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SMILES Parser

SMILES Parser#

(Open)SMILES parser implemented based on

  1. http://opensmiles.org/

  2. https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system

as of 03/2021

class autode.smiles.parser.Parser#
__init__() → None#

SMILES Parser

property charge#

Total charge on all the atoms

property mult#

Approximate spin multiplicity (2S+1). For multiple unpaired electrons will default to a singlet

property n_atoms#

Number of atoms in parsed, not including implicit hydrogens

property n_bonds#

Number of bonds parsed

parse(smiles: str)#

Parse a SMILES string e.g. ‘[He]’, ‘C’

property parsed#

Has the parser parsed every character of the SMILES string

property smiles#

SMILES string being parsed

autode.smiles.parser.atomic_charge(string)#

Parse a section of a SMILES string associated with an atom for the formal charge on the atom, will ignore anything but +, -. e.g.:

+   ->   1
-   ->  -1
++  ->   2
H+  ->   1
autode.smiles.parser.atomic_class(string: str) → int | None#

Extract the atomic class from a string i.e.:

H4:2 -> 2 :7 -> 7 :001 -> 1

autode.smiles.parser.atomic_n_hydrogens(string)#

Extract the number of hydrogens from a partial SMILES, i.e.:

H3-  ->  3
H    ->  1
C    ->  0
Returns:

Number of hydrogens

Return type:

(int)

autode.smiles.parser.atomic_sterochem(string)#

Extract the first occurring atomic stereochemistry from a partial SMILES i.e:

@H3  ->  @
@    ->  @
@@-  ->  @@
Returns:

Type of point stereochemistry

Return type:

(SMILESStereoChem)

autode.smiles.parser.next_char(string: str, idx: int) → str#

Get the next character in a string if it exists otherwise return an empty string

Returns:

Next character in the string

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