README.md

Simple Mols Programming Exercise

In this folder are files containing python code to manipulate molecules.

Intro

Two of the most common ways of storing molecules as data are smiles strings and sdf files. A smiles string is a series of characters used to represent a molecule, follow the link for more information. A smiles file ("*.smi") contains a list of smiles strings. An sdf file is a data format to store molecules with coordinates, to record a 2D or 3D configuration of a molecule, as well as it's basic structural information.

Files in this folder:

• The file simple_mol.py provides a class which holds molecules in basic python datatypes using numpy.
• The file example_script.py shows how to use the SimpleMol class and read functions to read in molecules and display their properties

Exercise 1

• Write a python script which reads the basic_mols.smi file from the molecules folder, creates 2 SimpleMol class objects from it, calculate the number of atoms in the molecule and print the result.

Ideas for other exercises

• Find an sdf file from someone, and recreate the example_script but for this new file
• Add code to the example script to save the molecules as smiles strings in a new file
• Write a function which replaces oxygen atoms with nitrogen atoms
• Write a function which finds carbon atoms with single bonds