I second Geoff's recommendation: It's not a good idea to use the order of
atoms in a SMILES for anything. For your problem, consider this:
N(O=N(O)CC)C1CCCCCCCCCCC(Cl)C=1Br
It's really not reasonable to try to analyze the string to figure out which
atoms are connected to the double bond, unless you want to build a full
SMILE parser. Note that this uses the legal but unusual syntax of marking
the double bond on the second of the pair of ring-closure digits. For
reference, here's what it looks like:
[image: Inline image 2]
There is also no reason to think that the atoms in the SMILES will be
written in the same order as the xyz file.
Craig
On Wed, Sep 13, 2017 at 5:35 AM, Volker Settels <volker.sett...@basf.com>
wrote:
> Hi Geoff,
>
>
>
> Thanks a lot for your help!
>
>
>
> I checked a couple of xyz files generated from SMILES. In these files, the
> hydrogens are always listed after the “heavy” atoms. If the “heavy” atoms
> always are listed in the same order than in the SMILES, counting characters
> to find double bonds could work. What would you think?
>
>
>
> My task is to perform a conformational search for a list of molecules. For
> this reason, I have to identify double bonds, which should be excluded from
> conformational search due to fixed stereochemistry (‘\’ or ‘/’ in SMILES).
> Assuming the following SMILES:
>
>
>
> CC\=\CCN=CC
>
>
>
> I have to think about a routine which gives me the atoms involved only in
> the first double bond of the SMILES above. After transforming the SMILES
> into a format including the 3D structure, I still have to gather the
> information about double bonds with specified stereochemistry. Is this
> possible in the sdf format? I am not used to this format.
>
>
>
> Best wishes
>
>
>
> Volker
>
>
>
> *Von:* Geoffrey Hutchison [mailto:geoff.hutchi...@gmail.com]
> *Gesendet:* Dienstag, 12. September 2017 22:04
> *An:* Volker Settels <volker.sett...@basf.com>
> *Cc:* openbabel-disc...@lists.sf.net
> *Betreff:* Re: [Open Babel] Conversion SMILES to XYZ
>
>
>
> That likely won't work, because in general the SMILES doesn't include
> hydrogens.
>
>
>
> If you want to follow double-bonds, I recommend converting to a file
> format with bonding information, e.g., SDF.
>
>
>
> Best regards,
>
> -Geoff
>
>
>
> this is a question regarding the conversion of SMILES to xyz. I have to
> identify atoms in the generated xyz file, which are involved in double
> bonds with fixed stereochemistry according to the SMILES. A fast solution
> would be just to count atoms until ‘/’ or ‘\’ is found in the SMILES. But
> this is only possible, if it is ensured that in every case the order of
> atoms within the xyz file is identical to the one in the SMILE string. Is
> this the case? Thanks a lot for your help!
>
>
>
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