Vexo

Make BigQuery and Google Sheets Chemistry Native

Installation

Running intall.sh at the top directory will create cloud functions for all of the cheminformatic functions. The caller of the script must have access to create assign roles, create cloud functions, and create BigQuery datasets. The default project configured to the gcloud cli will be used to create the cloud and bigquery functions.

Currently the cloud functions targetting Google Sheets are not authenticated. If you wish to authenticate them you will manually have to modify the install.sh script removing --allow-unauthenticated and adding a service account IAM binding like is done for the BigQuery functions.

BigQuery

The install.sh script will create a dataset in BigQuery names vexo. When it is complete there should be a function that matches each seen in biquery_functions.csv.

Examples

Canonical Smiles

Canononicalize smiles based on standard rdkit canonicalization.

SELECT vexo.canonical_smiles("C1=CC=CC=C1")

Iso-Canonical Smiles

Same as above but keep stereochemistry in the returned smiles.

SELECT vexo.iso_canonical_smiles("CC1(C)[C@@H]2C[C@@H](O)[C@@](C)(O)[C@H]1C2")

Substructure Search

Search for substructure match. The first argument is the pattern and the second the smiles. The pattern can also be a SMARTS pattern.

SELECT vexo.substructure_match("c1ccccc1", "CCO/C=N/c1ccccc1")

Sheets

The install.sh also installs a set of functions that are targetting more general HTML requests that also work directly in Google Sheets. This can be very valuable if you are a Chemist that is comfortable with Sheets but not with coding. It opens up most functionality available in rdkit to being called directly from a Sheet.

The deployed Cloud Function has this pattern: https://<REGION>-<PROJECT>.cloudfunctions.net/vexo-<FUNCTION>. Where:

1. is the GCP region configured in your CLI.
2. is the GCP project configured in your CLI.
3. is the vexo function installed from this repo.

Examples

In the below examples we will use us-east1 as the region and a placeholder project of vexo.

Structure PNG

This first example draws the structure of a molecule from the SMILES in a sheet. The function has this pattern:

=IMAGE(CONCAT("https://us-east1-vexo.cloudfunctions.net/vexo-smiles-png/", ENCODEURL(A2)), 1)

where A2 is the cell that contains the smiles.

Below is an example PNG of what you should expect: