Running the current OMG release on Centos 6.2 with composition C5H3ClN2O2 and requiring the fragment ClCCC#N (SMILES) gives many structures with pentavalent nitrogens e.g. O(OC(=CC#N)Cl)N=1=CC1 . Has anyone else observed this? Any suggestions for avoiding it, or filtering them out of the SDF output?
Thanks,
Peter.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
In the "MultiCore" implementation branch, there are more options available.
You can try "-filter" which removes some predefined "unusual"
structures. This is done on-the-fly and may even speed-up the process.
However, the filtered structures cannot be modified. I'm not sure if the
structure you mentioned would match any of the predefined ones.
You can also try the "-badlist" option to specify your own list of "bad"
structures that should be excluded. Note, however, that this filtering is
done a posteriori, which means it adds (slightly) to the computation time.
Regards
Mahdi
PS: Don't forget to cite the OMG and the PMG papers if you publish using
the tools! ;)
Running the current OMG release on Centos 6.2 with composition C5H3ClN2O2
and requiring the fragment ClCCC#N (SMILES) gives many structures with
pentavalent nitrogens e.g. O(OC(=CC#N)Cl)N=1=CC1 . Has anyone else observed
this? Any suggestions for avoiding it, or filtering them out of the SDF
output?
Hello there,
Running the current OMG release on Centos 6.2 with composition C5H3ClN2O2 and requiring the fragment ClCCC#N (SMILES) gives many structures with pentavalent nitrogens e.g. O(OC(=CC#N)Cl)N=1=CC1 . Has anyone else observed this? Any suggestions for avoiding it, or filtering them out of the SDF output?
Thanks,
Peter.
Hi Peter,
In the "MultiCore" implementation branch, there are more options available.
You can try "-filter" which removes some predefined "unusual"
structures. This is done on-the-fly and may even speed-up the process.
However, the filtered structures cannot be modified. I'm not sure if the
structure you mentioned would match any of the predefined ones.
You can also try the "-badlist" option to specify your own list of "bad"
structures that should be excluded. Note, however, that this filtering is
done a posteriori, which means it adds (slightly) to the computation time.
Regards
Mahdi
PS: Don't forget to cite the OMG and the PMG papers if you publish using
the tools! ;)
On Mon, Nov 3, 2014 at 10:41 AM, Peter Howe peterhowe@users.sf.net wrote:
Hi Mahdi,
Thanks - that's very helpful. Are those commands documented somewhere?
Cheers,
Peter.
Hi Peter,
If you run the application, you should get a help page. Not much more
documentation, I'm afraid.
Good luck
Mahdi
On Mon, Nov 3, 2014 at 1:28 PM, Peter Howe peterhowe@users.sf.net wrote: