[Open Babel] A couple of points

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[Open Babel] A couple of points

drc-2
I was testing all the comands in the user docs.

 >babel aceto_indes.fs aceto_results.sdf -s c1ccccc1Br -at5
5 molecules converted
However looking at the file it seems the molecule separator is missing?

MOL_00000105
 OpenBabel11140519413D

 10 10  0  0  0  0  0  0  0  0999 V2000
    1.1069   -0.0724    0.0000 C   0  0  0  0  0
    2.5552   -0.0724    0.0000 C   0  0  0  0  0
    0.3862    1.1552    0.0000 C   0  0  0  0  0
    0.3862   -1.3241    0.0000 C   0  0  0  0  0
    3.2724   -1.3241    0.0000 C   0  0  0  0  0
    3.2724    1.1552    0.0000 O   0  0  0  0  0
   -1.0276    1.1552    0.0000 C   0  0  0  0  0
   -1.0276   -1.3241    0.0000 C   0  0  0  0  0
   -1.7448   -0.0724    0.0000 C   0  0  0  0  0
   -3.1931   -0.0724    0.0000 Br  0  0  0  0  0
  1  2  1  0  0  0
  1  3  1  0  0  0
  1  4  2  0  0  0
  2  5  1  0  0  0
  2  6  2  0  0  0
  3  7  2  0  0  0
  4  8  1  0  0  0
  7  9  1  0  0  0
  8  9  2  0  0  0
  9 10  1  0  0  0
M  END
MOL_00000067
 OpenBabel11140519413D

 10 10  0  0  0  0  0  0  0  0999 V2000
   -0.3552    0.0483    0.0000 C   0  0  0  0  0

Should Inchi be amoungst the input/output formats?

In version 1 of babel there were various options for CML are they no longer available?

Are the descriptors that Nick England coded available?

The user docs are now upto 10 pages, do you want me to post them to this list or should I just send a file (what format) to you?

Thanks



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Re: [Open Babel] A couple of points

Geoffrey Hutchison

On Nov 14, 2005, at 2:51 PM, [hidden email] wrote:

> I was testing all the comands in the user docs.
> ...
> Should Inchi be amoungst the input/output formats?

The InChI code was only just recently made available under the LGPL.  
It is now possible for us to release OB-2.0 with InChI, so it will be  
added. I'm going to make a snapshot available ASAP.

> In version 1 of babel there were various options for CML are they  
> no longer available?

Yes. Try "babel -Hcml" to see the options. This is true for any  
format. Try "babel -Hxyz" to see options available for the XYZ format.

> Are the descriptors that Nick England coded available?

Do you mean:
mpd  Sybyl descriptor format
              [Molec_name]\t[atomtype];[layer]-[frequency]-
[neighbour_type];            Options: e.g. -xnc
              n prefix molecule names with name of file
              c use XML style separators instead
              i use IDX atom types of babel internal

Specification at: http://dx.doi.org/10.1021/ci034207y

> The user docs are now upto 10 pages, do you want me to post them to  
> this list or should I just send a file (what format) to you?

Why don't you post to the list in text or HTML. It's probably best to  
split them into multiple web pages, but thanks *very* much for doing  
this -- what you've posted so far is great. It really outlines how  
much functionality Chris Morley jammed into the new framework. :-)

Thanks,
-Geoff

P.S. Could you send me a copy of the iBabel documentation -- it'd be  
nice to have docs for the Mac and Windows GUIs too.


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