I'm sure this will be an easy question for you experts out there, but I have been searching the forum and working on this for a couple hours now and can't get it right.
I have a very messy data file that I am trying to tidy up - one of the issues is some records are split into multiple lines: ... (4 Replies)
Hi all,
I am developing an application in Tcl, inwhich i have to load many modules written in C. I am converting those C modules into shared object(.so) files, and wrap it with my application using SWIG, for which i had the interface file.
Now my question is, i have two different... (2 Replies)
Hi,
Can anyone know how to use perl to merge the following multi-line information which beginning with "BAM" into one line. For each line need to delete the return and add a space. Please see the red color line.
******Org. Multi-line)
BAM admin 101.203.57.22 ... (3 Replies)
Hi,
lets assume the following details..
file 1 has below details
abc|1234|xyz
abc1|1234|xyz1
abc2|1234|xyz2
and file 2 has below details
pqr|124|lskd
ebwer|325|dfb
wf|234|sdb
I need out put shown below
abc|1234|xyz
pqr|124|lskd
abc1|1234|xyz1
ebwer|325|dfb
abc2|1234|xyz2... (4 Replies)
Hello
I did do a search and the past threads doesn't really solve my issue. (using various awk commands)
I need to combine the output from java -version into 1 line, but I am having difficulties.
When you exec java -version, you get:
java version "1.5.0_06"
Java(TM) 2 Runtime... (5 Replies)
Hi all
I have spent half a day trying to create a shell script which reads a configuration file on a line by line basis.
The idea of the file is that each will contain server information, such as IP address and various port numbers. The line could also be blank (The file is user created). Here... (1 Reply)
example:
comment Now_TB.table column errac is for error messages
1 - first
2 - second
3 -third ;
in this example I need to be able to grab the comment as first word and ; as the last word and it might span a few lines. I need it to be put all in one line without line breaks so I can... (4 Replies)
Hi guys,
So i have a input file with several sequences aligned (fasta)
>NC_005930 241 bp
MNMINIFIINNIFDQFIPVKLSIFSLTSVGSIIA
LSWVWINTKTHWAISRSNTP-SLLLNSL
WTLLITNL-NEKTNPWAPWLFSLFLLCFSFNIMSLI-PYTF-SQ
TSHLSFTFGLSLPIWIMVNIAGFKNNWKKKISHLLPQGTPIYLVPVMII
IETISLFIQPLTLGFRLGANLLAGHLLIFLCSCTIWE... (6 Replies)
Hi all, I'm relatively new to scripting, I can do pretty basic things. I have a daily log file that looks like:
timestamp=2017-06-28-01.01.35.080576;
event status=0;
userid=user1;
authid=user1;
application id=10.10.10.10.11111.12345678901;
application name=GUI;
... (29 Replies)
Hi,
Can anyone help me for merge the following multi-line log which beginning with a " and line ending with ": into one line.
*****Original Log*****
087;2008-12-06;084403;"mc;;SYHLR6AP1D\LNZW;AD-703;1;12475;SYHLR6AP1B;1.1.1.1;0000000062;HGPDI:MSISDN=12345678,APNID=1,EQOSID=365;... (3 Replies)
Discussion started by: rajeshlinux2010
3 Replies
LEARN ABOUT DEBIAN
obrotate
obrotate(1) User's Reference Manual obrotate(1)NAME
obrotate -- batch-rotate dihedral angles matching SMARTS patterns
SYNOPSIS
obrotate 'SMARTS-pattern' filename atom1 atom2 atom3 atom4 angle
DESCRIPTION
The obrotate program rotates the torsional (dihedral) angle of a specified bond in molecules to that defined by the user. In other words, it
does the same as a user setting an angle in a molecular modelling package, but much faster and in batch mode (i.e. across multiple molecules
in a file).
The four atom IDs required are indexes into the SMARTS pattern, which starts at atom 0 (zero). The angle supplied is in degrees. The two
atoms used to set the dihedral angle <atom1> and <atom4> do not need to be connected to the atoms of the bond <atom2> and <atom3> in any way.
The order of the atoms matters -- the portion of the molecule attached to <atom1> and <atom2> remain fixed, but the portion bonded to <atom3>
and & <atom4> moves.
EXAMPLES
Let's say that you want to define the conformation of a large number of molecules with a pyridyl scaffold and substituted with an aliphatic
chain at the 3-position, for example for docking or 3D-QSAR purposes.
To set the value of the first dihedral angle to 90 degrees:
obrotate 'c1ccncc1CCC' pyridines.sdf 5 6 7 8 90
Here 6 and 7 define the bond to rotate in the SMARTS patter, i.e., c1-C and atoms 5 and 8 define the particular dihedral angle to rotate.
Since the atoms to define the dihedral do not need to be directly connected, the nitrogen in the pyridine can be used:
obrotate 'c1ccncc1CCC' pyridines.sdf 4 6 7 8 90
Keep the pyridyl ring fixed and moves the aliphatic chain:
obrotate 'c1ccncc1CCC' pyridines.sdf 5 6 7 8 90
Keep the aliphatic chain fixed and move the pyridyl ring:
obrotate 'c1ccncc1CCC' pyridines.sdf 8 7 6 5 90
SEE ALSO babel(1), obchiral(1), obfit(1), obgrep(1), obprop(1), obrotate(1).
The web pages for Open Babel can be found at: <http://openbabel.org/>
A guide for constructing SMARTS patterns can be found at: <http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html>
AUTHORS
The obgrep program was contributed by Fabien Fontaine
Open Babel is developed by a cast of many, including currrent maintainers Geoff Hutchison, Chris Morley, Michael Banck, and innumerable oth-
ers who have contributed fixes and additions. For more contributors to Open Babel, see <http://openbabel.org/wiki/THANKS>
COPYRIGHT
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison and other contributors.
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABIL-
ITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
Open Babel 2.2 July 4, 2008 Open Babel 2.2