[Open Babel] fixed format for Fenske-Hall z-matrix ?

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[Open Babel] fixed format for Fenske-Hall z-matrix ?

Vincent Favre-Nicolin-2
        Hi,

   I am using the Fenske-Hall z-matrix as input for my program. I just tried
converting a small protein using that format (pdb->fhz) but unfortunately OB
uses a fixed length of 3 digits for atom numbers, which limits to 999 atoms
(and has no space above 100 atoms).
e.g.:
............
C  99 1.441 92 124.927 91 178.1
C 100 1.508 99 109.285 92 295.7
O 101 1.233100 121.531 99 151.9
C 100 1.532 99 109.718 92 177.2
C 103 1.514100 114.835 99 307.0
C 104 1.523103 111.223100 247.7
N 105 1.465104 110.926103 255.3

............
   Is the Fenske-Hall z-matrix format strictly formated, or is it possible to
increase the width of the index of previous atoms ?
e.g.
sprintf(buffer,"%-2s %5d %6.3f %5d %8.3f %5d %6.1f",...
rather than
sprintf(buffer,"%-2s%3d%6.3f%3d%8.3f%3d%6.1f",...

        Vincent
--
Vincent Favre-Nicolin
Université Joseph Fourier
http://v.favrenicolin.free.fr
ObjCryst & Fox : http://objcryst.sourceforge.net


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Re: [Open Babel] fixed format for Fenske-Hall z-matrix ?

Geoffrey Hutchison

On Oct 7, 2005, at 6:59 PM, Vincent Favre-Nicolin wrote:

> converting a small protein using that format (pdb->fhz) but  
> unfortunately OB
> uses a fixed length of 3 digits for atom numbers, which limits to  
> 999 atoms
> (and has no space above 100 atoms).
> ............
>    Is the Fenske-Hall z-matrix format strictly formated, or is it  
> possible to
> increase the width of the index of previous atoms ?

The current versions of Fenske-Hall are available from Texas A&M:
http://www.chem.tamu.edu/jimp/
http://www.chem.tamu.edu/jimp2/

I suspect that the file format has changed--the "sample files" do not  
look at all like the old Babel format now in Open Babel. While the  
JIMP program looks like it supports well more than 999 objects, it is  
practically much easier to just create a "Fox" or "ObjCryst" format  
for your purposes. Make a copy of the fhformat.cpp, make your  
changes, and edit away.

Alternatively, use Open Babel as a library inside your program and  
you can read in any format you want -- access the OBMol object after  
reading in the file.

Cheers,
-Geoff


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