02-08-2013
Awesomeness thanks! works like a charm
10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
I have about 300 files which has the function getDBBackend().
How to write a program to change the empty function from the old format to the new format?
Old empty function format are either:
function getDBBackend()
{
// Not available
} // getDBBackend
or:
function... (0 Replies)
Discussion started by: powah
0 Replies
2. Shell Programming and Scripting
Hi Everyone,
# cat 1.txt
1321631,77770132976455,19,20091001011859,20091001011907
1321631,77770132976455,19,20091001011859,20091001011907
1321631,77770132976455,19,20091001011859,20091001011907
# cat 1.txt | awk -F, '{OFS=",";print $1,$3,$4,$5}'
1321631,19,20091001011859,20091001011907... (7 Replies)
Discussion started by: jimmy_y
7 Replies
3. Shell Programming and Scripting
Hello,
Can you tell me how can I change this format by awk
Input
0.2057422D-01
0.2463722D-01
-0.1068047D-02
Output
0.02057422
0.02463722
-0.001068047
Thanks
wan (8 Replies)
Discussion started by: wanchem
8 Replies
4. Shell Programming and Scripting
tenxun-glibc_code-x86-64-linux-20120713190049.root.tar.bz2
To
tenxun-glibc_code-x86-64-linux.root.tar.bz2 (3 Replies)
Discussion started by: yanglei_fage
3 Replies
5. Shell Programming and Scripting
Hi,
i have a file input.txt
Continent North America
Country USA Capital Washington D.C.
Country Canada Capital Ottawa
Continent South America
Country Argentina Capital Buenos Aires
Country Brazil Capital Brasília
Coutry Colombia Capital Bogotá
and i want to get an output.txt
... (3 Replies)
Discussion started by: fastlane3000
3 Replies
6. Shell Programming and Scripting
I have below date format in a CSV file. (dd/mm/yyyy)
Ex Input:
9/8/2013
Need to convert it into below format (yyyymmdd ) and redirect to new file.
Ex Output:
20130809
How do I use awk here to change the format and if leading 0 (zero) is not then add it.
Please help. Thanks. (8 Replies)
Discussion started by: vegasluxor
8 Replies
7. UNIX for Dummies Questions & Answers
Greetings!
I need a quick way to change the format in a table of data
Here is an example of the input:
10 72 Value=177 VDB=0.0245 Value4=0,0,171,0
10 274 Value=238 VDB=0.0433 Value4=29,0,205,0
10 312 Value=222 VDB=0.0384 Value4=8,0,190,19
10 540 Value=405 VDB=0.0391 Value4=13,30,153,195... (3 Replies)
Discussion started by: Twinklefingers
3 Replies
8. Shell Programming and Scripting
I have a csv file formatted like this:
2014-08-21 18:06:26,A,B,12345,123,C,1232,26/08/14 18:07and I'm trying to change it to MM/DD/YYYY HH:MM for both occurances.
I have got this:
awk -F, 'NR <=1 {print;next}{"date +%d/%m/%Y\" \"%H:%m -d\""$1 "\""| getline dte;$1=dte}1' OFS="," test.csvThis... (6 Replies)
Discussion started by: say170
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9. Shell Programming and Scripting
Example:
Input csv file
00245DLS,Sitel Ocala,12/31/2014,18:45,1.00,7.00,0.00,0.00
00245DLS,Sitel Ocala,12/31/2014,19:00,-1.00,-1.00,-1.00,-1.00
00245HB,Charlotte,01/01/2015,00:00,-1.00,-1.00,-1.00,0.00
Output csv file
00245DLS,Sitel Ocala,2014/12/31,18:45,1.00,7.00,0.00,0.00
00245DLS,Sitel... (8 Replies)
Discussion started by: adit
8 Replies
10. UNIX for Beginners Questions & Answers
Hi,
I have a file where I need to change the date format on the nth field from DD-MM-YYYY to YYYY-MM-DD so I can accurately sort the record by dates
From regex - Use sed or awk to fix date format - Stack Overflow, I found an example using nawk.
Test run as below:
$: cat xyz.txt
A ... (2 Replies)
Discussion started by: newbie_01
2 Replies
LEARN ABOUT DEBIAN
pdb2pqr
PDB2PQR(1) PDB2PQR Manual PDB2PQR(1)
NAME
pdb2pqr - Generate PQR files for use in electrostatics calculations
SYNOPSIS
pdb2pqr [--nodebump] [--noopt] [--chain] [--assign-only] [--clean] [--ffout=name] [--with-ph=ph] [--apbs-input] [--ligand=path]
[[--verbose] | [-v]] --ff=forcefield path output-path
pdb2pqr {--help | -h}
DESCRIPTION
pdb2pqr automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a utility for
converting protein files in PDB format (path) to PQR format (output-path). These tasks include:
o Adding a limited number of missing heavy atoms to biomolecular structures
o Determining side-chain pKas
o Placing missing hydrogens
o Optimizing the protein for favorable hydrogen bonding
o Assigning charge and radius parameters from a variety of force fields
OPTIONS
pdb2pqr accepts the following options:
--ff=forcefield
The forcefield to use. Current values are amber, charm, parse and tyl06.
--help, -h
Print a help message and exit.
--nodebump
Do not perform debumping operation.
--noopt
Do not perform hydrogen optimization.
--chain
Keep the chain ID in the output PQR file.
--assign-only
Only assigns charges to add atoms, debump, or optimize.
--clean
Do no optimization, atom addition, or parameter assignment, just return the original PDB file in alligned format.
--ffout=name
Instead of using the standard caninical naming scheme for residue and atom names, use the names from the given forcefield.
--with-ph=ph
Use propka to calculate pKas and apply them to the molecule given the pH value. Actual PropKa results will be output to
output-path.propka.
--apbs-input
Create an APBS input file based on the generated PQR file. Also create a Python pickle for using these parameters in other programs.
--ligand=path
Calculate the parameters for the ligand in MOL2 format at the given path. Pdb2pka must be compiled.
--verbose, -v
Print additional information to screen.
EXTENSIONS
Extensions add functionality to PDB2PQR and are called by passing a parameter to pdb2pqr. They put their results into files located in
output-path.
The following extensions can be used by pdb2pqr:
--phi
Print the per-residue backbone phi angle to output-path.phi.
--psi
Print the per-residue backbone psi angle to output-path.phi.
--hbond
Print a list of hygrogen bonds to output-path.hbond.
--chi
Print the per-residue backbone chi angle to output-path.chi.
--contact
Print a list of contacts to output-path.con.
--hbondwhatif
Print a list of hydrogen bonds to output-path.hbo.
--salt
Print a list of salt bridges to output-path.salt.
--rama
Print the per-residue phi and psi angles to outpath-path.rama.
CITING PDB2PQR
Please acknowledge your use of pdb2pqr by citing:
Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann
electrostatics calculations. Nucleic Acids Research, 32, W665-W667 (2004).
SEE ALSO
psize(1)
AUTHOR
Manuel Prinz <debian@pinguinkiste.de>
Wrote this manpage for the Debian System.
COPYRIGHT
Copyright (C) 2008 Manuel Prinz
pdb2pqr 2008-06-04 PDB2PQR(1)