Re: [Open Babel] Smiles for diphosphorus

2013-11-08 Thread Craig James
On Fri, Nov 8, 2013 at 8:57 AM, Scott McKechnie 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 p

Re: [Open Babel] Smiles for diphosphorus

2013-11-08 Thread Scott McKechnie
Hi Craig, Thanks for the reply. I used sdf: obabel -:'P#P' -osdf > P2.sdf --gen3d Best wishes, Scott On 8 November 2013 15:17, Craig James wrote: > On Fri, Nov 8, 2013 at 3:52 AM, scott_m wrote: > >> Hi all, >> >> When I use gen3d with P#P I get a molecule with two hydrogens. Should it >>

Re: [Open Babel] Smiles for diphosphorus

2013-11-08 Thread Craig James
On Fri, Nov 8, 2013 at 3:52 AM, scott_m 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. > Differe

[Open Babel] Smiles for diphosphorus

2013-11-08 Thread scott_m
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. Best wishes, Scott -- View this message in context: http://forum