I usually run 3D generation as follows:
obabel -:OCC(=O)[C@@]1(O)CC[C@@H]2[C@]1(C)C[C@H](O)[C@]1([C@H
]2CCC2=CC(=O)CC[C@]12C)F --gen3d -osdf
==============================
*** Open Babel Warning in OpenBabel::OBBuilder::CorrectStereoAtoms
Could not correct 3 stereocenter(s) in this molecule ()
with Atom Ids as follows: 8 16 17
So...three stereocentres are wrong.
This is discussed in the OB paper. 3D structure generation fails stereo in
many cases of bridged rings, as we use ring templates of a particular
stereo.
- Noel
On 9 May 2012 17:13, Thomas Womack <twom...@globalphasing.com> wrote:
> When I try obgen on
>
> OCC(=O)[C@@]1(O)CC[C@@H]2[C@]1(C)C[C@H](O)[C@]1([C@H]2CCC2=CC(=O)CC[C@
> ]12C)F
>
> I get a message
>
> WARNING: damped steplength 16.7257 to 2.25803
>
> on stdout rather than stderr (so dumped into the SDF file making it
> invalid)
>
>
> If I edit the SDF file to remove that message, and run obprop, I find that
> the generated structure is
>
> OCC(=O)[C@@]1(O)CC[C@H]2[C@]1(C)C[C@H](O)[C@@]1([C@@H]2CCC2=CC(=O)CC[C@
> ]12C)F
>
> (IE the wrong chirality at the second, fifth and sixth chiral carbons)
>
> For comparison, obgen from the released 2.3.1 produces something which
> obprop-svn4747 reports as
>
> CC(=O)[C@@]1(O)CC[C@H]2[C@]1(C)C[C@@H](O)[C@@]1([C@@H]2CCC2=CC(=O)CC[C@
> ]12C)F
>
> (IE the wrong chirality at the fourth chiral carbon)
>
> I realise that steroids are nasty test cases, but they are annoyingly
> pharmaceutically relevant
>
> Tom
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> OpenBabel-Devel mailing list
> OpenBabel-Devel@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-devel
>
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
