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 #####*
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
