How to Use the Molecule Working Set

Your molecule working set (MWS) is an in-memory list of small molecules that is the subject of your calculations and manipulations.

Install OpenAD

Find more detailed installation instructions here.

Bash

pip install openad

Note

To run this tutorial from a Jupyter Notebook, make sure to enable OpenAD magic commands and prepend every command with %openad.

About the MWS

Your "Molecule Working Set" or MWS functions like a bucket where you can add molecules from various sources, to then review, triage or manipulate them together and export them to a new file.

Warning

When you end your session or restart your Jupyter kernel, the MWS gets erased.

At any given time, you can list your molecules, or display them in the GUI (graphical user interface). In the beginning of your session, your MWS will be empty.

Bash

list molecules

Bash

show molecules

Loading Individual Molecules

To add the molecule CCCCCC=CC=CC(=O)OCC (Ethyl decadienoate or pear flavor) to your working set, simply run the command below. This will ask for confirmation, then create the molecule and fetch any available data from PubChem.

Bash

add mol CCCCCC=CC=CC(=O)OCC

Aside from any valid SMILES or InChI, if a molecule is available on PubChem you can add it by name, InChIKey or PubChem CID.

If you're using SMILES or InChI as identifier and you don't need the enrichment from PubChem, you can add the basic clause. And If you prefer to skip the confirmation step, you can add the force clause.

Let's add a few more flavors to our molecular fruit salad.

Bash

add mol InChI=1S/C7H14O2/c1-6(2)4-5-9-7(3)8/h6H,4-5H2,1-3H3 force

Bash

add mol Isobutylbenzene force

Bash

add mol 'ethyl methylphenylglycidate' force

Bash

add mol HUMNYLRZRPPJDN-UHFFFAOYSA-N force

Bash

add mol 21648 force

Now we have pear, banana, cherry, strawberry, cherry and raspberry in our MWS. Let's list our salad.

Bash

list mols

Or we can inspect them in the GUI.

Bash

show molecules

Loading Molecules in Batch

Of course most of the time you'll want to load many molecules at once, sometimes from different file formats. So that's what we'll do.

Download the sample files below and copy them into your workspace. Update the file path if needed.

• sample_molecules1.sdf
• sample_molecules2.csv
• sample_molecules3.smi

Bash

import from '~/Downloads/sample_molecules1.sdf' to 'sample_molecules1.sdf'

Bash

import from '~/Downloads/sample_molecules2.csv' to 'sample_molecules2.csv'

Bash

import from '~/Downloads/sample_molecules3.smi' to 'sample_molecules3.smi'

Once the files are in your workspace, you can easily load them into your MWS.

Don't forget the append clause.

Bash

load mols from file 'sample_molecules1.sdf'

Bash

load mols from file 'sample_molecules2.csv' append

Bash

load mols from file 'sample_molecules3.smi' append

Now when you inspect your MWS, you’ll see you have 34 molecules loaded.

Bash

show molecules

Continue Learning

Want to learn more about how to work with small molecules in OpenAD?
Check out the other small molecule tutorials.