Re: [Open Babel] Two smi conversion problems

I originally used "C=0" but using "[C-]#[O+]" gives the following roundtrip for me: [C-]#[O+] -> SDF -> [C-]#[OH] Since writing the above I tried installing the latest version of Open Babel and using "C=0" now gives an error and using "[C-]#[O+]" gives the correct result. Thanks for the help with

Re: [Open Babel] Two smi conversion problems

> Thanks for the reply, the sdf file was actually produced from a smiles string > using gen3d. OK, I guessed that, but what was the original SMILES? And what version of Open Babel are you using? The current development code roundtrips: [C-]#[O+] -> SDF -> [C-]#[O+] Thanks, -Geoff--

Re: [Open Babel] Two smi conversion problems

Thanks for the reply, the sdf file was actually produced from a smiles string using gen3d. Best wishes, Scott On 12 March 2014 22:05, Geoffrey Hutchison wrote: > 1. When converting a sdf file (see attached) for carbon monoxide to smi > format I get the following smi result: > > [C-]#[OH] > > >

Re: [Open Babel] Two smi conversion problems

1. When converting a sdf file (see attached) for carbon monoxide to smiformat I get the following smi result:[C-]#[OH]The SDF says it came through Open Babel.. presumably from some other format. It gives formal charges:M  CHG  2   1  -1   2   1This gives a -1 charge to the carbon and +1 to the oxyg

[Open Babel] Two smi conversion problems

Hi all, 1. When converting a sdf file (see attached) for carbon monoxide to smi format I get the following smi result: [C-]#[OH] 2. Hydrogens are inserted when converting the smiles P#P for the diphosphorus molecule to sdf format (see attached) using gen3d. Best wishes, Scott CO.sdf