[chimera-dev] No glue!

[Eric Pettersen]

Hi JD,
	I think there are two member functions of Molecule that you are  
interested in here:

     minimumRings(crossResidues = False)
     allRings(bool crossResidues, int allSizeThreshold)

They both return a list of Rings.  'crossResidues' controls whether  
rings are allowed to cross residue boundaries (usually you would want  
False, but if you're studying cycles formed by disulphide bonds...).   
'allSizeThreshold' is the maximum size ring that will be returned  
(zero = no limit).  For highly fused ring systems like nanotubes you  
would want to limit the ring size or else the ring-finding algorithm  
will not return in your lifetime.  'minimumRings' only returns rings  
that can't be decomposed into multiple subrings. So for anthracene,  
for example, 'minimumRings' would return 3 six-member rings whereas  
'allRings' would return 3 six-member rings, 2 ten-member rings, and 1  
fourteen-member ring.

Atoms and Bonds have similar functions if you are interested in the  
rings that a particular atom or bond participates in.

Rings have 'atoms' and 'bonds' attributes as well as 'orderedAtoms'  
and 'orderedBonds' attributes.  The latter two return the atoms/bonds  
in ring order.  There is also an 'aromatic()' member function.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu


On Feb 13, 2010, at 6:25 AM, Jean Didier Pie Marechal wrote:

> Dear all,
>
> I'd like to add an atom at the mass center of each aromatic fragment  
> of my ligand (I always want to add an atom don't I?).
>
> I know how to calculate cm, put an atom or point, select aromatic  
> ring BUT I am banging my head against the wall to define one entity  
> of each ring separately.
>
> Would it be a lot more complicate to do so for any cyclic moeity.
>
> Thanks for any help!
>
> best,
>
> JD
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