Practical Session 03

Note that you can install the course download script cdl in your own bin directory and use it like any other shell command:

mkdir ~/bin
cd ~/bin
curl -O http://becksteinlab.physics.asu.edu/pages/courses/2013/SimBioNano/03/cdl
cd
echo 'export PATH=${PATH}:${HOME}/bin' >> ~/.profile

When you open a new shell (or reload you bash configuration file with . ~/.profile) you will have updated your PATH and the shell will find cdl. To download a file:

cdl 03 Ar_L16_N64.xyz

These files will be available for the duration of the course.

	Name	Last modified	Size	Description
	Parent Directory		-
	Ar_L16_N64.xyz	2013-01-23 17:48	2.7K
	IntroductiontoPython/	2013-01-24 17:37	-
	Practical03IntroductiontoPython.pdf	2013-01-24 21:18	119K
	assignment_06.txt	2013-01-24 18:39	6.6K
	cdl	2013-01-23 18:22	1.6K
	p03_class.txt	2013-01-24 17:38	11K
	pdb_downloader.sh	2016-06-09 17:22	2.7K
	python.vimrc	2013-01-23 17:46	421
	test_06_0.xyz	2013-01-24 18:39	1.4K
	test_06_1.xyz	2013-01-24 18:39	2.7K

The notes for today's practical can be accessed in your browser Introduction to Python or as a PDF or text file, p03_class.txt.

Python

The Python programming language is versatile, not too hard to learn, and very useful. For learning Python see

• Getting started with Python has links to various useful pages
• The Python Tutorial
• A Byte of Python is a very good tutorial for Python and very much recommended for doing in your own time. Just note that it is written for Python 3.x whereas we are dealing with Python 2.6/2.7 because it is still much more widely used.

XYZ file format

The XYZ file format is a very simple format to store positions of particles. It is described in VMD's XYZ Plugin. Basically, a XYZ file looks like this:

N
title text
atom1   x y z
atom2   x y z
...
atomN   x y z

The first line is the number of atoms. The second a string. From the third line onwards, each line contains a symbol for the particle ("atomX") and the cartesian coordinates. All entries are white-space separated.