Re: [Jmol-users] Distances between centers of aromatic rings?

[Eric M. <em...@mi...>]

Thanks so much, Bob! This seems to be working perfectly.
The only change I had to make is that rings.length is an array of zeros. 
So I used rings.lines.count.

I was able to get His rings with
ringsh = {*}.find("SMARTS","c1cncn1", true)
and then make a single array

ringsall = rings + ringsh

Jmol continues to amaze and delight me!
Eric

On 2/10/15 5:47 PM, Robert Hanson wrote:
> This is what SMARTS searching does.
>
> rings = {*}.find("SMARTS","c1ccccc1", true)  // an array of atom sets
> centers = rings.xyz   // centers of those atom sets; still an array
> print centers[1]
> print centers[2]
> ...
>
>
> On Tue, Feb 10, 2015 at 3:59 PM, Eric Martz <em...@mi... 
> <mailto:em...@mi...>> wrote:
>
>     I would like to generate a list of distances between the centers of
>     aromatic rings, identifying the pair of residues that each distance
>     represents.
>
>     I believe the following reports the center of the 6-carbon ring of
>     Tyr3
>     in 1pgb:
>
>
> $ load =1pgb
> IMMUNOGLOBULIN BINDING PROTEIN          23-NOV-93   1PGB
> TWO CRYSTAL STRUCTURES OF THE B1 IMMUNOGLOBULIN-BINDING
> DOMAIN OF STREPTOCCOCAL PROTEIN G AND COMPARISON WITH NMR
> found biomolecule 1: A
>
> // all rings:
>
> $ rings = {*}.find("SMARTS","c1ccccc1", true)
> $ print rings.xyz
> {13.123668 14.505501 26.274666}
> {7.7295 15.019166 20.959}
> {1.7821666 16.910334 17.072166}
> {7.07 8.775001 16.5255}
> {15.482834 9.6655 22.505835}
> {11.408334 10.879166 21.280832}
>
> // just tyr
>
> $ rings = {tyr}.find("SMARTS","c1ccccc1", true)
> $ print rings.xyz
> {13.123668 14.505501 26.274666}
> {1.7821666 16.910334 17.072166}
> {15.482834 9.6655 22.505835}
>
> // with labels
>
> for (var i = 1; i <= rings.length; i++) {
>  print (rings[i])[1].label("%n%r") + " " + rings[i].xyz
> }
>
> TYR3 {13.123668 14.505501 26.274666}
> TYR33 {1.7821666 16.910334 17.072166}
> TYR45 {15.482834 9.6655 22.505835}
>
> If I had such lists, how would I generate a list of distances between
>
>     the ring-centers, being able to identify the two residues for each
>     distance?
>
>
> // use .xyz.distance  (average position...distance....)
>
>  for (var i = 1; i <= rings.length; i++) {
>   for (var j = i + 1; j <= rings.length; j++) {
>     print (rings[i])[1].label("%n%r") + "\t" + 
> (rings[j])[1].label("%n%r")  + "\t" + 
> rings[i].xyz.distance(rings[j].xyz).format("%6.3f")
>   }
> }
>
> TYR3    TYR33    14.802
> TYR3    TYR45     6.572
> TYR33    TYR45    16.423
>
>
> :)
>
>
>
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