Please reply to the list.
is this one record of the file or is this an entire file?
be sure and read the docs for doing this kind of thing:
perldoc -f open
--
basically you want to do something like this. this is enought to get you
started. you won't learn anything if i write it for you.
open(F, "<yourfile") or die "could not open: $!\n";
while (<FH>) {
s/^\s+//; # strip leading spaces
$header = $_ if /HEADER/; # grab header line
$auth = $_ if /AUTHOR/; #grap author line
push (@atom, $_) if /ATOM/; #push atom lines into an array
...
}
to further parse this and grab what you want like 'code', 'author name' ,
and the atom lines you want
perldoc -f split
perldoc -f substring
perldoc -f grep
> -----Original Message-----
> From: Baris Ozol [mailto:[EMAIL PROTECTED]]
> Sent: Tuesday, June 25, 2002 10:13 AM
> To: 'Kipp, James'
> Subject: RE: HElP ...me!
>
>
>
> Thanks for reply.. I put a small example of the file .. I just want to
> find header and write as
> 'this is an Oxygen Transport protein isolated at 08-DEC-97
> and its code
> is 1A00'
>
> And I want to get author name. AS the format I showed you.
>
> And I want to get ATOM (1 by 1) like 'in the 3rd order Atom is C. it's
> located on VAL' and so on.
>
>
> HEADER OXYGEN TRANSPORT 08-DEC-97 1A00
> TITLE HEMOGLOBIN (VAL BETA1 MET, TRP BETA37 TYR) MUTANT
> COMPND MOL_ID: 1;
> EXPDTA X-RAY DIFFRACTION
> AUTHOR J.S.KAVANAUGH,A.ARNONE
> REVDAT 1 18-MAR-98 1A00 0
> JRNL REF TO BE PUBLISHED
> REMARK 900 1A0X, 1A0Y, 1A0Z, 1A01.
> DBREF 1A00 A 1 141 SWS P01922 HBA_HUMAN 1 141
> SEQADV 1A00 MET B 1 SWS P02023 VAL 1 ENGINEERED
> SEQRES 1 A 141 VAL LEU SER PRO ALA ASP LYS THR ASN VAL LYS ALA ALA
> SEQRES 2 A 141 TRP GLY LYS VAL GLY ALA HIS ALA GLY GLU TYR GLY ALA
> SEQRES 4 B 146 ARG PHE PHE GLU SER PHE GLY ASP LEU SER THR PRO ASP
> HELIX 32 32 LEU D 81 THR D 84 14
> HELIX 33 33 ALA D 86 ASP D 94 19
> HELIX 34 34 PRO D 100 GLU D 121 522
> HELIX 35 35 PRO D 124 ALA D 142 119
> LINK FE HEM A 142 NE2 HIS A 87
> CRYST1 84.100 112.000 63.800 90.00 90.00 90.00 P 21 21 21 8
> 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 0.011891 0.000000 0.000000 0.00000
> SCALE2 0.000000 0.008929 0.000000 0.00000
> SCALE3 0.000000 0.000000 0.015674 0.00000
> MTRIX1 1 0.950670 -0.050560 0.306050 5.59928 1
> MTRIX2 1 -0.051200 -0.998670 -0.005940 90.78605 1
> MTRIX3 1 0.305940 -0.010020 -0.952000 -20.34795 1
> ATOM 1 N VAL A 1 101.601 38.534 -1.962 1.00 53.29 N
> ATOM 4514 OXT HIS D 146 74.219 58.700 -6.876 1.00 18.18 O
> TER 4515 HIS D 146
> HETATM 4516 FE HEM D 147 74.555 59.956 11.896 1.00
> 17.05 FE
> HETATM 4517 CHA HEM D 147 73.915 63.268 12.452 1.00 21.37 C
> HETATM 4518 CHB HEM D 147 71.553 59.151 13.248 1.00 17.90 C
> HETATM 4774 O HOH 473 72.622 28.948 11.969 1.00 24.04 O
> CONECT 650 648 649 1071
> CONECT 1071 650 1076 1087 1095
> MASTER 217 0 4 35 0 0 0 9 4770 4 180 46
> END
>
> -----Original Message-----
> From: Kipp, James [mailto:[EMAIL PROTECTED]]
> Sent: Tuesday, June 25, 2002 9:15 AM
> To: [EMAIL PROTECTED]
> Subject: RE: HElP ...me!
>
> can you tell us how the data is file is formatted currently? also and
> code
> you have done so far. and what you want to do with it?
>
> > -----Original Message-----
> > From: Baris Ozol [mailto:[EMAIL PROTECTED]]
> > Sent: Tuesday, June 25, 2002 9:10 AM
> > To: [EMAIL PROTECTED]
> > Subject: HElP ...me!
> >
> >
> > Hi everybody,
> >
> > Hopefully some of you will help to solve my problem!!
> > I'm trying to parse a flat file formatted file. It's a PDB
> > (Protein Data
> > Bank).
> >
> > But I didn't find any script on internet and perl.com.
> > If you'll help me, I will be happy and solve the problem..
> >
> > Thank you.
> >
> > Bryce
> >
> >
> >
> > --
> > To unsubscribe, e-mail: [EMAIL PROTECTED]
> > For additional commands, e-mail: [EMAIL PROTECTED]
> >
> >
>
>
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>
>
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