[EMBOSS] pdbparse format

Peter Robinson Peter.Robinson at t-online.de
Mon Jan 31 20:04:26 UTC 2005

Hi list,

I have been looking into the new pdbparse program and am writing a
routine to parse the output of that program into a Java program I am
writing to do some datamining on PDB files. For the moment at least I am
writing a parse routine based on column positions rather than on regular
expressions or some other approach.
I would appreciate some help in understanding the output format. I have
been looking at the function ajPdbWriteAll. 

ajFmtPrintF(outf, "%-2c%6S    %-4S%8.3f%9.3f%9.3f<snip>, 

this should print out the 
"%-2c":  1char AA (left-justified, 2 spaces)
"%6S    ": 3charAA (right-justified, 6 spaces, followed by 4 spaces)
"-4S": AtomType (e.g., CA) (left-justified, 4 spaces)
"%8.3" x coord, 8 spaces with 3 precision 
"%9.3" y coord  9 spaces with 3 precision
"%9.3" z coord  9 spaces with 3 precision

==> If I am reading this correctly, why does the x coord have one less
space than y and z?
==> Can one consider this output format fixed, or will it be subject to
==> Excuse what may seem like a trivial question, but I don't want my
program to break down "at an embarassing moment". 


Peter N. Robinson
peter.robinson at t-online.de
peter.robinson at charite.de

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