Python Scripting for Computational Molecular Science: Glossary

You can assign the values of several variables at once.

Indentation is very important in for loops and if statements. Don’t forget the : and to indent the items in the loop.

You should use the os.path module to work with file paths.

One of the most flexible ways to read in the lines of a file is the readlines() function.

An if statement can be used to find a particular string within a file.

The split() function can be used to seperate the elements of a string.

You will often need to recast data into a different data type when it was read in as a string.

Use the glob function in the python library glob to find all the files you want to analyze.

You can have multiple for loops nested inside each other.

Python can only print strings to files.

Don’t forget to close files so python will actually write them.

If you are reading in a file that is mostly numerical data, there are better ways to read in the data than using readlines().

The notation to refer to a particular element of an array is array_name[row,column].

Typically, you should not write a function to perform a standard math operation. The function probably already exists in numpy.

The matplotlib library is the most commonly used plotting library.

You can import libraries with shorthand names.

You can save a figure with the savefig command.

Matplotlib is highly customizable. You can change the style of your plot, and there are many kinds of plots.

Functions make your code easier to read, more reuseable, more portable, and easier to test.

If a function returns True or False, you can use it in an if statement as a condition.

You must import argparse in your code to accept user arguments.

You add must first create an argument parser using parser = argparse.ArgumentParser

You add arguments using parser.add_argument

You must import sys in your code to accept user arguments.

The name of the script itself is always sys.argv[0] so the first user input is normally sys.argv[1].

The python package pytest looks for functions that start with test to run.

It is particularly important to write tests for the edge and corner cases of your functions.

While writing tests can seem time consuming, they are essential to writing good code. Testing is particularly important when multiple people are collaborating on a complex code.

Version control keeps a complete, organized history of all work on a project. It is extremely useful whether you are working individually or on a team.

Good commit messages are critical to maintaining an organized and useful repository.

Putting your code on GitHub is the best way to easily share your code, collaborate, and track changes.