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Dear Grant,
computer programs split fields based on a 'field separator', usually
e.g. a space or tab or end-of-line. There is nothing to separate
"1.00201.10" into two fields, and you as a human only can read this
because you know that
a) these should be two numbers
b) the occupancy has a precision of two digits.
You need to read in the line as fixed format - in C this is
the family of scanf-function which might also exist in python.
You can use 'cut' with the '-c' option to split the fields as
preparation for your python program.
Cheers,
Tim
On 06/06/2013 06:37 AM, 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
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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