This concatenates your multiple lines and stores the single string in an array element:

#!perl

use 5.12.0;
use warnings;

my @joined = ();
my $index = 0;

while (<DATA>) {
    chomp;
    if (m{ \A line=ULMNm }msx && $. > 1) {
        ++$index;
    }
    $joined[$index] .= $_;
}

for (@joined) { say }

__DATA__
line=ULMNm  3  1fdy_07      N-ACETYLNEURAMINATE LYASE           user  
+ 1           3                                    
  RMSD =     1.06 A
  MATRIX:   -0.3862 -0.2080 -0.8987  0.6457  0.6347 -0.4244 -0.6587  0
+.7442  0.1108   -16.917   -91.429   -35.632  
                   D  47    SER       A  57    SER.?     
                   D  48    THR       A  56    THR.?     
                   D 165    LYS       A  33    LYS~?     
 
line=ULMNm  3  2tmd_00      TRIMETHYLAMINE DEHYDROGENASE        user  
+ 1           3                                    
  RMSD =     1.15 A
  MATRIX:    0.9011 -0.4313  0.0445 -0.1032 -0.3130 -0.9441 -0.4211 -0
+.8462  0.3266    52.913    23.262    25.449  
                   A 169    TYR       A  41    TYR~?     
                   A 172    HIS       A  95    HIS^?     
                   A 267    ASP       A  98    ASP~?

[download]

Outputs:

$ multiline_join_array.pl
line=ULMNm  3  1fdy_07      N-ACETYLNEURAMINATE LYASE           user  
+ 1           3                                      RMSD =     1.06 A
+  MATRIX:   -0.3862 -0.2080 -0.8987  0.6457  0.6347 -0.4244 -0.6587  
+0.7442  0.1108   -16.917   -91.429   -35.632                     D  4
+7    SER       A  57    SER.?                        D  48    THR    
+   A  56    THR.?                        D 165    LYS       A  33    
+LYS~?      
line=ULMNm  3  2tmd_00      TRIMETHYLAMINE DEHYDROGENASE        user  
+ 1           3                                      RMSD =     1.15 A
+  MATRIX:    0.9011 -0.4313  0.0445 -0.1032 -0.3130 -0.9441 -0.4211 -
+0.8462  0.3266    52.913    23.262    25.449                     A 16
+9    TYR       A  41    TYR~?                        A 172    HIS    
+   A  95    HIS^?                        A 267    ASP       A  98    
+ASP~?

[download]

I don't know what subsequent processing you want to do. I've just output each array element to the screen (say just tags on a newline).

-- Ken

In reply to Re^3: regex question: store multiple lines as a string by kcott
in thread regex question: store multiple lines as a string by nurulnad

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.