- class openff.pablo.residue.AtomDefinition(name: str, synonyms: tuple[str, ...], symbol: str, leaving: bool, charge: int, aromatic: bool, stereo: Literal['S', 'R'] | None)[source]
Bases:
objectDescription of an atom in a residue from the Chemical Component Dictionary (CCD).
Attributes
The canonical name of this atom
Other names this atom can have
The elemental symbol for this atom
Whether this atom is absent when a bond is formed between two residues.
The formal charge of this atom
Whether this atom is aromatic
The chirality of this atom
Constructor Methods
Construct a new atom definition, optionally using some default values.
Instance and Static Methods
Return a copy of
selfwith the specified attributes replaced.Properties
The set of the canonical name and all synonyms
- aromatic: bool
Whether this atom is aromatic
- charge: int
The formal charge of this atom
- leaving: bool
Whether this atom is absent when a bond is formed between two residues.
When a bond is formed between this residue and another, a “leaving fragment” must be removed to satisfy the valence model with the new bond. The leaving fragment is computed by identifying a single leaving atom bonded to each of the atoms forming the bond, as well as all leaving atoms bonded to those first leaving atoms.
- name: str
The canonical name of this atom
- replace(*, name: str | __UNSET__ = __UNSET__(), symbol: str | __UNSET__ = __UNSET__(), synonyms: Iterable[str] | __UNSET__ = __UNSET__(), leaving: bool | __UNSET__ = __UNSET__(), charge: int | __UNSET__ = __UNSET__(), aromatic: bool | __UNSET__ = __UNSET__(), stereo: Literal['S', 'R'] | None | __UNSET__ = __UNSET__()) Self[source]
Return a copy of
selfwith the specified attributes replaced.
- symbol: str
The elemental symbol for this atom