo.residue.ResidueDefinition.anon_from_molecule parameter), [1] (openff.pablo.residue.ResidueDefinition.anon_from_smiles parameter), [1] (openff.pablo.residue.ResidueDefinition.anon_from_smiles_marked_leaving parameter), [1] (openff.pablo.residue.ResidueDefinition.from_capped_molecule parameter), [1] (openff.pablo.residue.ResidueDefinition.from_molecule parameter), [1] (openff.pablo.residue.ResidueDefinition.from_smiles parameter), [1] (openff.pablo.ResidueDefinition attribute) (openff.pablo.ResidueDefinition.anon_from_molecule parameter), [1] (openff.pablo.ResidueDefinition.anon_from_smiles parameter), [1] (openff.pablo.ResidueDefinition.anon_from_smiles_marked_leaving parameter), [1] (openff.pablo.ResidueDefinition.from_capped_molecule parameter), [1] (openff.pablo.ResidueDefinition.from_molecule parameter), [1] (openff.pablo.ResidueDefinition.from_smiles parameter), [1] disambiguate_alt_ids() (in module openff.pablo.ccd.patches) DISULFIDE_BOND (in module openff.pablo.chem) E extra_definitions (openff.pablo.ccd.CcdCache parameter), [1] F file (openff.pablo.topology_from_pdb parameter), [1] fix_caps() (in module openff.pablo.ccd.patches) flipped() (openff.pablo.residue.BondDefinition method) format (openff.pablo.topology_from_pdb parameter), [1] from_capped_molecule() (openff.pablo.residue.ResidueDefinition class method) (openff.pablo.ResidueDefinition class method) from_molecule() (openff.pablo.residue.ResidueDefinition class method) (openff.pablo.ResidueDefinition class method) from_smiles() (openff.pablo.residue.ResidueDefinition class method) (openff.pablo.ResidueDefinition class method) G graph I ignore_synonym_clashes (openff.pablo.residue.ResidueDefinition.vary_protonation parameter), [1] (openff.pablo.ResidueDefinition.vary_protonation parameter), [1] is_anonymous (openff.pablo.residue.ResidueDefinition property) (openff.pablo.ResidueDefinition property) L leaving (openff.pablo.residue.AtomDefinition attribute) leaving atom leaving_atom_indices (openff.pablo.residue.ResidueDefinition.from_capped_molecule parameter), [1] (openff.pablo.ResidueDefinition.from_capped_molecule parameter), [1] leaving_atoms (openff.pablo.residue.ResidueDefinition.anon_from_smiles parameter), [1] (openff.pablo.residue.ResidueDefinition.from_smiles parameter), [1] (openff.pablo.ResidueDefinition.anon_from_smiles parameter), [1] (openff.pablo.ResidueDefinition.from_smiles parameter), [1] library_paths (openff.pablo.ccd.CcdCache parameter), [1] linking atom linking_bond (openff.pablo.residue.ResidueDefinition attribute) (openff.pablo.residue.ResidueDefinition.from_capped_molecule parameter), [1] (openff.pablo.residue.ResidueDefinition.from_molecule parameter), [1] (openff.pablo.residue.ResidueDefinition.from_smiles parameter), [1] (openff.pablo.ResidueDefinition attribute) (openff.pablo.ResidueDefinition.from_capped_molecule parameter), [1] (openff.pablo.ResidueDefinition.from_molecule parameter), [1] (openff.pablo.ResidueDefinition.from_smiles parameter), [1] M mapped_smiles (openff.pablo.residue.ResidueDefinition.from_smiles parameter), [1] (openff.pablo.ResidueDefinition.from_smiles parameter), [1] MissingAtomError module openff.pablo openff.pablo.ccd openff.pablo.ccd.patches openff.pablo.chem openff.pablo.exceptions openff.pablo.residue molecular graph molecule (openff.pablo.residue.ResidueDefinition.anon_from_molecule parameter), [1] (openff.pablo.residue.ResidueDefinition.from_capped_molecule parameter), [1] (openff.pablo.residue.ResidueDefinition.from_molecule parameter), [1] (openff.pablo.ResidueDefinition.anon_from_molecule parameter), [1] (openff.pablo.ResidueDefinition.from_capped_molecule parameter), [1] (openff.pablo.ResidueDefinition.from_molecule parameter), [1] N n_core_atoms (openff.pablo.residue.ResidueDefinition property) (openff.pablo.ResidueDefinition property) n_expected_atoms (openff.pablo.residue.ResidueDefinition property) (openff.pablo.ResidueDefinition property) name (openff.pablo.residue.AtomDefinition attribute) name_to_atom (openff.pablo.residue.ResidueDefinition property) (openff.pablo.ResidueDefinition property) names (openff.pablo.residue.AtomDefinition property) O openff.pablo module openff.pablo.ccd module openff.pablo.ccd.patches module openff.pablo.chem module openff.pablo.exceptions module openff.pablo.residue module order (openff.pablo.residue.BondDefinition attribute) P PabloError patch_his_sidechain_zwitterion() (in module openff.pablo.ccd.patches) patches (openff.pablo.ccd.CcdCache parameter), [1] PdbResidueMatchError PEPTIDE_BOND (in module openff.pablo.chem) PHOSPHODIESTER_BOND (in module openff.pablo.chem) preload (openff.pablo.ccd.CcdCache parameter), [1] product_crosslinks (openff.pablo.residue.ResidueDefinition.react parameter), [1] (openff.pablo.ResidueDefinition.react parameter), [1] product_descriptions (openff.pablo.residue.ResidueDefinition.react parameter), [1] (openff.pablo.ResidueDefinition.react parameter), [1] product_linking_bonds (openff.pablo.residue.ResidueDefinition.react parameter), [1] (openff.pablo.ResidueDefinition.react parameter), [1] product_residue_names (openff.pablo.residue.ResidueDefinition.react parameter), [1] (openff.pablo.ResidueDefinition.react parameter), [1] product_smarts (openff.pablo.residue.ResidueDefinition.react parameter), [1] (openff.pablo.ResidueDefinition.react parameter), [1] product_virtual_sites (openff.pablo.residue.ResidueDefinition.react parameter), [1] (openff.pablo.ResidueDefinition.react parameter), [1] protonated_at() (openff.pablo.residue.ResidueDefinition method) (openff.pablo.ResidueDefinition method) R react() (openff.pablo.residue.ResidueDefinition static method) (openff.pablo.ResidueDefinition static method) reactant_smarts (openff.pablo.residue.ResidueDefinition.react parameter), [1] (openff.pablo.ResidueDefinition.react parameter), [1] reactants (openff.pablo.residue.ResidueDefinition.react parameter), [1] (openff.pablo.ResidueDefinition.react parameter), [1] replace() (openff.pablo.residue.AtomDefinition method) (openff.pablo.residue.BondDefinition method) (openff.pablo.residue.ResidueDefinition method) (openff.pablo.ResidueDefinition method) residue_library (openff.pablo.topology_from_pdb parameter), [1] residue_name (openff.pablo.ccd.CcdCache.with_varied_protonation parameter), [1] (openff.pablo.residue.ResidueDefinition attribute) (openff.pablo.residue.ResidueDefinition.from_capped_molecule parameter), [1] (openff.pablo.residue.ResidueDefinition.from_molecule parameter), [1] (openff.pablo.residue.ResidueDefinition.from_smiles parameter), [1] (openff.pablo.ResidueDefinition attribute) (openff.pablo.ResidueDefinition.from_capped_molecule parameter), [1] (openff.pablo.ResidueDefinition.from_molecule parameter), [1] (openff.pablo.ResidueDefinition.from_smiles parameter), [1] ResidueDefinition (class in openff.pablo) (class in openff.pablo.residue) ResidueValidationError S set_hop3_leaving() (in module openff.pablo.ccd.patches) skip_errors (openff.pablo.residue.ResidueDefinition.vary_protonation parameter), [1] (openff.pablo.ResidueDefinition.vary_protonation parameter), [1] smiles (openff.pablo.residue.ResidueDefinition.anon_from_smiles parameter), [1] (openff.pablo.residue.ResidueDefinition.anon_from_smiles_marked_leaving parameter), [1] (openff.pablo.ResidueDefinition.anon_from_smiles parameter), [1] (openff.pablo.ResidueDefinition.anon_from_smiles_marked_leaving parameter), [1] STD_CCD_CACHE (in module openff.pablo) stereo (openff.pablo.residue.AtomDefinition attribute) (openff.pablo.residue.BondDefinition attribute) strip_linkless_leavers() (in module openff.pablo.ccd.patches) symbol (openff.pablo.residue.AtomDefinition attribute) synonyms (openff.pablo.residue.AtomDefinition attribute) T to_openff_molecule() (openff.pablo.residue.ResidueDefinition method) (openff.pablo.ResidueDefinition method) topology_from_pdb() (in module openff.pablo) U UnknownOrAmbiguousSerialInConectError use_canonical_names (openff.pablo.topology_from_pdb parameter), [1] V vary_protonation() (openff.pablo.residue.ResidueDefinition method) (openff.pablo.ResidueDefinition method) virtual_sites (openff.pablo.residue.ResidueDefinition attribute) (openff.pablo.residue.ResidueDefinition.anon_from_molecule parameter), [1] (openff.pablo.residue.ResidueDefinition.anon_from_smiles parameter), [1] (openff.pablo.residue.ResidueDefinition.anon_from_smiles_marked_leaving parameter), [1] (openff.pablo.residue.ResidueDefinition.from_capped_molecule parameter), [1] (openff.pablo.residue.ResidueDefinition.from_molecule parameter), [1] (openff.pablo.residue.ResidueDefinition.from_smiles parameter), [1] (openff.pablo.ResidueDefinition attribute) (openff.pablo.ResidueDefinition.anon_from_molecule parameter), [1] (openff.pablo.ResidueDefinition.anon_from_smiles parameter), [1] (openff.pablo.ResidueDefinition.anon_from_smiles_marked_leaving parameter), [1] (openff.pablo.ResidueDefinition.from_capped_molecule parameter), [1] (openff.pablo.ResidueDefinition.from_molecule parameter), [1] (openff.pablo.ResidueDefinition.from_smiles parameter), [1] visualize() (openff.pablo.residue.ResidueDefinition method) (openff.pablo.ResidueDefinition method) W with_() (openff.pablo.ccd.CcdCache method) with_defaults() (openff.pablo.residue.AtomDefinition class method) (openff.pablo.residue.BondDefinition class method) with_patch() (openff.pablo.ccd.CcdCache method) with_replaced() (openff.pablo.ccd.CcdCache method) with_synonyms() (openff.pablo.residue.ResidueDefinition method) (openff.pablo.ResidueDefinition method) with_varied_protonation() (openff.pablo.ccd.CcdCache method) with_virtual_sites() (openff.pablo.ccd.CcdCache method) with_vsite_water() (openff.pablo.ccd.CcdCache method) without() (openff.pablo.ccd.CcdCache method)