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Top Forums UNIX for Dummies Questions & Answers Extract paragraph that contains a value x<-30 Post 302970450 by Egy on Wednesday 6th of April 2016 04:36:47 PM
Old 04-06-2016
Extract paragraph that contains a value x<-30

I am using OSX. I have a multi-mol2 file (text file with coordinates and info for several molecules). An example of two molecules in the file is given below for molecule1 and molecule 2. The total file contains >50,000 molecules.

I would like to extract out and write to another file only the molecules that have a Grid Score < -30.0000. For the case below, it should only write for molecule1 (Grid Score = -43.6), but not molecule2 (Grid Score = -13.6).

Looking through the forum, I realized I need to do a paragraph grep or something analogous. The best I could determine is that I could use the awk command. But, I have no idea how to put in the condition for Grid Score < -30.

This is my first post, and I am very much an amateur. Any help to get me going in the right direction would be greatly appreciated. Forgive me if my post is not formatted correctly. Happy to take any criticism. Thanks.



Code:
########## Name:                molecule1
##########    Grid Score:          -43.616261
##########      Grid_vdw:          -38.348866
##########       Grid_es:           -5.267394
##########    Int_energy:            7.004528

@<TRIPOS>MOLECULE
molecule1
 50 50 1 0 0
SMALL
USER_CHARGES


@<TRIPOS>ATOM
      1 C1         23.3017   18.5209   24.1009 C.3     1  <0>        -0.1533
      2 C2         21.8869   18.3400   23.5472 C.3     1  <0>        -0.1225
      3 C3         21.8457   18.8065   22.0906 C.3     1  <0>        -0.1318
@<TRIPOS>BOND
     1     1     2    1
     2     1    21    1
@<TRIPOS>SUBSTRUCTURE
     1 <0>         1 TEMP              0 ****  ****    0 ROOT


########## Name:                molecule2
##########    Grid Score:          -13.616261
##########      Grid_vdw:          -18.348866
##########       Grid_es:           -1.267394
##########    Int_energy:            5.004528

@<TRIPOS>MOLECULE
molecule2
 50 50 1 0 0
SMALL
USER_CHARGES


@<TRIPOS>ATOM
      1 C1         23.3017   18.5209   24.1009 C.3     1  <0>        -0.1533
      2 C2         21.8869   18.3400   23.5472 C.3     1  <0>        -0.1225
      3 C3         21.8457   18.8065   22.0906 C.3     1  <0>        -0.1318
@<TRIPOS>BOND
     1     1     2    1
     2     1    21    1
@<TRIPOS>SUBSTRUCTURE
     1 <0>         1 TEMP              0 ****  ****    0 ROOT

 

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Locale::Maketext::Extract::Plugin::Perl(3)		User Contributed Perl Documentation		Locale::Maketext::Extract::Plugin::Perl(3)

NAME
Locale::Maketext::Extract::Plugin::Perl - Perl format parser SYNOPSIS
$plugin = Locale::Maketext::Extract::Plugin::Perl->new( $lexicon # A Locale::Maketext::Extract object @file_types # Optionally specify a list of recognised file types ) $plugin->extract($filename,$filecontents); DESCRIPTION
Extracts strings to localise (including HEREDOCS and concatenated strings) from Perl code. This Perl parser is very fast and very good, but not perfect - it does make mistakes. The PPI parser (Locale::Maketext::Extract::Plugin::PPI) is more accurate, but a lot slower, and so is not enabled by default. SHORT PLUGIN NAME
perl VALID FORMATS
Valid localization function names are: translate maketext gettext loc x _ __ KNOWN FILE TYPES
.pm .pl .cgi SEE ALSO
xgettext.pl for extracting translatable strings from common template systems and perl source files. Locale::Maketext::Lexicon Locale::Maketext::Extract::Plugin::Base Locale::Maketext::Extract::Plugin::PPI Locale::Maketext::Extract::Plugin::FormFu Locale::Maketext::Extract::Plugin::TT2 Locale::Maketext::Extract::Plugin::YAML Locale::Maketext::Extract::Plugin::Mason Locale::Maketext::Extract::Plugin::TextTemplate Locale::Maketext::Extract::Plugin::Generic AUTHORS
Audrey Tang <cpan@audreyt.org> COPYRIGHT
Copyright 2002-2008 by Audrey Tang <cpan@audreyt.org>. This software is released under the MIT license cited below. The "MIT" License Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. perl v5.16.2 2010-08-10 Locale::Maketext::Extract::Plugin::Perl(3)
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