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The Python Shell

In this module you can learn:

  • How to use Python as a pocket calculator
  • How to store data in variables
  • How to import functions from Python modules

Traces in the desert sand…

slot

Fill in dashed lines with appropriate values using the python interactive shell

>>> 1 _ _ 2
>>> 3
>>> 12 - _ _
4
>>> _ _ * 5
20
>>> _ _ ** 2
81

>>> camels = 9
>>> camels
_ _
>>> silk = camels *  _ _
>> silk
36
>>> math.sqrt(silk)
_ _
>>> math.pow(camels, _ _ )
81.0

The interactive Python shell

You can access the shell by typing python in a command-line terminal

$ python
Python 2.7.9 (default, Apr  2 2015, 15:33:21)
[GCC 4.9.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>>

You can leave the shell with Ctrl-D

Challenge #1 Open a Python interactive session (the Python shell):

  • Calculate the sum and difference of two numbers
  • Divide two numbers. Try 5/3.
  • Then try 5.0/3
  • Calculate 3x5
  • Calculate a power of 2


Variables

Variables are containers for data.

Variable names may be composed of letters, underscores and, after the first position, also digits.

>>> camels = 9
>>> camels
9
>>> silk = camels * 4
>> silk
36

The math module

Sometimes you need more complex mathematical constants and functions

  • square root
  • factorial
  • sine or cosine
  • pi
  • log

Python groups them together in a text file. You can access them by importing the file.

import math

Find the matching pairs of functions and x/y values.

slot

Components of Python

slot

Recap

The Dogma of Programming

  • First, make it work.
  • Second, make it nice.
  • Third, and only if it is really necessary, make it fast.

> **Challenge #2** --- >+ The diameter of a cell is 10 μm. >+ What volume does that cell have given it is a perfect sphere? >+ Use Python to do the calculation. >+ Use variables for the parameters. >+ Print the volume to the screen > ---

See the Solution to challenge #2

Challenge #3

Calculate the distance between two points in the 3D space

Given two points in the Cartesian space:

P1 = (43.64, 30.72, 88.95) P2 = (45.83, 31.11, 92.04)

  • Use Python to calculate their distance
  • Use variables for the parameters
  • Print the distance to the screen

The formula for calculating the distance is: slot

See the Solution to challenge #3

Challenge #4

Find cysteine bonds in the Insulin structure

  • Data in 2OMH.pdb
  • Lines containing 'SG'
  • x, y, z coordinates
  • Use what you learnt from Task 2
HEADER    HORMONE                                 22-JAN-07   2OMH
TITLE     STRUCTURE OF HUMAN INSULIN COCRYSTALLIZED WITH ARG-12 PEPTIDE IN
TITLE    2 PRESENCE OF UREA
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: INSULIN A CHAIN;
COMPND   3 CHAIN: A
COMPND   4 MOL_ID: 2;
COMPND   5 MOLECULE: INSULIN B CHAIN;
COMPND   6 CHAIN: B
ATOM      1  N   GLY A   1     -11.626  14.280   1.013  1.00 19.13           N  
ATOM      2  CA  GLY A   1     -12.164  13.430   2.116  1.00 18.24           C  
ATOM      3  C   GLY A   1     -11.587  13.815   3.470  1.00 17.90           C  
ATOM      4  O   GLY A   1     -10.907  14.833   3.590  1.00 18.08           O  
ATOM      5  N   ILE A   2     -11.836  12.995   4.484  1.00 17.57           N  
ATOM      6  CA  ILE A   2     -11.397  13.317   5.832  1.00 17.78           C  
ATOM      7  C   ILE A   2      -9.875  13.489   5.951  1.00 17.93           C  
ATOM      8  O   ILE A   2      -9.408  14.371   6.670  1.00 17.80           O  
ATOM      9  CB  ILE A   2     -11.922  12.289   6.869  1.00 17.86           C  
ATOM     10  CG1 ILE A   2     -11.767  12.855   8.281  1.00 17.66           C  
ATOM     11  CG2 ILE A   2     -11.242  10.918   6.680  1.00 18.86           C  
ATOM     12  CD1 ILE A   2     -12.434  12.031   9.365  1.00 19.10           C  
ATOM     13  N   VAL A   3      -9.110  12.680   5.224  1.00 18.04           N  
ATOM     14  CA  VAL A   3      -7.652  12.759   5.315  1.00 19.40           C  
ATOM     15  C   VAL A   3      -7.193  14.102   4.747  1.00 19.43           C  
ATOM     16  O   VAL A   3      -6.395  14.820   5.357  1.00 19.23           O

Challenge #5

The hydrolysis of one phosphodiester bond from ATP results in a standard Gibbs energy (ΔG0) of -30.5 kJ/mol. According to biochemistry textbooks, the real ΔG value depends on the concentration of the compounds and these concentrations can differ quite a lot among tissues.

The Gibbs energy as a function of the concentrations of the compounds can be written as:

ΔG = ΔG0 + RT * ln ( [ADP] * [Pi] / [ATP])

Knowing that:

R = 0.00831

T = 298

  • Use Python to calculate the real DG in the tissues reported in the table.
  • Use variables for the parameters.
  • Print the results to the screen.

See the Solution to challenge #5

Recap

  • You can use the Python shell as a pocket calculator.
  • Variables are containers for data.
  • Modules are containers for data and functions
  • You can leave the shell by Ctrl-D.