Smiles#

SMILES (Simplified Molecular Input Line Entry System) is a notation that allows a users to represent chemical structures in 2D notation. This notation can be used in Horus.

Smiles implementation in Horus

In order to control SMILES from Horus blocks, we use the SmilesAPI, a bridge built for communicating Blocks with the SMILES manager.

SmilesAPI#

SmilesAPI is a library for creating and manipulating molecular structures using SMILES notation in Horus. It is designed to be used within Blocks in order to add molecular structures represented by SMILES notation.

In order to control the SMILES interpreter within a Block action, you need to import the SmilesAPI class and use the desired methods.

from HorusAPI import SmilesAPI

my_smiles = "CCCO"

# Create the structure calling directly the Smiles API
SmilesAPI().addSmiles(my_smiles)

The SMILES actions will be applied in the same manner as Mol* actions, for more information, refer to the Molstar (Mol*) documentation page.

SmilesAPI methods#

The SmilesAPI module

class SmilesAPI(*args, **kwargs)#

API for interacting with the Smiles Manager inside Horus

addCSV(csv: str, group: str | None = None) → None#

Adds a CSV file to the smiles manager

Parameters:

csv – The CSV file path to add

addSmiles(smiles: str, group: str | None = None) → None#

Add a smiles string to the smiles manager

Parameters:

  • smiles – The smiles string to add

  • group – The group to add the smiles to

addSmilesWithData(smiles: list[dict]) → None#

Adds a list of full SMILES object to the smiles manager

Each object should be in the following keys:

  • smi: string -> SMILES as a string

  • label: string -> Label to display

  • extraInfo: string -> Extra info to display

  • group: string -> Group to add the smiles to

  • props: {key: value, …} -> Properties to add to the molecule (optional)

reset() → None#

Resets the visualizer