I can repeat the bug.
I did exactly the same steps as you did, so no other file formats / 3D
There is one difference, though:
Open Babel 1.100.2 -- Mar 17 2004 -- 09:15:41
Open Babel 1.100.1 -- Aug 3 2003 -- 12:04:24
So maybe the bug exists only in the newer version?
Regards and thanks for helping out,
At 17:58 23.8.2004 +0100, you wrote:
>At 17:31 19/08/2004 +0300, Winnie Wefelmeyer wrote:
>>Well, in that case I think it is a bug in OpenBabel.
>>The entire process was done with OpenBabel:
>>I converted a mol file into a cml file.
>>Both files were then converted into SMILES, which yielded the below
>>To me it also seems like the second structure is incorrect, since other
>>tools gave me the first structure out of both files (for example cdk).
>I cannot repeat the bug! My operations were:
>Open Babel 1.100.1 -- Aug 3 2003 -- 12:04:24
>Usage: src/babel [-i<input-type>] <name> [-o<output-type>] <name>
>Try `babel -H' for more information.
>D:\sourceforge\openbabel>src\babel -imdl test\C12308.mol -ocml test\C12308.cml
>D:\sourceforge\openbabel>src\babel -imdl test\C12308.mol -osmi test\C12308.smi
>D:\sourceforge\openbabel>src\babel -icml test\C12308.cml -osmi
>The output files are:
>(Note, however that there *DOES* appear to be a problem at one of the
>atoms. Can anyone reproduce this?)
>You will see that your file starts:
> ISISHOST08160423312D 1 1.00000 0.00000 14771
> 27 31 0 1 0 999 V2000
> 4.3958 -12.0458 0.0000 H 0 0 0 0 0 0 0 0 0
> 3.9875 -11.3291 0.0000 C 0 0 1 0 0 0 0 0 0
>and the 2D in line 2 asserts it is a 2D structure. AFAICS OB has
>transmitted this faithfully. It seems that at some stage you have
>converted it into a 3D format and then re-input it. Here are two examples
>of dangerous conversions:
>convert to PDB and then to SMI:
>(all bond orders are lost)
>convert to XYZ and then SMI:
>all bonds are lost.
>I think you must have converted to a format which only manages 3D
>coordinates and which then joined atoms in the 2D representation. It does
>not seem to be a MOL/CML/OpenBabel problem.
>try the steps I have given above and see if it works.
>>If anybody is interested, I could supply the mol file I used.
>>At 09:45 19.8.2004 +0100, you wrote:
>>>On Aug 19 2004, Winnie Wefelmeyer wrote:
>>>>thank you very much for your response. Unfortunately I don't know
>>>>whether the SMILES are identical.
>>>>I entered them at the below mentioned address, but the outcome was
>>>>Here they are: SMILE resulting from mol file:
>>>>SMILE resulting from cml, which has formerly been the same mol file as
>>>These are different molecules - the second has clearly 7 rings and its
>>>structure is unlikely to be correct.
>>>IFF you can track it to a problem in Openbabel (i.e. Openbabel is the
>>>only software used) then it may be a bug. My own guess is that it has 2D
>>>coordinates which are being presented to OB as 3D and it is making extra
>>>connections - that is a common problem with Molfiles. But it doesn't
>>>seem like an Openbabel or CML problems per se and I doubt the list can
>>>help much more.
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