Python fundamentals

Variables are names for values

Step through: a name appears when it is first assigned, and changes when assigned again.

Built-in names can be overwritten by accident

print = 1
print("123")

del print   # back to the built-in
print("123")

Numbers: /, //, %

/ always gives a float. // is how many whole rows fit, % is what is left over.

Every value has a type

type(x) tells which one.

Strings

Text in quotes. Characters are numbered from 0 from the left, and from −1 from the right.

formula = 'C2H5OH'

Operators and methods

'Hello ' + 'World'
'Hello' + str(1), 'A' * 5
'H' in formula, formula.count('H'), formula.find('OH')

'Hello' + 1

split turns one string into a list of strings

line = 'H, C, N, O, Fe'
line.split(', ')

line.upper(), line.lower(), len(line)

f-strings: values inside text

After the colon comes the format: alignment, width, decimals. Build one and watch the output cells.

n = 4
mass = 18.015
print(f'Water has {n} atoms and mass {mass:.1f}')

Files

with opens the file and closes it for you. readlines() gives one string per line, newline included.

with open('test.txt', 'w') as f:
    f.write('123\n')
    f.write('456')

with open('test.txt') as f:
    lines = f.readlines()
lines

with open('pyridine.xyz') as f:
    lines = f.readlines()
print(lines[0])
print(lines[2])
lines[2].split()

Lists and tuples

A list is an ordered, changeable collection. Click the statements in order.

elements = ['H', 'C', 'N', 'O', 'Fe']

Indexing and slicing work exactly as for strings

A list can mix types; a tuple is a list you cannot change

mixed = ['Hola', 123, True, 4.5]
for item in mixed:
    print(item, type(item))

t = ('H', 1, 1.008)
t[1] = 2

Two names, one list

b = a does not copy. Both names point to the same object; changing it through one name is visible through the other.

for, range, enumerate

The loop variable takes each value of the collection in turn. The indented block runs once per value.

range makes the numbers to loop over

stop is never included. range(5) means range(0, 5, 1).

Index and value together

Dictionaries: key → value

Look up by name instead of by position. Click the statements in order.

carbon = {'symbol': 'C', 'mass': 12.011, 'number': 6}

The dictionary used in the exercises and later today:

masses = {'H': 1.008, 'C': 12.011, 'N': 14.007, 'O': 15.999, 'Fe': 55.845}

Building a dictionary in a loop

Conditions: if / elif / else

Conditions are tested top to bottom; the first true one wins, the rest are skipped.

Comparisons and and, or, not

== compares values, is compares identity

Empty things count as False

text = ''
if text:
    print('not empty')
else:
    print('empty')

while: repeat as long as a condition holds

The condition is re-checked before every pass. Something inside must move it towards False.

Comprehensions: a loop that builds a list in one line

Hover a part to see where it goes.

for i in range(10):
    doubles.append(i * 2)

[i * 2 for i in range(10)]

for x in range(1, 11):
    if x % 2 == 0:
        squares.append(x**2)

[x**2 for x in range(1, 11) if x % 2 == 0]

The same for dictionaries

name_lengths = {}
for element in elements:
    name_lengths[element] = len(element)

{element: len(element) for element in elements}

positions = {}
for i, element in enumerate(elements):
    positions[element] = i

{element: i for i, element in enumerate(elements)}

Reading an error message

Read the last line first: the kind of error and what went wrong. Then find the arrow: where.

1 / 0

print(undefined_variable)

Functions

A function gets its own box of variables while it runs. return hands a value back; print only shows it.

print is not return

Docstrings: a comment the function carries with it

def product(a, b):
    """Return the product of a and b."""
    return a * b

product?

A loop inside a function

Several values come back as a tuple

def get_even_numbers(n):
    numbers = list(range(0, n, 2))
    return len(numbers), numbers

count, values = get_even_numbers(10)
count, values

Scope: what lives where

Names created inside a function disappear when it returns. Constants go at the top, in CAPITALS.

energy_kcal

def set_value():
    global value
    value = 5

set_value()
value

Default and keyword arguments

Positional arguments fill parameters left to right. Keywords go by name. Missing ones take their default.

*args collects extra positional, **kwargs extra keyword arguments

Recursion

A function may call itself. Each call gets its own box; they pile up, then unwind.

Scripts and sys.argv

A .py file is run from the terminal. The words after python arrive as a list of strings. Edit the command line.

# argv.py
import sys

print(sys.argv)

The homework template

# homework/hw1/count_atoms.py
import sys

if len(sys.argv) > 1:
    filename = sys.argv[1]
else:
    print("Filename not provided!")
    exit()

# filename is a string: open it, count the atoms