Hi,
in principle there should be no restriction on the under limit for the number
of atoms, so I can’t recall exactly why we did put this 'atoms < 3’ restriction
in the code in first instance. So I guess you can safely remove this check and
replace it with a lower limit like 1 or so.
Hans
On 08 Nov 2013, at 00:25, David Hall <li...@cowsandmilk.net> wrote:
> I know nothing about what spectrophores are, but I can tell you all the
> molecules you provided have 2 atoms.
>
> The code for spectrophores checks if your molecule has at least 3 atoms. And
> gives you the error you've listed if your molecule has less than 3 atoms:
> https://github.com/openbabel/openbabel/blob/master/src/spectrophore.cpp#L227
>
> Presumably, there is something about spectrophore calculation that requires 3
> atoms. Maybe someone from silicos-it can give some details.
>
> -David
>
>
>
> On Thu, Nov 7, 2013 at 5:05 PM, Wendy Hawley Carande <whaw...@gmail.com>
> wrote:
> Hello,
>
> I'm a relatively new Open Babel user. I looked through the archives, but I
> couldn't find help for this problem. I apologize if the answer has already
> been presented.
>
> I'm using obspectrophore on a large number of mol files. For most of the
> files, everything runs smoothly, but for a few I get an error message:
> OBSpectrophore::GetSpectrophore() error: not enough atoms in molecule
> Error calculating Spectrophore from molecule number 0 (counting starts at 0)!
>
> Below I will paste the mol files for reference. Please let me know if you
> have any suggestions. I have used both version 2.3.1 and the development
> version 2.3.90.
>
> Thank you for your time!
> Wendy
>
> ________________________
>
> 5160
> OpenBabel11061313593D
>
> 2 1 0 0 0 0 0 0 0 0999 V2000
> 0.5698 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.5698 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 3 0 0 0 0
> M CHG 2 1 -1 2 1
> M END
> ________________________
>
> 5666
> OpenBabel11061313593D
>
> 2 1 0 0 0 0 0 0 0 0999 V2000
> -1.2867 0.0000 0.0000 I 0 0 0 0 0 0 0 0 0 0 0 0
> 1.2867 0.0000 0.0000 I 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0 0 0 0
> M END
> ________________________
>
> 5819
> OpenBabel11061313593D
>
> 2 1 0 0 0 0 0 0 0 0999 V2000
> -0.5585 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> 0.5585 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 3 0 0 0 0
> M END
> ________________________
>
> 5843
> OpenBabel11061313593D
>
> 2 1 0 0 0 0 0 0 0 0999 V2000
> -0.9900 0.0000 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
> 0.9901 0.0000 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0 0 0 0
> M END
> ________________________
>
> ------------------------------------------------------------------------------
> November Webinars for C, C++, Fortran Developers
> Accelerate application performance with scalable programming models. Explore
> techniques for threading, error checking, porting, and tuning. Get the most
> from the latest Intel processors and coprocessors. See abstracts and register
> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
> _______________________________________________
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
> ------------------------------------------------------------------------------
> November Webinars for C, C++, Fortran Developers
> Accelerate application performance with scalable programming models. Explore
> techniques for threading, error checking, porting, and tuning. Get the most
> from the latest Intel processors and coprocessors. See abstracts and register
> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk_______________________________________________
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
------------------------------------------------------------------------------
November Webinars for C, C++, Fortran Developers
Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss