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
> ________________________
>
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