Counting rotors

[Richard West-2]

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

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[Geoffrey Hutchison-5]

On Oct 16, 2009, at 6:54 PM, Richard West wrote:

> (i.e. is there an open-babel function to count the number of
> rotors in a statistical mechanics sense?)

No, it counts the number of rotors in a cheminformatics (i.e., quick-
and-dirty) way.

You can also try this, which finds rotatable bonds based on SMARTS  
patterns:
       OpenBabel::OBRotorList rl;
       OpenBabel::OBMol obmol = m_molecule->OBMol();
       rl.Setup(obmol);
       cout << "# of Rotors" << rl.Size();

Hope that helps,
-Geoff

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