Python_SmallWorld_API

This is Unofficial. So please do not abuse it or use it when you cannot legally use the site!

An (unofficial) Python3 module to query the SmallWorld chemical space search server (https://sw.docking.org/search.html).

Overview

The SmallWorld server (https://sw.docking.org/search.html) allows one to search for similar compounds to a give SMILES in one of many databases —a very complex feat.

The API points of the site are described in wiki.docking.org/index.php/How_to_use_SmallWorld_API.

This Python3 module allows one to search it.

Usage

from rdkit import Chem
from rdkit.Chem import PandasTools
import pandas as pd  # for typehinting below

from smallworld_api import SmallWorld

aspirin = 'O=C(C)Oc1ccccc1C(=O)O'
sw = SmallWorld()
results : pd.DataFrame = sw.search(aspirin, dist=5, db='WorldDrugs-20Q2-3004')

from IPython.display import display
display(results)

The first two lines are optional. The code works without rdkit, but if pandas gets imported before PandasTools and Chem imported not in main then display issues happen.

So it's up to you to remember to run:

PandasTools.AddMoleculeColumnToFrame(results,'smiles','molecule',includeFingerprints=True)

Debug

The instantiation is set up so for debugging, namely it has two attributes of interest:

• sw.last_reply, a requests.Response instance
• sw.hit_list_id an integer representing the search (AKA. hlid in the server responses)

As a result if something goes wrong and one is in a Jupyter notebook one can do sw.show_reply_as_html().

Also, as a shorthand, mol: Chem.Mol = SmallWorld.check_smiles(aspirin) can be called to check if the molecules is fine.

Generally if you get status code 500, it is best to try again tomorrow as the server is having a hard time and is probably not okay on the web.

Choices

The database choices can seen with the preset list SmallWorld.db_choices. But also this can be recached via the classmethod SmallWorld..retrieve_databases().

Two databases, REAL_Space_21Q3_2B(public) and REAL_DB_20Q2, are Enamine REAL databases (aka. Enamine will make the compound if you buy it). Previously, the repository, enamine-real-search was good for this, but unfortunately Enamine changed their endpoints. So I wrote this to take its place!

Likewise, the attribute SmallWorld.sf_choices (type list) and the classmethod SmallWorld.retrieve_scorefun_options() do the same. The values are less and are: ['Atom Alignment', 'SMARTS Alignment', 'ECFP4', 'Daylight'], but these are activated by default and will be visible as columns in the resulting dataframe from a search call.

Here is the full list of databases:

import pandas as pd

choices: pd.DataFrame = SmallWorld.retrieve_databases()

display(choices)

Which will return (as of writing on the 9th Dec 2021):