My understanding now is that OBMol.NumRotors() counts the number of
rotors that lead to different conformers. Rotating about either of the
two C-C bonds in propane does not yield any different conformers, and
thus I get
>>> propane = pybel.readstring('smi','CCC')
>>> propane.OBMol.NumRotors()
0
butane however gives 1
>>> pybel.readstring('smi','CCCC').OBMol.NumRotors()
1
However, in terms of statistical mechanics, both C-C bonds in propane
are internal rotors, and I would want a rotor count of 2. For straight-
chain alkanes it's tempting to just add 2 to the NumRotors() answer.
However, this will not work in general. Neopentane should gave 4
internal rotors.
>>> neopentane = pybel.readstring('smi','CC(C)(C)C')
>>> neopentane.OBMol.NumRotors()
0
I can find another way (count the number of non-terminal non-cyclic
single bonds in non-linear molecules) but is this re-inventing the
wheel? (i.e. is there an open-babel function to count the number of
rotors in a statistical mechanics sense?)
Also, is there documentation for NumRotors that I overlooked? It took
me a little while to realise that this is not what I wanted and why.
Thanks
------------------------------------------------------------------------------
Come build with us! The BlackBerry(R) Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9 - 12, 2009. Register now!
http://p.sf.net/sfu/devconference
_______________________________________________
OpenBabel-scripting mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
