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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