Atom

---

bigsmiles.data_structures.bigsmiles.Atom(id_, symbol, isotope=None, stereo=None, hydrogens=None, charge=0, valence=None, class_=None, parent=None, **kwargs)

this class represents an atom

ATTRIBUTE	DESCRIPTION
id_	id of atom (id is limited to atoms). Range: [1, inf] TYPE: int
symbol	symbol symbol (e.g., H, C, O, Zn) TYPE: str
isotope	isotope (e.g., [13C]) TYPE: int | None
stereo	stereochemistry [None, "@", "@@"] (None means not defined) TYPE: str | None
hydrogens	number of explict hydrogens (e.g., [CH2]) TYPE: int | None
charge	symbol charge (e.g., [Fe+3]) TYPE: int
valence	The capacity to form bonds with other atoms TYPE: int
class_	index of class (e.g., [C:1] class_ = 1) TYPE: int | None
parent	the owner of the atom TYPE: BigSMILES | Branch | StochasticFragment | None
kwargs	any additional keyword arguments are accepted and set as additional attributes

bond_capacity: float property

total capacity of the atom account for charge

bonds: list[Bond] property writable

list of bonds (excludes implicit hydrogens)

bonds_available: float property

number bonds that remain open for bonding

details: str property

long string representation

full_valence: bool property

returns true if the atom valence is full

implicit_hydrogens: float property

number of implicit hydrogens. (zero if explict hydrogens have been specified)

number_of_bonds: float property

number of bonds already formed (not including implicit hydrogens; but including explicit hydrogens)

ring_indexes: list[int] property

list of ring index

root: BigSMILES property

the owner at the top of the parent tree

__eq__(other)

equality is based on the following parameters:

• id_
• symbol
• isotope
• stereo
• hydrogens
• charge
• valence
• aromatic
• bonds ~ bond.id_

delete_bond(delete_bond)

delete bond or bonds

PARAMETER	DESCRIPTION
delete_bond	TYPE: Bond | list[Bond]