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P:\test>perl -MO=Deparse 376142-dl.pl >376142.pl
376142-dl.pl syntax OK

if ($line =~ 
    /$atomid.*\s*\w+\s+$resid\s+$atomidmatch.* \w+\s+$residmatch\s+\d\
+./ 
...
    print OUTFILE "array2[$el]\n";
    last;
}

sub outputIf {
    my( $line, $atomid, $atomidmatch, 
...
    }
    return 0;
}

last if outputIf( $line, $atomid, $atomidmatch, $1, $2, $array2[$el], 
+\*OUTFILE );

if ($array2[$el + 10] =~ /resid (\d+) and name (H\w+\d*).?\)/ 
and $array2[$el     ] =~ /resid (\d+) and name (H\w+\d*).?\)/) {
...
        }
    }
}

@array2 = <KATFILE>;
chomp @array2;
...
    print OUTFILE "$array2[$el]\n";
}

sub whileIf {
    my( $arrayRef, $el, $offset, $distfile, $outfile ) = @_;
...
    }
    return 0;
}

$katfile = '/remote/belgarath/tpukala/pegasus/xplor/signif/25jun2.kat2
+';
$outfile = 'temp.kat';
...
    }
    return 0;
}