BondDefinition — OpenFF Pablo 0.0.0.dev0+versionmissing documentation

class openff.pablo.residue.BondDefinition(atom1: str, atom2: str, order: int, aromatic: bool, stereo: Literal['E', 'Z'] | None)[source]

Bases: object

Description of a bond in a residue from the Chemical Component Dictionary (CCD).

Attributes

`atom1`	The canonical name of the first atom in this bond
`atom2`	The canonical name of the second atom in this bond
`order`	The bond order of this bond (1 for single bond, 2 for double bond, etc.)
`aromatic`	`True` if this bond is aromatic, `False` otherwise
`stereo`	The stereochemistry of this bond.

Constructor Methods

with_defaults

Construct a new bond definition, optionally using some default values.

Instance and Static Methods

`flipped`	The same bond, but with the atoms in the opposite order
`replace`	Return a copy of `self` with the specified attributes replaced.

aromatic: bool: True if this bond is aromatic, False otherwise

atom1: str: The canonical name of the first atom in this bond

atom2: str: The canonical name of the second atom in this bond

flipped() → Self[source]: The same bond, but with the atoms in the opposite order

order: int: The bond order of this bond (1 for single bond, 2 for double bond, etc.)

replace(*, atom1: str | __UNSET__ = __UNSET__(), atom2: str | __UNSET__ = __UNSET__(), order: int | __UNSET__ = __UNSET__(), aromatic: bool | __UNSET__ = __UNSET__(), stereo: Literal['E', 'Z'] | None | __UNSET__ = __UNSET__()) → Self[source]: Return a copy of self with the specified attributes replaced.

stereo: Literal['E', 'Z'] | None: The stereochemistry of this bond.

classmethod with_defaults(atom1: str, atom2: str, *, order: int = 1, aromatic: bool = False, stereo: Literal['E', 'Z'] | None = None) → Self[source]: Construct a new bond definition, optionally using some default values.