In so far as I have tested this, it works and gives the same output as my script.
Just to illustrate the difference between a working solution and a well formed solution, my script took 16+ minutes to reformat a file,
The code posted by Chubler_XL processed the same file in just over 1 second.
Thanks, this will save many hours of waiting for my code to finish.
LMHmedchem
This User Gave Thanks to LMHmedchem For This Post:
why do inode indices starts from 1 unlike array indexes which starts from 0
its a question from "the design of unix operating system" of maurice j bach
id be glad if i get to know the answer quickly
:) (0 Replies)
brothers why inode index starts from 1 unlike array inex which starts from 0
its a question from the design of unix operating system of maurice j.bach
i need to know the answer urgently...someone help please (1 Reply)
I come across the problems when assigning the array in the script below . How to use the array with the 'string index' correctly ? When I assign a new string index , the array elements that are previously assigned are all changed .:eek::eek::eek:
$ array=211
$ echo ${array}
211
$... (4 Replies)
hi folks
i am facing problom while trying to access sql variable as array index ina unix shell script....script goes as below..
#!/bin/ksh
MAX=3
for elem in alpha beeta gaama
do
arr=$elem
((x=x+1))
Done
SQL_SERVER='servername'
/apps/sun5/utils/sqsh -S $SQL_SERVER -U user -P pwd -b -h... (1 Reply)
Hi,
I'm just trying to use a dynamic index for some array elements that I'm accessing within a loop. Specifically, I want to access an array at variable position $counter and then also at location $counter + 1 and $counter + 2 (the second and third array positions after it) but I keep getting... (0 Replies)
Hi,
I am using KSH shell to do some programming.
I want to search array and print index value of the array.
Example..
nodeval4workflow="DESCRIPTION ="" ISENABLED ="YES" ISVALID ="YES" NAME="TESTVALIDATION"
set -A strwfVar $nodeval4workflow
strwfVar=DESCRIPTION=""... (1 Reply)
Hi,
I am new to perl and I have the following query please help here.
I have following array variables declaration
@pld1 = qw(00 01 02 03 04 05);
@pld2 = qw(10 11 12 13 14 15);
for(my $k=1;$k<=2;$k++)
{
//I want here to use @pld1 if $k is 1
// and @pld2 if $k is 2. How to do... (3 Replies)
I am trying to reformat the table by filling any missing rows. The final table will have consecutive IDs in the first column. My problem is the index of the associate array in the awk script.
infile:
S01 36407 53706 88540
S02 69343 87098 87316
S03 50133 59721 107923... (4 Replies)
I am trying to assign indexes to an associative array in a for loop but I have to use an eval command to make it work, this doesn't seem correct I don't have to do this with regular arrays
For example, the following assignment fails without the eval command:
#! /bin/bash
read -d "\0" -a... (19 Replies)
Discussion started by: Riker1204
19 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