hi,
the fields can not be splitted using /s because some fields have common
boundaries, i.e. some fields are from column 31-38 and the next field starts
from 39.. As in
COLUMNS DATA TYPE FIELD DEFINITION
---------------------------------------------------------------------------------
1 - 6 Record name "ATOM "
7 - 11 Integer serial Atom serial number.
these are the 1st two fields.
On 5/9/05, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
>
>
>
> ----- Original Message -----
> From: Aditi Gupta <[EMAIL PROTECTED]>
> Date: Monday, May 9, 2005 11:41 am
> Subject: extracting coordinates
>
> > Hi everyone,
> Hello Aditi,
>
> >
> > That code is working...
> > But my specific problem is as follows:
> >
> > i have a file in which data is stored as
> >
> > HELIX 4 4 VAL 74 LEU 84 1 11
> > CRYST1 33.020 33.750 75.670 90.00 90.00 90.00 P 21 21 21 4
> > ORIGX1 1.000000 0.000000 0.000000 0.00000
> > ORIGX2 0.000000 1.000000 0.000000 0.00000
> > ORIGX3 0.000000 0.000000 1.000000 0.00000
> > SCALE1 0.030285 0.000000 0.000000 0.00000
> > SCALE2 0.000000 0.029630 0.000000 0.00000
> > SCALE3 0.000000 0.000000 0.013215 0.00000
> > ATOM 1 N LEU 2 -10.586 -14.055 54.397 1.00 49.37 N
> > ATOM 2 CA LEU 2 -9.711 -13.341 53.419 1.00 48.40 C
> > ATOM 3 C LEU 2 -10.401 -12.068 52.928 1.00 46.56 C
> > ATOM 4 O LEU 2 -11.440 -12.138 52.267 1.00 47.05 O
> > ATOM 5 CB LEU 2 -9.417 -14.253 52.223 1.00 51.90 C
> > ATOM 6 CG LEU 2 -7.974 -14.441 51.748 1.00 54.45 C
> > ATOM 7 CD1 LEU 2 -7.365 -13.109 51.342 1.00 53.43 C
> > ATOM 8 CD2 LEU 2 -7.160 -15.095 52.852 1.00 55.22 C
> > ATOM 9 N THR 3 -9.833 -10.909 53.259 1.00 42.49 N
> > ATOM 10 CA THR 3 -10.405 -9.634 52.826 1.00 40.93 C
> > ATOM 11 C THR 3 -10.060 -9.403 51.362 1.00 41.24 C
> >
> >
> >
> > the fields of records having ATOM as 1st field are as follows:
> >
> > COLUMNS DATA TYPE FIELD DEFINITION
> > -------------------------------------------------------------------
> > --------------
> > 1 - 6 Record name "ATOM "
> >
> > 7 - 11 Integer serial Atom serial number.
> >
> > 13 - 16 Atom name Atom name.
> >
> > 17 Character altLoc Alternate location
> > indicator.
> > 18 - 20 Residue name resName Residue name.
> >
> > 22 Character chainID Chain identifier.
> >
> > 23 - 26 Integer resSeq Residue sequence number.
> >
> > 27 AChar iCode Code for insertion of
> > residues.
> > 31 - 38 Real(8.3) x Orthogonal
> > coordinates for X in
> > Angstroms.
> >
> > 39 - 46 Real(8.3) y Orthogonal
> > coordinates for Y in
> > Angstroms.
> >
> > 47 - 54 Real(8.3) z Orthogonal
> > coordinates for Z in
> > Angstroms.
> >
> > 55 - 60 Real(6.2) occupancy Occupancy.
> >
> > 61 - 66 Real(6.2) tempFactor Temperature factor.
> >
> > 73 - 76 LString(4) segID Segment identifier,
> > left-justified.
> >
> > 77 - 78 LString(2) element Element symbol, right-
> > justified.
> > 79 - 80 LString(2) charge Charge on the atom.
> >
> >
> >
> > I have to get the x,y,z coordinates of records whose atom name is
> > 'CA'(highlighted as blue).
> >
> > I wrote a code but its giving many errors..
> >
> > The code is:
> >
> >
> >
> > #!usr/bin/perl
> > use warnings;
> >
> > $filename = "1a32.txt";
> > chomp $filename;
>
> The above line is useless, perldoc -f chomp
>
> > open (FILEHANDLE, "$filename") or die "couldn't open $filename:$!";
> > @file= <FILEHANDLE>;
> > close (FILEHANDLE);
> >
> > $a= "ATOM";
> > $c= "CA";
> >
> > foreach $line(@file)
> > {
> > if(my $line =~ /^/$a/\s*
> > (\s*\d+)
> > \s*/$c/\s*
> > \d*
> > \w+
> > \s
> > \w
> > (\s*\d+)
> > \w*
> > (\s*\d*)
> > (\s*\d*)
> > (\s*\d*)
> > (\s*\d*)
> > (\s*\d*)
> > (\w*\s*)
> > (\s*\w*)
> > (\s*\w*)/)
>
> Youch, that is way to long of a regular expression [ atleast for me ], you
> may consider a shorter nested version such as my @fields =~ /([\w+\s+])/g.
> In any case I think split would work the best here [ my @fields = split
> /\s/,$line ], since your fields are locked into place. In general you PAD
> data, untill you get it all uniformed such as yours. Below is some simple
> code that should help you on your way, feel free to modify at will.
>
> >
> > {
> > my $x= substr($line,30,8);
> > my $y= substr($line,38,8);
> > my $z= substr($line,46,8);
> >
> > print "$x\t$y\t$z\n";
> > }
> > }
> >
> > #-------------------------------------------------
> >
> >
> >
> > The errors that i'm getting are:
> >
> > Scalar found where operator expected at two.pl line 15, near "/^/$a"
> > (Missing operator before $a?)
> > Unrecognized escape \d passed through at two.pl line 15.
> > Unrecognized escape \s passed through at two.pl line 15.
> > Unrecognized escape \w passed through at two.pl line 17.
> > Unrecognized escape \s passed through at two.pl line 17.
> > Unrecognized escape \w passed through at two.pl line 17.
> > Unrecognized escape \s passed through at two.pl line 17.
> > Backslash found where operator expected at two.pl line 22, near
> > "(\s*\" (Might be a runaway multi-line ** string starting on line 17)
> > (Missing operator before \?)
> > Unquoted string "d" may clash with future reserved word at two.pl
> > line 22.
> > Backslash found where operator expected at two.pl line 23, near ")
> > \"
> > (Missing operator before \?)
> > Unquoted string "w" may clash with future reserved word at two.pl
> > line 23.
> > Unrecognized escape \s passed through at two.pl line 24.
> > Backslash found where operator expected at two.pl line 25, near
> > "(\s*\" (Might be a runaway multi-line ** string starting on line 24)
> > (Missing operator before \?)
> > Unquoted string "d" may clash with future reserved word at two.pl
> > line 25.
> > Unrecognized escape \s passed through at two.pl line 26.
> > Backslash found where operator expected at two.pl line 27, near
> > "(\s*\" (Might be a runaway multi-line ** string starting on line 26)
> > (Missing operator before \?)
> > Unquoted string "d" may clash with future reserved word at two.pl
> > line 27.
> > Unrecognized escape \w passed through at two.pl line 28.
> > Backslash found where operator expected at two.pl line 29, near
> > "(\w*\" (Might be a runaway multi-line ** string starting on line 28)
> > (Missing operator before \?)
> > Unrecognized escape \w passed through at two.pl line 29.
> > syntax error at two.pl line 15, near "/^/$a"
> > Substitution replacement not terminated at two.pl line 31.
> >
> > Please help me..
> >
>
> #!usr/bin/perl
> use warnings;
> use strict;
> my $filename = "1a32.txt";
> my $Atom='CA';
>
> open (FILEHANDLE, "$filename") or die "couldn't open $filename:$!";
> @file= <FILEHANDLE>;
> close (FILEHANDLE);
>
> foreach my $line ( @file ){
>
> my @fields = split /\s/,$line;
> print "X: $fields[-4] Y: $fields[-3] Z: $fields[-2]\n" if uc $fields[2] eq
> '$Atom;
>
> }
>
> HTH,
> Mark G.
>
>
