Re: [Open Babel] OpenBabel calculating wrong formula

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Hi Noel,

Thanks for the response.

Would it be hard to add a command line switch for the CML and/or SMILES
reader(s) to suppress any attempts to add implict hydrogens?

I have structures coming from QM calculations and thefore I know all
hydrogens and don't want any to be added (even my SMILES have explicit
hydrogens).
Some of my structures have even free valencies and I want to make sure that
they get SMILES that are different from the hydrogenated analogs (e.g.
[Si][Si] vs. [SiH3][SiH3]).

Currently I'm  comparing the formula calculated by OB to the one from the
QM file to find cases where the structure gets messed up. It's a bit
frustrating that in those three cases from my previous mail the SMILES is
actually correct, but only the formula gets messed up.

Oliver

On Tuesday, December 9, 2014, Noel O'Boyle <bao...@gm...> wrote:

> Hi Oliver,
>
> You are hitting an OB bug. The SMILES reader (among others) does not
> set the implicit hydrogen correctly. I've done some work on sorting
> this out, but it's kind of "on the long finger" now.
>
> Regards,
> - Noel
>
> On 9 December 2014 at 19:53, Oliver Stueker
> <rev...@us... <javascript:;>> wrote:
> > Hi,
> >
> > I'm trying to use OpenBabel (Open Babel 2.3.2 -- Jan 21 2014 -- 23:20:09
> > from Ubuntu 14.04)
> > to generate normalized SMILES strings.
> >
> > I've noticed that for some cases, it generates wrong a formula (which I
> want
> > to use as a sanity check).
> >
> > Here are the offending formulas that I have found so far:
> >
> > Formula     SMILES                     Formula(obabel)
> > B2H6        [BH2]12[H][BH2]2[H]1       B2H8
> > CHP         [CH]=P                     CH2P
> > P4          [P]P1P=P1                  H2P4
> >
> > At the bottom are commands to verify the behaviour.
> >
> > As one can see the SMILES to SMILES conversion is correct as well as the
> > generated SDF file,
> > but the formula property has too many hydrogen atoms.
> >
> > Can someone figure out what exactly is going on there?
> >
> > Also please see the issues I have filed regarding the automatic
> implication
> > of hydrogen atoms when reading CML files, that can't be turned off:
> > http://sourceforge.net/p/openbabel/bugs/947/
> > http://sourceforge.net/p/openbabel/feature-requests/172/
> >
> >
> > Thanks,
> > Oliver
> >
> >
> ------------------------------------------------------------------------------------------------
> >
> ------------------------------------------------------------------------------------------------
> >
> ------------------------------------------------------------------------------------------------
> > $ echo "[BH2]12[H][BH2]2[H]1" | obabel -i smi -o can
> > [BH2]12[H][BH2]1[H]2
> > 1 molecule converted
> > ##### SMILES to SMILES: OK #####
> >
> ------------------------------------------------------------------------------------------------
> > $ echo "[BH2]12[H][BH2]2[H]1" | obabel -i smi  --add formula -o sdf
> > ==============================
> > *** Open Babel Warning  in WriteMolecule
> >   No 2D or 3D coordinates exist. Stereochemical information will be
> stored
> > using an Open Babel extension. To generate 2D or 3D coordinates instead
> use
> > --gen2D or --gen3D.
> >
> >  OpenBabel12041410482D
> >
> >   8  9  0  0  0  0  0  0  0  0999 V2000
> >     0.0000    0.0000    0.0000 B   0  0  0  0  0  0  0  0  0  0  0  0
> >     0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
> >     0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
> >     0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
> >     0.0000    0.0000    0.0000 B   0  0  0  0  0  0  0  0  0  0  0  0
> >     0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
> >     0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
> >     0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
> >   1  2  1  0  0  0  0
> >   1  3  1  0  0  0  0
> >   1  8  1  0  0  0  0
> >   1  4  1  0  0  0  0
> >   1  5  1  0  0  0  0
> >   4  5  1  0  0  0  0
> >   5  6  1  0  0  0  0
> >   5  7  1  0  0  0  0
> >   5  8  1  0  0  0  0
> > M  END
> >>  <formula>
> > B2H8
> >
> > $$$$
> > 1 molecule converted
> > ##### SMILES to Formula: NOT OK #####
> >
> ------------------------------------------------------------------------------------------------
> >
> ------------------------------------------------------------------------------------------------
> >
> ------------------------------------------------------------------------------------------------
> > $ echo "[CH]=P" | obabel -i smi -o can
> > [CH]=P
> > 1 molecule converted
> > ##### SMILES to SMILES: OK #####
> >
> ------------------------------------------------------------------------------------------------
> > $ echo "[CH]=P" | obabel -i smi  --add formula -o sdf
> > ==============================
> > *** Open Babel Warning  in WriteMolecule
> >   No 2D or 3D coordinates exist. Stereochemical information will be
> stored
> > using an Open Babel extension. To generate 2D or 3D coordinates instead
> use
> > --gen2D or --gen3D.
> >
> >  OpenBabel12051413272D
> >
> >   3  2  0  0  0  0  0  0  0  0999 V2000
> >     0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
> >     0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
> >     0.0000    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
> >   1  2  1  0  0  0  0
> >   1  3  2  0  0  0  0
> > M  RAD  1   1   2
> > M  END
> >>  <formula>
> > CH2P
> >
> > $$$$
> > 1 molecule converted
> > ##### SMILES to Formula: NOT OK #####
> >
> ------------------------------------------------------------------------------------------------
> >
> ------------------------------------------------------------------------------------------------
> >
> ------------------------------------------------------------------------------------------------
> > $ echo "[P]P1P=P1" | obabel -i smi -o can
> > [P]P1P=P1
> > 1 molecule converted
> > ##### SMILES to SMILES: OK #####
> >
> ------------------------------------------------------------------------------------------------
> > $ echo "[P]P1P=P1" | obabel -i smi -o sdf --add formula
> > ==============================
> > *** Open Babel Warning  in WriteMolecule
> >   No 2D or 3D coordinates exist. Stereochemical information will be
> stored
> > using an Open Babel extension. To generate 2D or 3D coordinates instead
> use
> > --gen2D or --gen3D.
> >
> >  OpenBabel12091416012D
> >
> >   4  4  0  0  0  0  0  0  0  0999 V2000
> >     0.0000    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
> >     0.0000    0.0000    0.0000 P   0  0  3  0  0  0  0  0  0  0  0  0
> >     0.0000    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
> >     0.0000    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
> >   1  2  1  0  0  0  0
> >   2  4  1  1  0  0  0
> >   2  3  1  1  0  0  0
> >   3  4  2  0  0  0  0
> > M  RAD  1   1   3
> > M  END
> >>  <formula>
> > H2P4
> >
> > $$$$
> > 1 molecule converted
> > ##### SMILES to Formula: NOT OK #####
> >
> ------------------------------------------------------------------------------------------------
> >
> >
>

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