Python tutorialfeb152012

A Tutorial on the Python
Programming Language
Moshe Goldstein
Most of it based on a Python Presentation by Michael DiRamio - 2005

Which of these languages do you know?
• C or C++
• Java
• Perl
• Scheme
• Fortran
• Python
• Matlab

Presentation Overview
• Running Python and Output
• Data Types
• Input and File I/O
• Control Flow
• Functions
• Then, Why Python in Scientific Computation?
• Binary distributions Scientific Python

Hello World
>>> 'hello world!'
'hello world!'
•Open a terminal window and type “python”
•If on Windows open a Python IDE like IDLE
•At the prompt type ‘hello world!’

Python Overview
From Learning Python, 2nd Edition:
• Programs are composed of modules
• Modules contain statements
• Statements contain expressions
• Expressions create and process objects

The Python Interpreter
•Python is an interpreted
language
•The interpreter provides an
interactive environment to
play with the language
•Results of expressions are
printed on the screen
>>> 3 + 7
10
>>> 3 < 15
True
>>> 'print me'
'print me'
>>> print 'print me'
print me
>>>

The print Statement
>>> print 'hello'
hello
>>> print 'hello', 'there'
hello there
•Elements separated by
commas print with a space
between them
•A comma at the end of the
statement (print ‘hello’,) will
not print a newline character

Documentation
>>> 'this will print'
'this will print'
>>> #'this will not'
>>>
The ‘#’ starts a line comment

Variables
• Are not declared, just assigned
• The variable is created the first time you assign it
a value
• Are references to objects
• Type information is with the object, not the
reference
• Everything in Python is an object

Everything is an object
• Everything means
everything, including
functions and classes
(more on this later!)
• Data type is a property
of the object and not of
the variable
>>> x = 7
>>> x
7
>>> x = 'hello'
>>> x
'hello'
>>>

Numbers: Integers
• Integer – the equivalent of
a C long
• Long Integer – an
unbounded integer value.
>>> 132224
132224
>>> 132323 ** 2
17509376329L
>>>

Numbers: Floating Point
• int(x) converts x to an
integer
• float(x) converts x to a
floating point
• The interpreter shows
a lot of digits
>>> 1.23232
1.2323200000000001
>>> print 1.23232
1.23232
>>> 1.3E7
13000000.0
>>> int(2.0)
2
>>> float(2)
2.0

Numbers: Complex
• Built into Python
• Same operations are
supported as integer and
float
>>> x = 3 + 2j
>>> y = -1j
>>> x + y
(3+1j)
>>> x * y
(2-3j)

Numbers are immutable
>>> x = 4.5
>>> y = x
>>> y += 3
>>> x
4.5
>>> y
7.5
x 4.5
y
x 4.5
y 7.5

String Literals
• Strings are immutable
• There is no char type like
in C++ or Java
• + is overloaded to do
concatenation
>>> x = 'hello'
>>> x = x + ' there'
>>> x
'hello there'

String Literals: Many Kinds
• Can use single or double quotes, and three double
quotes for a multi-line string
>>> 'I am a string'
'I am a string'
>>> "So am I!"
'So am I!'
>>> s = """And me too!
though I am much longer
than the others :)"""
'And me too!nthough I am much longernthan the others :)‘
>>> print s
And me too!
though I am much longer
than the others :)‘

Substrings and Methods
>>> s = '012345'
>>> s[3]
'3'
>>> s[1:4]
'123'
>>> s[2:]
'2345'
>>> s[:4]
'0123'
>>> s[-2]
'4'
• len(String) – returns the
number of characters in the
String
• str(Object) – returns a
String representation of the
Object
>>> len(x)
6
>>> str(10.3)
'10.3'

String Formatting
• Similar to C’s printf
• <formatted string> % <elements to insert>
• Can usually just use %s for everything, it will
convert the object to its String representation.
>>> "One, %d, three" % 2
'One, 2, three'
>>> "%d, two, %s" % (1,3)
'1, two, 3'
>>> "%s two %s" % (1, 'three')
'1 two three'
>>>

Lists
• Ordered collection of data
• Data can be of different
types
• Lists are mutable
• Issues with shared
references and mutability
• Same subset operations as
Strings
>>> x = [1,'hello', (3 + 2j)]
>>> x
[1, 'hello', (3+2j)]
>>> x[2]
(3+2j)
>>> x[0:2]
[1, 'hello']

Lists: Modifying Content
• x[i] = a reassigns the
ith element to the
value a
• Since x and y point to
the same list object,
both are changed
• The method append
also modifies the list
>>> x = [1,2,3]
>>> y = x
>>> x[1] = 15
>>> x
[1, 15, 3]
>>> y
[1, 15, 3]
>>> x.append(12)
>>> y
[1, 15, 3, 12]

Lists: Modifying Contents
• The method
append modifies
the list and returns
None
• List addition (+)
returns a new list
>>> x = [1,2,3]
>>> y = x
>>> z = x.append(12)
>>> z == None
True
>>> y
[1, 2, 3, 12]
>>> x = x + [9,10]
>>> x
[1, 2, 3, 12, 9, 10]
>>> y
[1, 2, 3, 12]
>>>

Tuples
• Tuples are immutable
versions of lists
• One strange point is the
format to make a tuple with
one element:
‘,’ is needed to differentiate
from the mathematical
expression (2)
>>> x = (1,2,3)
>>> x[1:]
(2, 3)
>>> y = (2,)
>>> y
(2,)
>>>

Dictionaries
• A set of key-value pairs
• Dictionaries are mutable
>>> d = {1 : 'hello', 'two' : 42, 'blah' : [1,2,3]}
>>> d
{1: 'hello', 'two': 42, 'blah': [1, 2, 3]}
>>> d['blah']
[1, 2, 3]

Dictionaries: Add/Modify
>>> d
{1: 'hello', 'two': 42, 'blah': [1, 2, 3]}
>>> d['two'] = 99
>>> d
{1: 'hello', 'two': 99, 'blah': [1, 2, 3]}
>>> d[7] = 'new entry'
>>> d
{1: 'hello', 7: 'new entry', 'two': 99, 'blah': [1, 2, 3]}
• Entries can be changed by assigning to that entry
• Assigning to a key that does not exist adds an entry

Dictionaries: Deleting Elements
• The del method deletes an element from a dictionary
>>> d
{1: 'hello', 2: 'there', 10: 'world'}
>>> del(d[2])
>>> d
{1: 'hello', 10: 'world'}

Copying Dictionaries and Lists
• The built-in list
function will
copy a list
• The dictionary
has a method
called copy
>>> l1 = [1]
>>> l2 = list(l1)
>>> l1[0] = 22
>>> l1
[22]
>>> l2
[1]
>>> d = {1 : 10}
>>> d2 = d.copy()
>>> d[1] = 22
>>> d
{1: 22}
>>> d2
{1: 10}

Data Type Summary
• Lists, Tuples, and Dictionaries can store any type
(including other lists, tuples, and dictionaries!)
• Only lists and dictionaries are mutable
• All variables are references

Data Type Summary
• Integers: 2323, 3234L
• Floating Point: 32.3, 3.1E2
• Complex: 3 + 2j, 1j
• Lists: l = [ 1,2,3]
• Tuples: t = (1,2,3)
• Dictionaries: d = {‘hello’ : ‘there’, 2 : 15}

Input
• The raw_input(string) method returns a line of
user input as a string
• The parameter is used as a prompt
• The string can be converted by using the
conversion methods int(string), float(string), etc.

Input: Example
print "What's your name?"
name = raw_input("> ")
print "What year were you born?"
birthyear = int(raw_input("> "))
print "Hi %s! You are %d years old!" % (name, 2011 - birthyear)
~: python input.py
What's your name?
> Michael
What year were you born?
>1980
Hi Michael! You are 31 years old!

Files: Input
inflobj = open(‘data’, ‘r’) Open the file ‘data’
for input
S = inflobj.read() Read whole file into
one String
S = inflobj.read(N) Reads N bytes
(N >= 1)
L = inflobj.readlines() Returns a list of line
strings

Files: Output
outflobj = open(‘data’, ‘w’) Open the file ‘data’
for writing
outflobj.write(S) Writes the string S to
file
outflobj.writelines(L) Writes each of the
strings in list L to file
outflobj.close() Closes the file

Booleans
• 0 and None are false
• Everything else is true
• True and False are aliases for 1 and 0 respectively

Boolean Expressions
• Compound boolean expressions
short circuit
• and and or return one of the
elements in the expression
• Note that when None is returned
the interpreter does not print
anything
>>> True and False
False
>>> False or True
True
>>> 7 and 14
14
>>> None and 2
>>> None or 2
2

Moving to Files
• The interpreter is a good place to try out some code,
but what you type is not reusable
• Python code files can be read into the interpreter
using the import statement

Moving to Files
• In order to be able to find a module called myscripts.py,
the interpreter scans the list sys.path of directory names.
• The module must be in one of those directories.
>>> import sys
>>> sys.path
['C:Python26Libidlelib', 'C:WINDOWSsystem32python26.zip',
'C:Python26DLLs', 'C:Python26lib', 'C:Python26libplat-win',
'C:Python26liblib-tk', 'C:Python26', 'C:Python26libsite-packages']
>>> import myscripts
Traceback (most recent call last):
File "<pyshell#2>", line 1, in <module>
import myscripts.py
ImportError: No module named myscripts.py

No Braces
• Python uses indentation instead of braces to
determine the scope of expressions
• All lines must be indented the same amount to be part
of the scope (or indented more if part of an inner
scope)
• This forces the programmer to use proper indentation
since the indenting is part of the program!

If Statements
import math
x = 30
if x <= 15 :
y = x + 15
elif x <= 30 :
y = x + 30
else :
y = x
print ‘y = ‘,
print math.sin(y)
In file ifstatement.py
>>> import ifstatement
y = 0.999911860107
>>>
In interpreter

While Loops
x = 1
while x < 10 :
print x
x = x + 1
>>> import whileloop
1
2
3
4
5
6
7
8
9
>>>
In whileloop.py
In interpreter

Loop Control Statements
break Jumps out of the closest
enclosing loop
continue Jumps to the top of the closest
enclosing loop
pass Does nothing, empty statement
placeholder

The Loop Else Clause
• The optional else clause runs only if the loop exits
normally (not by break)
x = 1
while x < 3 :
print x
x = x + 1
else:
print 'hello'
~: python whileelse.py
1
2
hello
Run from the command line
In whileelse.py

The Loop Else Clause
x = 1
while x < 5 :
print x
x = x + 1
break
else :
print 'i got here'
~: python whileelse2.py
1
whileelse2.py

For Loops
• Similar to perl for loops, iterating through a list of values
~: python forloop1.py
1
7
13
2
for x in [1,7,13,2] :
print xforloop1.py
~: python forloop2.py
0
1
2
3
4
for x in range(5) :
print xforloop2.py
range(N) generates a list of numbers [0,1, …, n-1]

For Loops
• For loops also may have the optional else clause
for x in range(5):
print x
break
else :
print 'i got here'
~: python elseforloop.py
1
elseforloop.py

Function Basics
def max(x,y) :
if x < y :
return x
else :
return y
>>> import functionbasics
>>> max(3,5)
5
>>> max('hello', 'there')
'there'
>>> max(3, 'hello')
'hello'
functionbasics.py

Functions are first class objects
• Can be assigned to a variable
• Can be passed as a parameter
• Can be returned from a function
• Functions are treated like any other variable in
Python, the def statement simply assigns a
function to a variable

Function names are like any variable
• Functions are objects
• The same reference
rules hold for them as
for other objects
>>> x = 10
>>> x
10
>>> def x () :
... print 'hello'
>>> x
<function x at 0x619f0>
>>> x()
hello
>>> x = 'blah'
>>> x
'blah'

Functions as Parameters
def foo(f, a) :
return f(a)
def bar(x) :
return x * x
>>> from funcasparam import *
>>> foo(bar, 3)
9
Note that the function foo takes two
parameters and applies the first as a
function with the second as its
parameter
funcasparam.py

Higher-Order Functions
map(func,seq) – for all i, applies func(seq[i]) and returns the
corresponding sequence of the calculated results.
def double(x):
return 2*x
>>> from highorder import *
>>> lst = range(10)
>>> lst
[0,1,2,3,4,5,6,7,8,9]
>>> map(double,lst)
[0,2,4,6,8,10,12,14,16,18]
highorder.py

filter(boolfunc,seq) – returns a sequence containing all those items
in seq for which boolfunc is True.
def even(x):
return ((x%2 == 0)
>>> lst = range(10)
>>> lst
[0,1,2,3,4,5,6,7,8,9]
>>> filter(even,lst)
[0,2,4,6,8]
highorder.py

reduce(func,seq) – applies func to the items of seq, from left to
right, two-at-time, to reduce the seq to a single value.
def plus(x,y):
return (x + y)
>>> lst = [‘h’,’e’,’l’,’l’,’o’]
>>> reduce(plus,lst)
‘hello’
highorder.py

Functions Inside Functions
• Since they are like any other object, you can have
functions inside functions
def foo (x,y) :
def bar (z) :
return z * 2
return bar(x) + y
>>> from funcinfunc import *
>>> foo(2,3)
7
funcinfunc.py

Functions Returning Functions
def foo (x) :
def bar(y) :
return x + y
return bar
# main
f = foo(3)
print f
print f(2)
~: python funcreturnfunc.py
<function bar at 0x612b0>
5
funcreturnfunc.py

Parameters: Defaults
• Parameters can be
assigned default
values
• They are overridden if
a parameter is given
for them
• The type of the default
doesn’t limit the type
of a parameter
>>> def foo(x = 3) :
... print x
...
>>> foo()
3
>>> foo(10)
10
>>> foo('hello')
hello

Parameters: Named
• Call by name
• Any positional
arguments must
come before
named ones in a
call
>>> def foo (a,b,c) :
... print a, b, c
...
>>> foo(c = 10, a = 2, b = 14)
2 14 10
>>> foo(3, c = 2, b = 19)
3 19 2

Anonymous Functions
• A lambda
expression returns a
function object
• The body can only
be a simple
expression, not
complex statements
>>> f = lambda x,y : x + y
>>> f(2,3)
5
>>> lst = ['one', lambda x : x * x, 3]
>>> lst[1](4)
16

Modules
• The highest level structure of Python
• Each file with the py suffix is a module
• Each module has its own namespace

Modules: Imports
import mymodule Brings all elements
of mymodule in, but
must refer to as
mymodule.<elem>
from mymodule import x Imports x from
mymodule right into
this namespace
from mymodule import * Imports all elements
of mymodule into
this namespace

Then,
why Python in Scientific
Computation?
python.pdf

Python and mgTinker
Now we will analyze some Python scripts which
are part of the mgTINKER package.

Scientific Computation-
oriented Python Distributions
Python(x,y)-2.7.2.1.exe – only Windows binary
distribution.
Enthought Python Distribution (epd-7-2-2-win-
x86.msi) – Windows, Unix/Linux, and Mac binary
distributions. The full version is completely free
for academic use.
…
Include most of the existent Python modules for
Scientific Computation, graph ploting, etc.

A simple example
An atom located in some place in 3D space, may be
represented by a tuple
atom1 = (atomname, xcoord, ycoord, zcoord)
or by a list
atom1 = [atomname, xcoord, ycoord , zcoord]
Given a set of atoms a1, a2, …, aN, that compose a
molecule mol, a geometric conformation of this molecule
will be represented by a list of atoms represented as above
mol = [a1, a2, a3, …, aN]
Having several conformations of a given molecule, we will
be able to write Python functions of our interest.

Python tutorialfeb152012

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