Re: [Open Babel] NumRotors (was Reference LogP / PSA)

[Geoffrey H. <ge...@ge...>]

On Sep 11, 2007, at 9:25 AM, Noel O'Boyle wrote:
>> [Amide / rotatable bond]
>>
>>> Regarding "Is amide bond considered as a rotatable bond?". Uh...this
>>> requires looking at the code, which says:
...
>> http://www.daylight.com/dayhtml_tutorials/languages/smarts/ 
>> smarts_examples.html#ROTATE
>>
>> Rotatable bond   [!$(*#*)&!D1]-!@[!$(*#*)&!D1]
>> "An atom which is not triply bonded and not one-connected  
>> i.e.terminal
>> connected by a single non-ring bond to and equivalent atom."


One "catch" about rotatable bonds in Open Babel is that there's  
essentially two methods for determining the number of rotatable  
bonds. What you describe is something like the "descriptor" method.  
In this case, the documentation clearly states what is a rotatable  
bond: (No need to read the code)

http://openbabel.SourceForge.net/api/2.1.0/
> Currently, this function classifies any bond with at least one  
> heavy atom, no sp-hybrid atoms (e.g., a triple bond somewhere) not  
> in a ring as a potential rotor. No other bond typing is attempted.
>
Now I don't know if the Open Babel definition matches "standard QSAR  
practice." If not, let's add a new function.

But the reason OBMol::NumRotors() and OBBond::IsRotor() overestimate  
whether a bond is rotatable is for rotamer/conformer searching (i.e.,  
using OBRotamerList, OBRotorList, and OBRotorRules). These classes  
can define a set of SMARTS patterns and likely dihedral angles. It's  
better to consider an amide as a bond to attempt to rotate, than to  
miss out on low-energy conformers.

Yes, this means that OBMol::NumRotors() serves double duty. If there  
needs to be a new "descriptor" version which returns the expected  
answer, that sounds like a good idea. But I'd also like to see the  
OBRotorRules database enhanced with some potential conformer  
searching rules too. This can be used to get a number of rotatable  
bonds too:

OBRotorList rl;
rl.Setup(mol);

cerr << " Number of rotors: " << rl.Size() << endl;

Cheers,
-Geoff