Introduction to Linux/Unix

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NMR Spectroscopy and Protein Structures Chem 991A
Special Topics in Physical Chemistry Lectures
MWF 1030am-1120am, Rm 733 Hamilton Hall Class
Projects Exams Thur. 600-800pm, Rm 733
Hamilton Hall COURSE OUTLINE Instructor Dr.
Robert Powers
Office Labs Address 722 HaH 721
HaH Phone [phone] Phone [phone] e-mailrp
owers3_at_unl.edu web page http//bionmr.unl.edu/
Office Hours 1130-1230 am MWF or by Special
Appointment. Required Text J. N. S. Evans,
Biomolecular NMR Spectroscopy, Oxford University
Press Recommended Text M. H.
Levitt, Spin Dynamics Basics of Nuclear
Magnetic Resonance, Wiley
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Course Outlined (cont.)
Some Other Recommended Resources
NMR of Proteins and Nucleic Acids Kurt
Wuthrich Protein NMR Spectroscopy Principals
and Practice John Cavanagh, Arthur Palmer,
Nicholas J. Skelton, Wayne Fairbrother
Principles of Protein Structure G. E. Schulz
R. H. Schirmer Introduction to Protein
Structure C. Branden J. Tooze Enzymes A
Practical Introduction to Structure, Mechanism,
and Data Analysis R. Copeland Biophysical
Chemistry Parts I to III, C. Cantor P.
Schimmel Principles of Nuclei Acid Structure
W. Saenger
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Course Outlined (cont.)
Some Important Web Sites
RCSB Protein Data Bank (PDB) Database of NMR
X-ray Structures http//www.rcsb.org/pdb/ BMRB
(BioMagResBank) Database of NMR resonance
assignments http//www.bmrb.wisc.edu/ CATH
Protein Structure Classification Classification
of All Proteins in PDB http//www.cathdb.info/ SC
OP Structural Classification of Proteins
Classification of All Structures into
http//scop.berkeley.edu Families, Super
Families etc. PDBeFold Compares 3D-Stuctures
of Proteins to http//www.ebi.ac.uk/msd-srv/ssm/
Determine Structural Similarities of New
Structures NMR Information Server NMR
Groups, News, Links, Conferences,
Jobs http//www.spincore.com/nmrinfo/ NMR
Knowledge Base A lot of useful NMR
links http//www.spectroscopynow.com/
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Course Outlined (cont.)
Course Work Oral Reports (2) 100
pts (variable due dates) Ubiquitin
Assignment 100 pts (due Dec. 13) Problem
Set 100 pts (due Dec. 13) Exam 1 100
pts (Thur., Oct. 3) Exam 2 100 pts (Thur.,
Nov. 7) Final Exam 200 pts (Fri, Dec. 20,
10am-12pm) Total 700 pts.
Answer keys for the problem sets and exams will
be posted on BlackBoard.
Grading scale A95 A90 A-85 B80
B75 B-70
C65 C60 C-55 D50 D-45 F40
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Course Outlined (cont.)

• Class Participation
• Reading assignments should be completed prior to
  each lecture. The required text will only
  supplement the lecture material. A vast majority
  of the material for the class will come from the
  lectures.
• You are expected to participate in ALL classroom
  discussions
• Exams
• All exams (except the final) will take place at 6
  pm in Hamilton Hall Rm. 733 on the scheduled
  date.
• The length of each exam (except the final) will
  be open-ended. You will have as much time as
  needed to complete the exam.
• Bring TI-89 style calculator or a simpler model,
  and an approved translator if required.
• A review session will take place during the
  normal class time prior to each exam.
• ALWAYS SHOW ALL WORK!!!!

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Lecture Topics (Tentative Schedule) Date T
opic Chapter I. Overview of Protein
Structures Aug 26 Introduction Aug 28 Linux
and Awk Aug 30 Protein Structures from an NMR
Perspective 4 Sept 4 Sept 6 Sept 9 Sept
11 Sept 13 Sept 16 Sept 18 Sept 20 Sept
23 Sept 25 Protein Modeling
Software 3.9 Sept 27 Sept 30 Oct 2 Oct
3 EXAM 1 Oct 4 Molecular Mechanics and
Dynamics 3.5-3.9 Oct 7 Oct 9 Comparison of
X-ray and NMR Structures Oct 11 Oct 14 Isotope
Labeling of Proteins 4.2.2 4.2.3 Oct 16 II.
NMR Assignment Problem 2 Oct 18 NMR
Software 3.9 Oct 21 to Oct 22 Fall Break
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Lecture Topics (continue) Date Topic
Chapter Oct 23 Oct 25 2D NMR 2.1 Oct
28 Oct 30 3D NMR 2.2 Nov 1 4D
NMR 2.3 III. NMR Structure Determination 3
Nov 4 NOEs 3.1 Nov 6 Nov 7 EXAM 2 Nov
8 Nov 11 Chemical shifts, Coupling constants,
Amide Exchanges 4.1.4, 3.2, 4.1.3, 5.2 Nov
13 Nov 15 Stereospecific assignments,
RDCs 4.1.2 Nov 18 Quality of NMR
Structures 3.10 Nov 20 IV. Protein
Dynamics 1.3,1.4, Nov 22 T1,T2, NOE
S2 Nov 25 Nov 27 to Nov 29 Thanksgiving V.
Protein-Ligand Structures 6.3 Dec 2 SAR by
NMR, Other 1D and 2D Methods Dec 4 Transfer
NOE 6.5 Dec 6 Filtered edited NMR
experiments Dec 9 Metabolomics 6.7 Dec
11 Dec 13 Problem Set Ubiquitin Assignment
due Dec 20 FINAL EXAM
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ORAL PRESENTATION OF STRUCTURE PAPERS

• Two 20 minute Oral Presentations
• Thursday Evenings at 6pm in HaH 733
• Audience Participation is Expected (like a
  journal club)
• Presentation Dates Randomly Assigned (see
  syllabus page 4)
• 50 points per presentation total of 100 points
• Paper of Your Choice
• A Protein Structure Should be a Major Focus of
  the Paper
• The Paper Topic Should be of General Interest and
  of Significant Impact
• Send an Electronic Copy of the Paper to the Class
  Prior to Your Presentation
• Some Recommended Sources
• Nature Structural Biology, Science, Nature, Cell,
  Molecular Cell, Structure, Protein Science, PNAS,
  Journal of Molecular Biology, Biochemistry, and
  Journal of Biomolecular NMR.
• The paper may cover a protein structure or a
  protein-complex (small molecule, protein, DNA,
  RNA, etc).

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ORAL PRESENTATION OF STRUCTURE PAPERS

• Presentation Goal
• Present a Clear Understanding of the Goals and
  Findings of the Paper to the Class
• Why was the particular protein the target of the
  paper?
• How was the structure determined? Were there any
  challenging issues?
• What structure was determined for the protein
  (fold?)
• What are some interesting features of the
  structure (dynamics)?
• Are there any unique structural differences
  compared to other members of the family?
• What structural features are important to
  function?
• How was the structure used to support or refute
  the biological focus of the paper?
• Does the structure actually support the
  conclusion or did the authors over interpret the
  data?
• Does the data/structure suggest other equally
  plausible conclusions?

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ORAL PRESENTATION OF STRUCTURE PAPERS

• Grading
• Combination of My Assessment and the Other
  Students Assessment
• Each Student will be Limited to Giving
  Approximately 30 As, 55 Bs, And 15 Cs
• Default Grade is a B, an A or C will Require
  Justification
• All the assessments will be averaged together to
  determine the number of points
• Assessing the Presenter
• How well did the presenter understand the
  material?
• How clearly did the presenter discuss the
  material?
• Was the chosen paper of general interest and
  biologically significant?
• Was the structure relevant and important to the
  paper?
• How well did the presenter answer questions?
• Did the paper lead to an interesting discussion?

Average Assessed Grade A 50pts, B 45pts, B
40pts, B- 35pts, C 30pts, C 25pts
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ORAL PRESENTATION OF STRUCTURE PAPERS
Tentative Schedule
Oral Presentation Schedule Oral Presentation Schedule Oral Presentation Schedule Oral Presentation Schedule Oral Presentation Schedule
9/5 9/12 9/19 9/26 10/10
Jonathan Catazaro Mark Carter Bradley Worley Teklab Gebregiworgis Jonathan Catazaro
Jeffrey Jeppson Jessica Periago Shulei Lei Darrell Marshall Jeffrey Jeppson
         
10/17 10/24 11/14 11/21 12/5
Mark Carter   Bradley Worley Teklab Gebregiworgis  
Jessica Periago   Shulei Lei Darrell Marshall  
         
12/12        
         
         
         
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Course Assignments

• Two Separate Graded Assignments
• A standard problem set included at the end of
  the syllabus
• An NMR assignment problem
• Due data for both assignments is the beginning of
  class on Fri. Dec. 13
• Late Problem Sets will NOT be accepted
• Grading - General
• Each Assignment is worth 100 pts. (200 pts.
  total)
• Show ALL work to receive full credit
• You must submit your own set of answers
• Some Additional Considerations
• Please start both assignments NOW!
• Please work together
• Please visit my office hours for assistance

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Course Assignments

• The Standard Problem Set Has Two Sections
• Writing simple AWK programs to manipulate files
• Using Xplor and other software to analyze protein
  structures
• Due date for both assignments is the beginning of
  class on Fri. Dec. 13
• Late Problem Sets will NOT be accepted
• Grading Standard Problem Set
• No unique answer for programing section, either
  it works or it doesnt
• E-mail me your scripts and I will run them
• If it works full credit, if not zero points
• The analysis of the protein structures section
  will have defined answers
• Please submit the answers to the protein
  structure section on the due date

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Course Assignments

• NMR Assignment Problem Set
• Determine the backbone NMR Assignments for
  Ubiquitin

1 10 20 30
40 Sequence MQIFVKTLTG KTITLEVEPS
DTIENVKAKI QDKEGIPPDQ 50
60 70 76 QRLIFAGKQL EDGRTLSDYN
IQKESTLHLV LRLRGG

• The completed project should include a cover page
  that summarizes your assignments using the
  following template
•  
• Res HN 15N Ca Cb Ca(i-1) Cb(i-1) CO(i-1)
• M1
• Q2
• I3
• .
• .
• .
• G76
• Include peak-pick list from the six spectra used
  to assign the protein

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Course Assignments

• NMR Assignment Problem Set
• You will ALL have access to a standard dataset of
  NMR spectra
• 2D 1H-15HSQC, 2D 1H-13C HSQC, 3D HNCO, 3D HNCA,
  3D CBCANH, and 3D CBCACONH
• Data will be available on the computers in the
  Research Instrument NMR Facility (HaH 832)
• All the necessary software for the processing and
  analyzing of the data will also be available on
  these computers
• Goal
• Assign the minimal set of backbone resonances
  (HN, 15N, 13CO, Ca, Cb)
• Provide practical experience with using NMR data
  to assign a protein
• Complete as much of the backbone assignments as
  possible
• Grading NMR Assignment Problem Set
• Based on how complete the assignments are
• Scaled based on overall success of the class

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Introduction to Linux/Unix
Linux A UNIXlike operating system developed as
a free and open source software User interface
is a traditional and cumbersome command line in a
shell (window) There are a number of flavors
(distributions) of Linux with different graphical
user interfaces (GUI) or desktop interfaces
(attempt to be Mac or Windows-like) - Debian,
Fedora, Ubuntu, Mageia, Mint Linux, etc.
Similarly, there are a number of PC-look-a-like
software programs (free commercial) (WORD,
EXCEL, etc). Initially thought it would replace
the Windows PC Very popular in academia because
it is free and open for development
Linux is for Adults Stephan Grzesiek
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Introduction to Linux/Unix
Typical Linux Windows Environment
Typical Linux Shell Environment
Simple command line execution of programs or
editing of files
Mimics PC/Mac desktop GUI environment
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Introduction to Linux/Unix
Connecting from a PC by a Terminal Emulation
Software (PuTTY)
Connecting from a PC by Samba
command line environment
PC/Mac folder environment
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Introduction to Linux/Unix

• Graphical User Interface (GUI) or PC/MAC Desktop
  Environment
• You can use the Desktop like a PC, but can be
  cumbersome
• Minimal (if any ) standards, everything in the
  environment needs to be configured
• Downside of open-source (free) software many
  contributors with little to no managers
• More common to work in a shell using the command
  line
• Primitive (Old School)
• Minimal mouse functions, pull down menus or other
  common features we are accustom to
• Need to memorize commands and options (flags)
• Need to open a Terminal, Window or Shell
• Right click mouse and select open terminal

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Introduction to Linux/Unix

• Three Common Linux Commands pwd, ls and cd
• pwd identifies the current path or directory
• ls list the files and folders in the current
  directory
• cd path - move to the defined path (change
  directory)
• cd .. (move up one directory),
• cd ../.. ( move up two directories)

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Introduction to Linux/Unix

• For a Complete List of Linux Commands and
  Explanations see
• http//linuxcommand.org/
• Or the book Linux in a Nutshell
• Some Other Common Commands
• echo text display or print text
• exit close a terminal
• clear clear all text in a terminal
• mkdir - make a new directory
• rm - remove/delete file
• mv - moves files
• cp - copies files
• ps lists all active user programs and display a
  PID (process identification number)
• kill pid - will kill (stop) the process with the
  listed pid number
• man command - will display the manual for the
  listed command
• cat file display the contents of a file (also
  used to combine or concatenate
  multiple files)
• vi file will open file with a primitive text
  editor
• chmod file flags will change or set
  permissions for file defined by flags

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Introduction to Linux/Unix

• It Gets More Complicated!
• A number of commands have a range of options that
  are implemented on the command line with a flag
• ls l - lists files and folders with associated
  permissions
• rm R - remove/delete folder
• mv i prompt before overwriting an existing
  file with the same name
• cp n do not overwrite an existing file with
  the same name
• cp u only overwrite an older file with the
  same name
• ps axu lists the detailed status of every
  process on the system with the name of the user
• chmod 755 file change files permission such
  that file's owner may read, write, and execute
  the file. All others may only read and execute
  the file.
• Multiple flags can be used simultaneously
• Again, man pages, Linux web site and reference
  books provide more details

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Introduction to Linux/Unix

• One More Very Useful Command
• sort
• Quickly re-order or sort the rows of a tabular
  file with n number of columns
• sort rn n filename gt newfilename
• - n the number of the column that will be
  sorted
• - r sort in reverse order
• - n sort based on numeric value of the string

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Permissions

• You cant read, write, edit or execute a file
  without permission!

Size of file in kilobytes
Directory
File Owner
Filename
Number of files in Directory
Group Owner belongs to
File Date or Time Stamp
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Permissions

• Reading and understanding permissions

Permissions
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Permissions

• Where did the 755 come from in the chmod command?

Think of the permission settings as a series of
bits rwx rwx rwx 111 111 111 rw- rw- rw-
110 110 110 rwx --- --- 111 000 000 and so
on... rwx 111 in binary 7 rw- 110 in
binary 6 r-x 101 in binary 5 r-- 100 in
binary 4 -xx 011 in binary 3 -x- 010 in
binary 2 --x 001 in binary 1 --- 000 in
binary 0
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Pipes and Redirection

• (pipe) - passes output of one Linux command to
  the input of a second command
• Example ls wc (wc counts the number of
  characters, words and lines)
• Not limited to just one pipe, can string
  multiple pipes together
• gt, lt - redirection of files
• command gt filename output of command (or
  program) is sent to a file called filename
  instead of being displayed on the screen
• Example ls gt file_list
• command lt filename the file filename is the
  input to the command or program
• Example xplor lt psf.inp

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Background Calculations

• For long calculations dont want the process
  directly associated with the window or shell
• Window must remain open and active during
  calculation
• Window is locked until the program is finished
• Calculations will be stopped if the window is
  closed
• A intense calculation can overwhelm the shell
  environment, leading to the window crashing or
  even slow down your computer
• Output displays on window can be lost, lock
  window or crash computer
• Instead, submit your job to the background
• Lowers the calculations priority to access the
  CPU
• Any interactive calculation has the highest
  priority
• Example background - xplor lt psf.inp gt psf.out
  
• interactive - xplor lt psf.inp
• Use ps command to monitor status of background
  jobs

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vi Primitive Text Editor

• Opens any text based file for reading, editing
  and writing
• Only simple text or ASCII files can be edited
  with vi
• You will see gibberish with .doc, .pdf, etc.
• Like Linux, vi uses a number of simple command
  line functions
• A number of the functions require a key
  combination (ctrl key another key)
• For a Complete List of Vi Commands and
  Explanations see
• The Vi Lovers Home Page http//thomer.com/vi/vi.
  html
• Or Learning the vi Editor by L. Lamb, OReilly
  Associates, Inc
• vi filename
• If filename exists, vi will open the file for
  editing
• If filename doesnt exist, vi will create the
  file for editing

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vi Primitive Text Editor
Cursor
What part of the text is shown All Top Bot Percen
tage
Line number
Column number
Editing Mode
Cursor Location
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vi Primitive Text Editor

• Working with files
• q quits only if no changes to the file have
  been made
• q! force vi to quit without saving any changes
• wq filename quits and writes the contents of
  the file to a new file named filename
• wq! quits and writes the file to the current
  filename
• r filename inserts the contents of the file
  filename into the current file at the cursor
  location
• Moving around the file
• number jumps to the specified line number in
  the text
• G or - jump to last line
• Ctrl-g gives current line number
• Ctrl-f or Ctrl-d move forward
• Ctrl-b or Ctrl-u move back
• Arrow Keys allows you to move around the file
  and position the cursor

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vi Primitive Text Editor

• Adding to a file
• Enter Key adds a blank line at the cursor
  position
• Esc key exits or leaves the active vi function
• i or a enters insert mode, allows text to be
  typed into the file at the location of the cursor
• R enters replace mode, allows text to be typed
  into the file at the location of the cursor
  replacing any existing text
• Deleting
• dd deletes the line at the position of the
  cursor
• dw deletes the word at the position of the
  cursor
• x deletes the character under the cursor
• r replace the character under the cursor
• D deletes from the cursor position to the end
  of the line
• u undo the last edit or change
• U undo all the edits on a single line
• Place a number in front of command and the
  command will be executed that many times

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vi Primitive Text Editor

• Copying and Pasting Text
• number yy yanks (copy) the specified number of
  lines (starting at the cursor)
• p put (pastes) the previously yanked (copied)
  lines in the text after the cursor
• J joins two lines at the position of the cursor
• Global Search and Replace
• /text moves the cursor to the next location of
  text in the file
• n moves to the next occurrence of text in the
  file
• s/search_string/replacement_string/g globally
  replace search_string with replacement_string

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Awk/Nawk Primitive (but Powerful) Programing
language

• Interpreted (not compiled) language
• C-like
• A file containing the software code needs to be
  passed to Awk
• awk_script.awk the Awk program
• infilename the file used by the Awk program
• outfilename the output generated by the Awk
  program
• Awk significantly simplifies writing a quick
  program
• Automatically handles opening and reading files
  and inputing data into standard variables
• Structured to read a file composed of rows and
  columns
• IMPORTANT sequentially reads each row as it
  executes the program
• If 10 rows, the program gets executed 10 times
  major source of confusion

awk f awk_script.awk infilename gt
outfilename
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Awk Program Structure
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BEGIN/END
This script politely introduces itself BEGIN
print Hello, world Main Does Nothing,
but still reads file END print Bye,
world

• All of the commands in the section defined by
  BEGIN occurs BEFORE the file is read
• All of the commands in the section defined by END
  occurs AFTER the file is read
• To comment out a line of text from a script add
  before text
• - Line is skipped by Awk

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BEGIN CAmax0 "65.52" CAmin0
"43.00" CBmax0 "38.70" CBmin0 "0.00"
Res0"A i1 While getline lt ref.pck gt 0)
CArefi 1 CBrefi 2 i Ma
in Does Nothing, but still reads file
BEGIN/END

• The BEGIN section is commonly used to set or
  define the value of variables used by the MAIN
  program
• Also, to open an input data or information from
  other files
• The END section is commonly used to print out the
  results of the Awk Program

END For (i 1 i lt NR i) print
CAi,CBi
38

• The various functions of AWK performs the tasks
  you want as the program sequentially reads the
  input file

Consider the following input file
PkID NH N15 CA CB CAi CBi COi
1.00 9.35 126.75 53.19 40.06 63.53 69.87 172.90
2.00 9.10 126.69 59.42 31.90 52.92 43.03 174.94 3
.00 9.73 126.68 60.73 38.11 54.64 31.38 171.92 4.0
0 7.80 126.57 57.28 33.99 56.10 30.75 172.60 5.00
8.84 126.52 58.35 28.58 53.25 40.03 173.12 6.00 8.
14 125.85 65.85 31.89 53.03 41.07 173.12 7.00 9.01
125.35 62.57 42.15 52.70 41.84 171.99 8.00 8.15 1
25.24 54.86 40.69 55.79 30.35 171.17
1 2 3 4
5 6 7 8

• Awk sequentially reads each row redefining the
  value of each standard variable (1 to 8)
• NF is set to the number of fields (columns), 8 in
  this example
• NR is set to the number of rows, 9 in this
  example
• 0 is a string corresponding to the entire row

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MAIN

• The primary Awk functions can be grouped into 5
  categories
• Logic statements
• Arithmetic
• Looping
• Arrays
• Printing

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BEGIN CAmax0 "65.52" CAmin0
"43.00" CBmax0 "38.70" CBmin0 "0.00"
Res0"A" PkID1 NH2 N153 CAiatom4
CBiatom5 CAatom6 CBatom7 COi8 CAupsqrt(C
Amax0 Caiatom) CBdn CBiatom/CBmin0 CO2
Coi2

• As the file is being read in, you can now write
  instructions to test, change or manipulate the
  original data
• You can define your own variable names
• You can do any number of arithmetic functions (
• Basic math ,-,,/,
• General functions cos(x), exp(x), sqrt(x), etc.

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Functions

• Logic statements
• if (logical test of a parameter/variable)
• Probably most important logic command
• General call structure is
• if (statement to test) action
• Example if (1 HAPPY)
• Reads if column 1 equals HAPPY
• If this is true then we do something
• else
• Used to perform an action when the if statement
  is false
• else action
• Example
• BEGIN
• 1 HAPPY
• if (1 HAPPY) print I am HAPPY
• else print I am SAD

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Functions

• Logic statements
• ! (not) true if not a match
• Example if (1 !HAPPY)
• True if 1 NOT EQUAL to HAPPY
• (and) true only if both conditions are met
• Example if (1 gt 2 1 gt 3)
• True if 1 is larger than BOTH 2 and 3
• (or) true if one of multiple conditions are
  met
• Example if (1 gt 2 1 gt 3)
• 1 only needs to be larger than either 2 or 3
  for the statement to be true

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BEGIN While getline lt ref.pck gt 0)
CArefi 1 CBrefi 2 i
Functions

• Loops allows you to repeat a set of
  instructions until a condition is met
• Major source of problem infinite loop
• The exit condition is never met
• Two loop functions
• For
• While

For (i 1 i lt NF i) if (i gt
54.0 lt 55.0) count
END For (i 1 i lt NR i) print
CAi,CBi
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Functions
BEGIN i1 PkIDi1 NHi2
N15i3 Caiatomi4 Cbiatomi5 Caatom
i6 Cbatomi7 Coii8 i

• Arrays allows you to assign multiple values to
  a single variable
• Effectively allows you to sort or group
  information
• Two types of Arrays
• 1D CA0
• 2D CB0,0

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Functions

• printf primary mechanism of reporting the
  results of the Awk program to the user
• Extremely flexible number of options available to
  format output
• Can do calculations within print statement
• Can be frustrating to get it right.
• Two types of print statements
• print no formatting, just prints the value of
  the valuable
• printf full range of formats available

BEGIN stateHAPPY For (i 1
i lt 10 i) print i print ii printf
(s\n, state)
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Functions

• Examples of different formatting options with
  printf
• Each variable needs a type definition
• d - decimal
• s - string
• f floating point
• e floating point with scientific notation
• Formatting is literal
• printf (ss\n, 1,2)
• print all the characters in column 1 (s) and
  column 2 (s)
• \n print new line
• no spacing
• 1 HAPPY and 2 SAD the output would be
  HAPPYSAD

47
Functions

• Examples of different formatting options with
  printf
• Spacing , Tabs and justifications
• The number of spaces between type definitions
  will be printed
• \t Tab, using system defined tab locations
• \n print new line
• Can use any number or combination of tabs, spaces
  and new lines
• Default printing is right justified
• For left justification, place a in front of the
  type classification (e.g. -10s)
• printf (s s\n, 1,2)
• single space
• 1 HAPPY and 2 SAD the output would be HAPPY
  SAD
• printf (s \ts\n\n, 1,2)
• five space then tab
• 1 HAPPY and 2 SAD the output would be HAPPY
  SAD
• Followed by two new lines

48
Functions

• Examples of different formatting options with
  printf
• Precision Modifier
• Fine tunes how the variable is printed
• Defines both spacing and number of characters or
  significant figures printed
• Simply, place a number in front of the type
  classification (e.g. 5.3f)
• printf (10s5s\n, 1,2)
• 10 spaces for the first string and 5 spaces for
  second string
• Spaces include the number of characters in the
  string
• 1 HAPPY and 2 SAD the output would be
  HAPPY SAD
• 5 spaces in front of HAPPY (5 spaces 5
  characters in HAPPY 10)
• 2 spaces in front of SAD ( 2 spaces 3
  characters in SAD 5)
• OR printing of 1 will end on column 10 and
  printing of 2 will end on column 15
• printf (f 5.3f\n, 1,1)
• 1 1/3, the output would be 0.333333 0.333
• f all the characters are printed
• 5 in 5.3 indicates a total of 5 characters are
  printed (including decimal point)
• 3 in 5.3 indicates a total of 3 characters are
  printed to the left of decimal point

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Functions

• Examples of different formatting options with
  printf
• Printing is literal
• Anything within the quotes is printed
• printf (s HELLO s\n, 1,2)
• 1 HAPPY and 2 SAD the output would be HAPPY
  HELLO SAD
• printf (Hello World\n)
• Dont need to print a variable
• The output would simply be Hello World
• Print to a File
• Simply redirect the output of the print or printf
  statement to a file name
• printf (Hello World\n) gt helloworld.txt

50
Functions

• Examples of different formatting options with
  printf
• Can do Math within the print and printf statement
• printf (d d\n, 12,sqrt(2))
• 1 1/3, the output would be 0.111111 0.577
• This is a general feature of Awk, functions can
  be imbedded within other functions
• For More information on Awk, see
• The book sed and awk by Dale Dougherty OReilly
  and Associates
• The GNU Awk Users Guide http//www.gnu.org/softwa
  re/gawk/manual/gawk.html
• Effective Awk Programming http//www.gnu.org/soft
  ware/gawk/manual/

51
Linux AWK Final Thoughts

• These Lectures have only meant to serve as a
  general introduction to both Linux and Awk
• There is a lot more detail and other topics that
  simply were not covered. Entire courses are
  dedicated to these topics. I did not present
  everything there is to know about Linux and Awk
  or programming in general
• Mastering an operating system and computer
  programming will only come from extensive effort
  and practice
• The best way to learn is by doing!!