SOLVED:problems with pattern match

paola82 has asked for the wisdom of the Perl Monks concerning the following question:

.I'll paste only the part of the script that I need to parse..I want to extract the residue that do hydrophobic and hydrogen bond..

%!PS-Adobe-3.0
%%Creator: Ligplot v.4.1
%%DocumentNeededResources: font Times-Roman Symbol
%%BoundingBox: (atend)
%%Pages: 1
%%EndComments
%%BeginProlog
....
#a lot of settings of the background
....
% Hydrophobic contact

Hydrophname_col   
Zero_linewidth W
G Background_col    
 189.17  329.15  189.17  317.71  235.30  317.71  235.30  329.15 Pl4
 212.23  323.43 moveto
(Trp 401(A)) Hydrophnam_size Center
(Trp 401(A)) Hydrophnam_size Print

% Hydrophobic contact

Hydrophname_col   
Zero_linewidth W
G Background_col    
 404.14  338.82  404.14  327.38  450.28  327.38  450.28  338.82 Pl4
 427.21  333.10 moveto
(Val 440(A)) Hydrophnam_size Center
(Val 440(A)) Hydrophnam_size Print

% Hydrophobic contact

Hydrophname_col   
Zero_linewidth W
G Background_col    
 280.94  601.38  280.94  589.94  327.08  589.94  327.08  601.38 Pl4
 304.01  595.66 moveto
(Gly 463(A)) Hydrophnam_size Center
(Gly 463(A)) Hydrophnam_size Print
....
#a lot of setting
....
% Residue names

gsave
Ligresname_col    
 244.91  185.50 moveto
(Atp 1) Ligresname_size Center
(Atp 1) Ligresname_size Print
Nligresname_col   
 139.01  612.49 moveto
(Lys 464(A)) Nligresnam_size Center
(Lys 464(A)) Nligresnam_size Print
Nligresname_col   
 133.08  424.57 moveto
(Thr 465(A)) Nligresnam_size Center
(Thr 465(A)) Nligresnam_size Print
Nligresname_col   
 448.11  410.46 moveto
(Ser 466(A)) Nligresnam_size Center
(Ser 466(A)) Nligresnam_size Print
Nligresname_col   
 447.88  472.27 moveto
(Gly 461(A)) Nligresnam_size Center
(Gly 461(A)) Nligresnam_size Print
Nligresname_col   
 395.22  557.76 moveto
(Thr 460(A)) Nligresnam_size Center
(Thr 460(A)) Nligresnam_size Print
Nligresname_col   
 271.30  555.87 moveto
( MG 2) Nligresnam_size Center
( MG 2) Nligresnam_size Print
Nligresname_col   
 112.85  502.47 moveto
(Ala 462(A)) Nligresnam_size Center
(Ala 462(A)) Nligresnam_size Print
grestore
....
....
[download]

paste the correct code to help beginners like me

#!/usr/local/bin/perl
use strict;
use warnings;
use LWP::Simple;
open (DATA, "</your_path/your_file.pl") || die "impossibile apr
+ire il file";

my ( @hydrophobic , @residue );

while ( my $r = <DATA> )
{
  if ( $r=~ m/Hydrophnam_size Center/ .. $r =~ /Hydrophnam_size/ )
  {
    push @hydrophobic , $r;
    next;
  }

  if( $r=~ m/Nligresnam_size Center/ .. $r =~ /Nligresnam_size/)
  {
    push @residue , $r;
  }
}

printf "legami idrofobici: %s\n" , join '' , @hydrophobic;

printf "legami idrogeno: %s\n" , join '' , @residue;

__DATA__
[download]

Comment on SOLVED:problems with pattern match Select or Download Code

Replies are listed 'Best First'.
Re: problems with pattern match by linuxer (Curate) on Apr 21, 2009 at 09:29 UTC
Hi, please insert the closing `</code>` in your post. additionally please put that code section into `<readmore>` tags. See Markup in the Monastery for details. Read more... (305 Bytes) Your description is unclear. So you want to parse the Postscript data and extract some information. But you didn't tell us, what you want to extract. Can you please add more details?	[reply] [d/l] [select]
Re^2: problems with pattern match by paola82 (Sexton) on Apr 21, 2009 at 10:11 UTC
sorry but I've done the update and in the preview it seems ok....what happend I put my code between "code" script "/code" and the the comment between "p" and "/p"	[reply]
Re: problems with pattern match by parv (Parson) on Apr 21, 2009 at 11:07 UTC
Could you please adopt a style, any style, for your programs? See perlstyle for some guidance & search around here on the topic. Problem is that you seem to have data on multiple lines that you are trying to match, but you are reading & matching only one line at a time. Try this ... Read more... (1481 Bytes)	[reply] [d/l]
Re^2: problems with pattern match by paola82 (Sexton) on Apr 21, 2009 at 11:49 UTC
Thank you, but I tried but it doesn't work...It only print legami idrofobici: legami idrogeno: so the script runs but it doesn't do what I want... #!/usr/local/bin/perl use strict; use warnings; use LWP::Simple; open (IN, "</home/nerone/Desktop/lig/1xmj.pl") \|\| die "impossibile apr +ire il file"; my ( @hydrophobic , @residue ); while ( my $r = <DATA> ) { if ( $r=~ m/Hydrophnam_size Center/ .. $r =~ /Hydrophnam_size/ ) { push @hydrophobic , $r; next; } if( $r=~ m/Nligresnam_size Center/ .. $r =~ /Nligresnam_size/) { push @residue , $r; } } printf "legami idrofobici: %s\n" , join '' , @hydrophobic; printf "legami idrogeno: %s\n" , join '' , @residue; __DATA__ [download] I don't know well that synthax....but it doesn't work	[reply] [d/l]
Re^3: problems with pattern match by parv (Parson) on Apr 21, 2009 at 11:57 UTC
`[...]` I tried but it doesn't work...It only print legami idrofobici: legami idrogeno: so the script runs but it doesn't do what I want. `... open (IN, "</home/nerone/Desktop/lig/1xmj.pl") \|\| die "impossibile apr +ire il file"; my ( @hydrophobic , @residue ); while ( my $r = <DATA> ) { ... }` [download] I used `DATA` file handle so that portion of your own input could be appended to the program itself to form self contained example. Given your changes, the program expectedly did not print anything. Please read about open function and DATA file handle (under "Special Literals" subsection). You need to replace `DATA` file handle with `IN` (not the other way around) and try again. After seeing "SOLVED" & posted code in OP: emphasised the replacement & added parenthetical clarification for good measure. sigh	[reply] [d/l] [select]