On Fri, Nov 8, 2013 at 8:57 AM, Scott McKechnie <mckec...@tcd.ie> wrote:
> Thanks for the reply. I used sdf:
>
> obabel -:'P#P' -osdf > P2.sdf --gen3d
>
When I do this, I get a molecule with four hydrogens, not two. However, I
still think it's wrong. The SMILES specification says that the "normal
valence" for phosphorus is three or five. That means it should have been
happy with the triple bond, but apparently it decided to add hydrogens to
bring it up to five.
I don't know if that's correct chemically (I'm not a chemist), but that's
what the SMILES spec says.
Craig
>
> Best wishes,
>
> Scott
>
>
> On 8 November 2013 15:17, Craig James <cja...@emolecules.com> wrote:
>
>> On Fri, Nov 8, 2013 at 3:52 AM, scott_m <js...@cam.ac.uk> wrote:
>>
>>> Hi all,
>>>
>>> When I use gen3d with P#P I get a molecule with two hydrogens. Should it
>>> not
>>> be the diphosphorus molecule with chemical formula P2? Using [P]#[P]
>>> produces the desired result but I wanted to find out why gen3d does this.
>>>
>>
>> Different file readers (SMILES, SDF, MOL2, InChI ...) have different
>> rules for hydrogens. Which did you use? Or was this a C++ program that you
>> wrote?
>>
>> Craig
>>
>>
>>>
>>> Best wishes,
>>>
>>> Scott
>>>
>>>
>>>
>>> --
>>> View this message in context:
>>> http://forums.openbabel.org/Smiles-for-diphosphorus-tp4656815.html
>>> Sent from the General discussion mailing list archive at Nabble.com.
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> 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
