Overview

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Constructors are used to build BigSMILES objects. There are three types of the constructor available:

Constructor

Base constructor that requires full parse information.

There are two approaches to building a BigSMILES object:

• build it step-by-step

  1. open branch
  2. add atoms
  3. close branch

• build it in chunks

  1. build the branch in a separate BigSMILES object
  2. attach the branch at a specified position

Examples

add_atom(parent, symbol, isotope, stereo, hydrogens, charge, valence, class_, kwargs)

Constructor String

Wraps several of the base constructor constructors. Performs parsing of string inputs before passing values to the base constructor functions.

Methods are appended with '_str' to denote the methods that accept strings.

Examples

add_atom(parent, symbol_str, kwargs)

Constructor Tokens

Converts a list[Tokens] into a BigSMILES leveraging the 'constructor string'. These function control more of the flow of constructing a BigSMILES; i.e., knowing when to call what constructor function given the situation.

Example

"C(C)C" --> [Token(TokenKind.Atom, "C"), Token(TokenKind.BranchStart, "("), Token(TokenKind.Atom, "C"), Token(TokenKind.BranchEnd, ")"), Token(TokenKind.Atom, "C")]

"[13C@H+:1]" --> {"symbol": "C", "isotope": 13, "stereo": "@", "hydrogens": 1, "charge": 1, "class_": 1}

Tokenizer

The tokenizer receives BigSMILES strings, Atom strings, or Bonding Descriptor strings and breaks it up into the individual tokens or parses in to a dictionary of distinct values.

Reaction

The reaction tokenizer parses and tokenized the reaction string. Molecules are constructed via BigSMILES --> Constructor Tokens.