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#638 SP and TB stereochemistry

2.3.x
open
nobody
Library Functions (223)
4
2012-10-23
2010-09-13
Anonymous
No

I've tried converting FPt@SP1(Cl)Cl to 3D using babel --gen3D -ismi <file> -oxyz <file>, and the structure that comes out reminds me of a octahedral platin missing two equatorial groups [see file attached].

On the other hand, if I input FPt@TB(F)(Cl)Cl, it is not converted, but replacing TB with SP1 yields the adequate trigonal bipyramidal geometry.

I got these results with the 2010-08-18 and 2010-08-13 snapshots and with today's SVN version.

Open Babel 2.2.99 -- Sep 13 2010 -- 12:02:15
Ubuntu 10.04 Netbook Remix

Discussion

  • Geoff Hutchison

    Geoff Hutchison - 2010-10-18

    I've looked through the code carefully, and both of these will need to fall under new features. This means, unfortunately, it won't be fixed in time for the 2.3.0 release next week.

    1) There currently isn't a special case to enforce SP geometry or stereochemistry in the builder. So as far as I can see, it defaults to octahedral.

    2) There isn't support for TB stereochemistry, although as you see, the builder does have support for TB geometries.

    I suspect both of these bugs will be fixed for v2.3.1.