ATOM records have fixed format so you can (and should) use string
slicing instead, like so (one-liner)
serial, aname, altloc, resn, chid, resi, insCode, x, y, z, occ, b,
element, q = line[6:11], line[12:16], line[16], line[17:20], line[21],
line[22:26], line[26], line[30:38], line[38:46], line[46:54],
line[54:60], line[60:66], line[76:78], line[78:80]
or with more explicit typing
serial, aname, altloc, resn, chid, resi, insCode, x, y, z, occ, b,
element, q = int(line[6:11]), line[12:16].strip(), line[16].strip(),
line[17:20].strip(), line[21], int(line[22:26]), line[26],
float(line[30:38]), float(line[38:46]), float(line[46:54]),
float(line[54:60]), float(line[60:66]), line[76:78].strip(), line[78:80]
Cheers,
Ed.
On Thu, 2013-06-06 at 04:37 +0000, GRANT MILLS wrote:
> Dear CCP4BB,
>
> I'm trying to write a simple python script to retrieve and manipulate
> PDB data using the following code:
>
> #for line in open("PDBfile.pdb"):
> # if "ATOM" in line:
> # column=line.split()
> # c4=column[4]
>
> and then writing to a new document with:
>
> #with open("selection.pdb", "a") as myfile:
> # myfile.write(c4+"\n")
>
> Except for if the PDB contains columns which run together such as the
> occupancy and B-factor in the following:
>
> ATOM 608 SG CYS A 47 12.866 -28.741 -1.611 1.00201.10
> S
> ATOM 609 OXT CYS A 47 14.622 -24.151 -1.842 1.00100.24
> O
>
> My script seems to miscount the columns and read the two as one
> column, does anyone know how to avoid this? (PS, I've googled this
> like crazy but I either don't understand or the link is irrelevant)
>
> Any advice would help.
> Thanks for your time,
> Grant
>
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
----------------------------------------------
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------ / Lao Tse /
