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SMILES Base

SMILES Base#

class autode.smiles.base.RingBond(idx_i, symbol, bond_idx=None)#

Dangling bond created when a ring is found

__init__(idx_i, symbol, bond_idx=None)#

Initialise the bond with a non-existent large index

Parameters:

  • symbol (str) – Symbol of this bond, in bond_order_symbols

  • bond_idx (None | int) – Index for this bond in the bond list

close(idx, symbol)#

Close this bond using an atom index

in_ring(rings_idxs)#

Is this bond a constituent of a ring

Return type:

(bool)

class autode.smiles.base.SMILESAtom(label: str, stereochem: SMILESStereoChem = SMILESStereoChem.NONE, n_hydrogens: int | None = None, charge: int = 0, atom_class: int | None = None)#

Atom in a SMILES string

__init__(label: str, stereochem: SMILESStereoChem = SMILESStereoChem.NONE, n_hydrogens: int | None = None, charge: int = 0, atom_class: int | None = None)#

SMILES atom initialised at the origin

determined implicitly

Parameters:

  • stereochem – Point stereochemistry around this atom (R, S)

  • charge – Formal charge on this atom

  • atom_class – Class of an atom. See §3.1.7 in the SMILES spec http://opensmiles.org/opensmiles.html

property has_stereochem#

Does this atom have associated stereochemistry?

invert_stereochem()#

Invert the stereochemistry at this centre

property is_aromatic#

Is this atom ‘aromatic’?

is_pi(valency: int = 0) → bool#

Determine if this atom is a ‘π-atom’ i.e. is unsaturated. Only approximate! Example:

>>> import autode as ade
>>> ade.Atom('C').is_pi(valency=3)
True
>>> ade.Atom('H').is_pi(valency=1)
False
Return type:

(bool)

property is_shifted#

Has this atom been shifted from the origin?

property n_bonded#

How many atoms are bonded to this one?

class autode.smiles.base.SMILESBond(idx_i: int, idx_j: int, symbol: str)#

Bond in a SMILES string

__init__(idx_i: int, idx_j: int, symbol: str)#

Bond between two atoms from a SMILES string, sorted from low to high

Parameters:

  • idx_j (int) –

  • symbol (str) – Bond order symbol

property atom_indexes#

Atom indexes for the atoms in this bond

distance(atoms)#

Distance of this bond (Å) given a set of atoms

in_ring(rings_idxs)#

Is this bond a constituent of a ring

Return type:

(bool)

is_cis(atoms)#

Is this bond a cis double bond?

is_trans(atoms)#

Is this bond a trans double bond?

Undefined stereochemistry defaults to trans

property symbol#

SMILES symbol for this bond e.g. # for a triple bond

class autode.smiles.base.SMILESBonds(iterable=(), /)#
append(bond: SMILESBond)#

Add another SMILESBond to this list

first_involving(*args)#

First bond that includes some atom indexes

insert(index: SupportsIndex, bond: SMILESBond)#

Insert a bond into this list if it does not already exist

involving(*args)#

Get all the bonds involving a particular atom (given as a index)

Return type:

(list(autode.smiles.SMILESBond))

n_involving(idx)#

How many bonds does an atom (given as a index) have?

class autode.smiles.base.SMILESStereoChem(value)#

An enumeration.

ALKENE_DOWN = -2#
ALKENE_UP = 2#
NONE = 0#
TET_INVERTED = -1#
TET_NORMAL = 1#
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